Starting phenix.real_space_refine on Sun Aug 24 23:57:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r17_14233/08_2025/7r17_14233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r17_14233/08_2025/7r17_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7r17_14233/08_2025/7r17_14233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r17_14233/08_2025/7r17_14233.map" model { file = "/net/cci-nas-00/data/ceres_data/7r17_14233/08_2025/7r17_14233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r17_14233/08_2025/7r17_14233.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 27 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 dihedrals: 15 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.07, per 1000 atoms: 0.26 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: 1.96 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.19 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: 5.65 Time building geometry restraints manager: 2.65 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: 13462 17.98 - 35.95: 939 35.95 - 53.93: 197 53.93 - 71.90: 41 71.90 - 89.88: 20 Dihedral angle restraints: 14659 sinusoidal: 6001 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 14656 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.540 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 12.980 89.879 8973 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 aren 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 covalent geometry : bond 0.00362 (24162) covalent geometry : angle 0.52673 (32862) SS BOND : bond 0.00176 ( 38) SS BOND : angle 0.89211 ( 76) hydrogen bonds : bond 0.23125 ( 874) hydrogen bonds : angle 8.09062 ( 2457) link_BETA1-4 : bond 0.00020 ( 1) link_BETA1-4 : angle 1.23213 ( 3) link_NAG-ASN : bond 0.00439 ( 21) link_NAG-ASN : angle 2.31363 ( 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 : 1.007 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: 0.8390 (m-10) cc_final: 0.8118 (m-10) REVERT: A 774 GLN cc_start: 0.8683 (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: 0.1626 time to fit residues: 63.7751 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 : 1.019 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3826 r_free = 0.3826 target = 0.117167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.078274 restraints weight = 63328.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081608 restraints weight = 33989.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081973 restraints weight = 19411.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082528 restraints weight = 15214.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082689 restraints weight = 13415.367| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1127 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= 0.116 Angle : 0.517 9.986 33004 Z= 0.271 Chirality : 0.043 0.308 3783 Planarity : 0.004 0.059 4226 Dihedral : 6.016 59.572 3649 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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 aren not related in a simple way. whole: 0.46 (0.16), residues: 2917 helix: 2.78 (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 0.006 0.000 ARG B 509 TYR 0.022 0.001 TYR B1067 PHE 0.039 0.001 PHE A 275 TRP 0.023 0.002 TRP B 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00251 (24162) covalent geometry : angle 0.51006 (32862) SS BOND : bond 0.00212 ( 38) SS BOND : angle 0.75712 ( 76) hydrogen bonds : bond 0.05055 ( 874) hydrogen bonds : angle 5.89918 ( 2457) link_BETA1-4 : bond 0.00085 ( 1) link_BETA1-4 : angle 1.25809 ( 3) link_NAG-ASN : bond 0.00465 ( 21) link_NAG-ASN : angle 1.86382 ( 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 194 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7800 (t70) cc_final: 0.7560 (t70) REVERT: A 144 TYR cc_start: 0.8964 (t80) cc_final: 0.8502 (t80) REVERT: A 153 MET cc_start: 0.7785 (mmp) cc_final: 0.7561 (mmm) REVERT: A 224 GLU cc_start: 0.8505 (mp0) cc_final: 0.8102 (mp0) REVERT: A 396 TYR cc_start: 0.8556 (m-10) cc_final: 0.8349 (m-10) REVERT: A 774 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8497 (mm-40) REVERT: B 265 TYR cc_start: 0.8069 (p90) cc_final: 0.7695 (p90) REVERT: B 342 PHE cc_start: 0.7685 (m-80) cc_final: 0.6885 (m-80) REVERT: B 418 ILE cc_start: 0.2401 (OUTLIER) cc_final: 0.2133 (mp) REVERT: B 436 TRP cc_start: 0.8323 (p-90) cc_final: 0.8011 (p-90) REVERT: B 740 MET cc_start: 0.8898 (tpp) cc_final: 0.8678 (tpt) REVERT: B 1141 LEU cc_start: 0.9170 (tp) cc_final: 0.8967 (tt) REVERT: C 237 ARG cc_start: 0.7223 (ttm110) cc_final: 0.7002 (ttm110) REVERT: C 421 TYR cc_start: 0.8495 (m-10) cc_final: 0.8007 (m-10) REVERT: C 979 ASP cc_start: 0.8855 (m-30) cc_final: 0.8606 (m-30) outliers start: 15 outliers final: 7 residues processed: 188 average time/residue: 0.1514 time to fit residues: 47.9435 Evaluate side-chains 168 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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: 0.8980 chunk 97 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 280 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 287 optimal weight: 2.9990 chunk 223 optimal weight: 0.0770 chunk 228 optimal weight: 5.9990 chunk 155 optimal weight: 0.3980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN B 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.117329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078488 restraints weight = 63170.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.081877 restraints weight = 31770.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082464 restraints weight = 17217.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082834 restraints weight = 14427.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083169 restraints weight = 13255.926| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1429 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= 0.102 Angle : 0.471 7.245 33004 Z= 0.246 Chirality : 0.042 0.263 3783 Planarity : 0.004 0.061 4226 Dihedral : 5.306 55.414 3647 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.81 % Allowed : 8.90 % Favored : 90.30 % 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 aren not related in a simple way. whole: 0.52 (0.16), residues: 2917 helix: 2.82 (0.21), residues: 619 sheet: 0.60 (0.20), residues: 609 loop : -0.74 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1091 TYR 0.022 0.001 TYR C 904 PHE 0.033 0.001 PHE A 275 TRP 0.012 0.001 TRP C 886 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00225 (24162) covalent geometry : angle 0.46490 (32862) SS BOND : bond 0.00181 ( 38) SS BOND : angle 0.71766 ( 76) hydrogen bonds : bond 0.04341 ( 874) hydrogen bonds : angle 5.26933 ( 2457) link_BETA1-4 : bond 0.00292 ( 1) link_BETA1-4 : angle 1.03661 ( 3) link_NAG-ASN : bond 0.00394 ( 21) link_NAG-ASN : angle 1.66446 ( 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 208 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7734 (t70) cc_final: 0.7452 (t70) REVERT: A 144 TYR cc_start: 0.8951 (t80) cc_final: 0.8499 (t80) REVERT: A 224 GLU cc_start: 0.8398 (mp0) cc_final: 0.8022 (mp0) REVERT: A 374 PHE cc_start: 0.8449 (m-80) cc_final: 0.7750 (m-80) REVERT: A 774 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8522 (mm-40) REVERT: B 265 TYR cc_start: 0.7990 (p90) cc_final: 0.7594 (p90) REVERT: B 342 PHE cc_start: 0.7852 (m-80) cc_final: 0.7260 (m-80) REVERT: B 418 ILE cc_start: 0.2433 (OUTLIER) cc_final: 0.2231 (mp) REVERT: B 436 TRP cc_start: 0.8296 (p-90) cc_final: 0.7982 (p-90) REVERT: B 740 MET cc_start: 0.8948 (tpp) cc_final: 0.8736 (tpt) REVERT: B 983 ARG cc_start: 0.8505 (ttp-170) cc_final: 0.7829 (ttp-170) REVERT: B 1141 LEU cc_start: 0.9195 (tp) cc_final: 0.8992 (tt) REVERT: C 237 ARG cc_start: 0.7180 (ttm110) cc_final: 0.6963 (ttm110) REVERT: C 421 TYR cc_start: 0.8244 (m-10) cc_final: 0.7910 (m-10) REVERT: C 979 ASP cc_start: 0.8820 (m-30) cc_final: 0.8542 (m-30) outliers start: 21 outliers final: 11 residues processed: 201 average time/residue: 0.1524 time to fit residues: 51.2730 Evaluate side-chains 179 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1027 THR 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 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: 7.9990 chunk 227 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 218 optimal weight: 0.5980 chunk 121 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN C 207 HIS C 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076507 restraints weight = 63686.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079736 restraints weight = 33405.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080235 restraints weight = 18625.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080874 restraints weight = 15507.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080983 restraints weight = 13624.950| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1619 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= 0.157 Angle : 0.508 10.149 33004 Z= 0.263 Chirality : 0.042 0.262 3783 Planarity : 0.004 0.060 4226 Dihedral : 5.044 52.931 3646 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.30 % Allowed : 11.00 % Favored : 87.69 % 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 aren not related in a simple way. whole: 0.43 (0.16), residues: 2917 helix: 2.74 (0.21), residues: 615 sheet: 0.50 (0.20), residues: 609 loop : -0.75 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.022 0.001 TYR C1067 PHE 0.022 0.001 PHE B 823 TRP 0.014 0.001 TRP C 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00366 (24162) covalent geometry : angle 0.50178 (32862) SS BOND : bond 0.00266 ( 38) SS BOND : angle 0.82536 ( 76) hydrogen bonds : bond 0.04637 ( 874) hydrogen bonds : angle 5.18456 ( 2457) link_BETA1-4 : bond 0.00218 ( 1) link_BETA1-4 : angle 1.03596 ( 3) link_NAG-ASN : bond 0.00368 ( 21) link_NAG-ASN : angle 1.67726 ( 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 205 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8990 (t80) cc_final: 0.8571 (t80) REVERT: A 153 MET cc_start: 0.7842 (mmm) cc_final: 0.7433 (mmm) REVERT: A 224 GLU cc_start: 0.8445 (mp0) cc_final: 0.7820 (mp0) REVERT: A 374 PHE cc_start: 0.8512 (m-80) cc_final: 0.8208 (m-80) REVERT: A 380 TYR cc_start: 0.8736 (m-10) cc_final: 0.8503 (m-10) REVERT: A 661 GLU cc_start: 0.6975 (pp20) cc_final: 0.6610 (pp20) REVERT: A 774 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8568 (mm-40) REVERT: B 265 TYR cc_start: 0.8041 (p90) cc_final: 0.7561 (p90) REVERT: B 342 PHE cc_start: 0.7972 (m-80) cc_final: 0.7152 (m-80) REVERT: B 418 ILE cc_start: 0.2476 (OUTLIER) cc_final: 0.2215 (mp) REVERT: B 436 TRP cc_start: 0.8333 (p-90) cc_final: 0.8017 (p-90) REVERT: B 983 ARG cc_start: 0.8519 (ttp-170) cc_final: 0.7941 (ttp-170) REVERT: B 1141 LEU cc_start: 0.9186 (tp) cc_final: 0.8986 (tt) REVERT: C 105 ILE cc_start: 0.7988 (mp) cc_final: 0.7745 (mp) REVERT: C 118 LEU cc_start: 0.9150 (tp) cc_final: 0.8839 (mm) REVERT: C 237 ARG cc_start: 0.7206 (ttm110) cc_final: 0.6951 (ttm110) REVERT: C 238 PHE cc_start: 0.8378 (p90) cc_final: 0.8112 (p90) REVERT: C 417 ASN cc_start: 0.9178 (m-40) cc_final: 0.8841 (p0) REVERT: C 421 TYR cc_start: 0.8277 (m-10) cc_final: 0.7988 (m-10) REVERT: C 568 ASP cc_start: 0.8476 (p0) cc_final: 0.8254 (p0) REVERT: C 979 ASP cc_start: 0.8863 (m-30) cc_final: 0.8569 (m-30) outliers start: 34 outliers final: 16 residues processed: 195 average time/residue: 0.1557 time to fit residues: 50.3192 Evaluate side-chains 171 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 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 524 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 278 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 189 optimal weight: 0.0000 chunk 190 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN B 115 GLN C1071 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.115482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076497 restraints weight = 62595.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.079623 restraints weight = 33462.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.080139 restraints weight = 19181.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.080646 restraints weight = 15835.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081049 restraints weight = 14183.001| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24222 Z= 0.178 Angle : 0.519 9.057 33004 Z= 0.270 Chirality : 0.043 0.260 3783 Planarity : 0.004 0.058 4226 Dihedral : 4.934 52.878 3646 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.38 % Allowed : 12.12 % Favored : 86.50 % 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 aren not related in a simple way. whole: 0.32 (0.15), residues: 2917 helix: 2.59 (0.21), residues: 621 sheet: 0.43 (0.20), residues: 609 loop : -0.82 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1014 TYR 0.023 0.001 TYR C1067 PHE 0.023 0.001 PHE B 823 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00415 (24162) covalent geometry : angle 0.51080 (32862) SS BOND : bond 0.00212 ( 38) SS BOND : angle 1.32692 ( 76) hydrogen bonds : bond 0.04812 ( 874) hydrogen bonds : angle 5.15658 ( 2457) link_BETA1-4 : bond 0.00184 ( 1) link_BETA1-4 : angle 1.12841 ( 3) link_NAG-ASN : bond 0.00363 ( 21) link_NAG-ASN : angle 1.68187 ( 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 193 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8910 (t80) cc_final: 0.8424 (t80) REVERT: A 153 MET cc_start: 0.7992 (mmm) cc_final: 0.7622 (mmm) REVERT: A 374 PHE cc_start: 0.8381 (m-80) cc_final: 0.8068 (m-80) REVERT: A 380 TYR cc_start: 0.8762 (m-10) cc_final: 0.8494 (m-10) REVERT: A 661 GLU cc_start: 0.7133 (pp20) cc_final: 0.6696 (pp20) REVERT: A 774 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8565 (mm-40) REVERT: B 200 TYR cc_start: 0.8001 (m-80) cc_final: 0.7738 (m-80) REVERT: B 265 TYR cc_start: 0.8118 (p90) cc_final: 0.7614 (p90) REVERT: B 342 PHE cc_start: 0.8046 (m-80) cc_final: 0.7174 (m-80) REVERT: B 418 ILE cc_start: 0.2594 (OUTLIER) cc_final: 0.2330 (mp) REVERT: B 436 TRP cc_start: 0.8343 (p-90) cc_final: 0.8018 (p-90) REVERT: B 983 ARG cc_start: 0.8504 (ttp-170) cc_final: 0.8210 (ttp80) REVERT: B 1141 LEU cc_start: 0.9131 (tp) cc_final: 0.8925 (tt) REVERT: C 105 ILE cc_start: 0.8058 (mp) cc_final: 0.7854 (mp) REVERT: C 118 LEU cc_start: 0.9243 (tp) cc_final: 0.9027 (mm) REVERT: C 237 ARG cc_start: 0.7305 (ttm110) cc_final: 0.7034 (ttm110) REVERT: C 238 PHE cc_start: 0.8444 (p90) cc_final: 0.8159 (p90) REVERT: C 417 ASN cc_start: 0.9068 (m-40) cc_final: 0.8779 (p0) REVERT: C 421 TYR cc_start: 0.8322 (m-10) cc_final: 0.8056 (m-10) REVERT: C 568 ASP cc_start: 0.8483 (p0) cc_final: 0.8214 (p0) REVERT: C 979 ASP cc_start: 0.8827 (m-30) cc_final: 0.8537 (m-30) outliers start: 36 outliers final: 27 residues processed: 182 average time/residue: 0.1423 time to fit residues: 43.7533 Evaluate side-chains 178 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 515 PHE 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 329 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 515 PHE 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 198 ASP 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 778 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 10 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 100 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 281 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.116747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.081125 restraints weight = 62803.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.080507 restraints weight = 36137.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081446 restraints weight = 24903.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.082639 restraints weight = 20123.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.082559 restraints weight = 17365.047| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24222 Z= 0.109 Angle : 0.483 8.980 33004 Z= 0.248 Chirality : 0.042 0.249 3783 Planarity : 0.004 0.057 4226 Dihedral : 4.572 53.211 3646 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.53 % Allowed : 13.04 % 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 aren not related in a simple way. whole: 0.46 (0.16), residues: 2917 helix: 2.73 (0.21), residues: 620 sheet: 0.51 (0.20), residues: 621 loop : -0.74 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 815 TYR 0.019 0.001 TYR C1067 PHE 0.024 0.001 PHE B 823 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00245 (24162) covalent geometry : angle 0.47571 (32862) SS BOND : bond 0.00362 ( 38) SS BOND : angle 1.18047 ( 76) hydrogen bonds : bond 0.04244 ( 874) hydrogen bonds : angle 4.93990 ( 2457) link_BETA1-4 : bond 0.00285 ( 1) link_BETA1-4 : angle 1.16802 ( 3) link_NAG-ASN : bond 0.00347 ( 21) link_NAG-ASN : angle 1.58798 ( 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 209 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8863 (t80) cc_final: 0.8452 (t80) REVERT: A 153 MET cc_start: 0.7889 (mmm) cc_final: 0.7478 (mmm) REVERT: A 374 PHE cc_start: 0.8206 (m-80) cc_final: 0.7951 (m-80) REVERT: A 380 TYR cc_start: 0.8766 (m-10) cc_final: 0.8478 (m-10) REVERT: A 661 GLU cc_start: 0.7072 (pp20) cc_final: 0.6630 (pp20) REVERT: A 774 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8469 (mm-40) REVERT: B 200 TYR cc_start: 0.7962 (m-80) cc_final: 0.7720 (m-80) REVERT: B 265 TYR cc_start: 0.8060 (p90) cc_final: 0.7521 (p90) REVERT: B 342 PHE cc_start: 0.8008 (m-80) cc_final: 0.7157 (m-80) REVERT: B 396 TYR cc_start: 0.8723 (m-80) cc_final: 0.8344 (m-80) REVERT: B 418 ILE cc_start: 0.2583 (OUTLIER) cc_final: 0.2313 (mp) REVERT: B 436 TRP cc_start: 0.8301 (p-90) cc_final: 0.7984 (p-90) REVERT: B 983 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.8224 (ttp80) REVERT: C 238 PHE cc_start: 0.8426 (p90) cc_final: 0.8096 (p90) REVERT: C 417 ASN cc_start: 0.9020 (m-40) cc_final: 0.8794 (p0) REVERT: C 421 TYR cc_start: 0.8304 (m-10) cc_final: 0.8065 (m-10) REVERT: C 568 ASP cc_start: 0.8509 (p0) cc_final: 0.8228 (p0) REVERT: C 979 ASP cc_start: 0.8804 (m-30) cc_final: 0.8528 (m-30) outliers start: 40 outliers final: 27 residues processed: 194 average time/residue: 0.1596 time to fit residues: 51.5677 Evaluate side-chains 179 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 515 PHE 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 515 PHE 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 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 560 LEU 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: 0.6980 chunk 16 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 51 optimal weight: 0.0570 chunk 8 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.116932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081438 restraints weight = 62197.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.080669 restraints weight = 36277.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081759 restraints weight = 24793.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.082167 restraints weight = 20095.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082320 restraints weight = 18159.642| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24222 Z= 0.109 Angle : 0.487 9.729 33004 Z= 0.249 Chirality : 0.042 0.242 3783 Planarity : 0.004 0.056 4226 Dihedral : 4.393 53.143 3646 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.30 % Allowed : 13.42 % Favored : 85.28 % 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 aren not related in a simple way. whole: 0.49 (0.16), residues: 2917 helix: 2.73 (0.21), residues: 620 sheet: 0.57 (0.20), residues: 596 loop : -0.70 (0.15), residues: 1701 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 B 823 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00246 (24162) covalent geometry : angle 0.48071 (32862) SS BOND : bond 0.00182 ( 38) SS BOND : angle 1.06977 ( 76) hydrogen bonds : bond 0.04124 ( 874) hydrogen bonds : angle 4.86277 ( 2457) link_BETA1-4 : bond 0.00177 ( 1) link_BETA1-4 : angle 1.16501 ( 3) link_NAG-ASN : bond 0.00333 ( 21) link_NAG-ASN : angle 1.58228 ( 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: 34 poor density : 164 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8788 (t80) cc_final: 0.8322 (t80) REVERT: A 153 MET cc_start: 0.7858 (mmm) cc_final: 0.7383 (mmm) REVERT: A 380 TYR cc_start: 0.8787 (m-10) cc_final: 0.8512 (m-10) REVERT: A 508 TYR cc_start: 0.7527 (m-10) cc_final: 0.7263 (m-10) REVERT: A 661 GLU cc_start: 0.7059 (pp20) cc_final: 0.6617 (pp20) REVERT: A 774 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8495 (mm-40) REVERT: B 200 TYR cc_start: 0.7921 (m-80) cc_final: 0.7672 (m-80) REVERT: B 265 TYR cc_start: 0.8045 (p90) cc_final: 0.7573 (p90) REVERT: B 342 PHE cc_start: 0.7986 (m-80) cc_final: 0.7135 (m-80) REVERT: B 396 TYR cc_start: 0.8708 (m-80) cc_final: 0.8366 (m-80) REVERT: B 418 ILE cc_start: 0.2597 (OUTLIER) cc_final: 0.2172 (mp) REVERT: B 436 TRP cc_start: 0.8269 (p-90) cc_final: 0.7944 (p-90) REVERT: B 983 ARG cc_start: 0.8582 (ttp-170) cc_final: 0.8349 (ttp-110) REVERT: C 238 PHE cc_start: 0.8488 (p90) cc_final: 0.8177 (p90) REVERT: C 421 TYR cc_start: 0.8267 (m-10) cc_final: 0.7991 (m-10) REVERT: C 568 ASP cc_start: 0.8537 (p0) cc_final: 0.8267 (p0) REVERT: C 896 ILE cc_start: 0.9635 (tp) cc_final: 0.9434 (tt) REVERT: C 979 ASP cc_start: 0.8805 (m-30) cc_final: 0.8524 (m-30) outliers start: 34 outliers final: 28 residues processed: 186 average time/residue: 0.1471 time to fit residues: 46.6753 Evaluate side-chains 186 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 515 PHE 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 515 PHE 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 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 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU 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: 2.9990 chunk 207 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.115557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076785 restraints weight = 62845.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080077 restraints weight = 34046.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080301 restraints weight = 19112.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080866 restraints weight = 16667.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.081264 restraints weight = 14801.435| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24222 Z= 0.164 Angle : 0.517 9.194 33004 Z= 0.266 Chirality : 0.043 0.246 3783 Planarity : 0.004 0.055 4226 Dihedral : 4.496 52.768 3646 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.69 % Allowed : 13.61 % Favored : 84.70 % 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 aren not related in a simple way. whole: 0.39 (0.16), residues: 2917 helix: 2.53 (0.21), residues: 628 sheet: 0.45 (0.20), residues: 595 loop : -0.72 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1014 TYR 0.022 0.001 TYR C1067 PHE 0.022 0.001 PHE B 823 TRP 0.008 0.001 TRP C 353 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00384 (24162) covalent geometry : angle 0.51016 (32862) SS BOND : bond 0.00203 ( 38) SS BOND : angle 1.11292 ( 76) hydrogen bonds : bond 0.04553 ( 874) hydrogen bonds : angle 4.93245 ( 2457) link_BETA1-4 : bond 0.00314 ( 1) link_BETA1-4 : angle 1.20628 ( 3) link_NAG-ASN : bond 0.00329 ( 21) link_NAG-ASN : angle 1.62815 ( 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 192 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8921 (t80) cc_final: 0.8504 (t80) REVERT: A 153 MET cc_start: 0.8082 (mmm) cc_final: 0.7773 (mmm) REVERT: A 380 TYR cc_start: 0.8864 (m-10) cc_final: 0.8597 (m-10) REVERT: A 661 GLU cc_start: 0.7210 (pp20) cc_final: 0.6728 (pp20) REVERT: A 774 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8508 (mm-40) REVERT: B 200 TYR cc_start: 0.7953 (m-80) cc_final: 0.7724 (m-80) REVERT: B 265 TYR cc_start: 0.8097 (p90) cc_final: 0.7533 (p90) REVERT: B 342 PHE cc_start: 0.8041 (m-80) cc_final: 0.7306 (m-80) REVERT: B 396 TYR cc_start: 0.8926 (m-80) cc_final: 0.8566 (m-80) REVERT: B 418 ILE cc_start: 0.2500 (OUTLIER) cc_final: 0.2234 (mp) REVERT: B 436 TRP cc_start: 0.8409 (p-90) cc_final: 0.8095 (p-90) REVERT: B 983 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8321 (ttp80) REVERT: C 84 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8187 (mm) REVERT: C 421 TYR cc_start: 0.8236 (m-10) cc_final: 0.7972 (m-10) REVERT: C 568 ASP cc_start: 0.8472 (p0) cc_final: 0.8155 (p0) REVERT: C 767 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8365 (mm) REVERT: C 979 ASP cc_start: 0.8835 (m-30) cc_final: 0.8533 (m-30) outliers start: 44 outliers final: 34 residues processed: 182 average time/residue: 0.1423 time to fit residues: 44.1127 Evaluate side-chains 180 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 495 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 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 662 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 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 938 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 267 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.115204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079831 restraints weight = 62720.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078659 restraints weight = 38510.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079696 restraints weight = 27004.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081255 restraints weight = 21707.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.081131 restraints weight = 17849.573| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24222 Z= 0.164 Angle : 0.519 9.714 33004 Z= 0.268 Chirality : 0.043 0.250 3783 Planarity : 0.004 0.054 4226 Dihedral : 4.548 52.944 3646 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.38 % Allowed : 14.11 % Favored : 84.51 % 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 aren not related in a simple way. whole: 0.34 (0.16), residues: 2917 helix: 2.45 (0.21), residues: 629 sheet: 0.45 (0.20), residues: 587 loop : -0.74 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1014 TYR 0.022 0.001 TYR C1067 PHE 0.022 0.001 PHE B 823 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00383 (24162) covalent geometry : angle 0.51222 (32862) SS BOND : bond 0.00211 ( 38) SS BOND : angle 1.04803 ( 76) hydrogen bonds : bond 0.04651 ( 874) hydrogen bonds : angle 4.94278 ( 2457) link_BETA1-4 : bond 0.00086 ( 1) link_BETA1-4 : angle 1.18608 ( 3) link_NAG-ASN : bond 0.00330 ( 21) link_NAG-ASN : angle 1.63788 ( 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 : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8893 (t80) cc_final: 0.8472 (t80) REVERT: A 153 MET cc_start: 0.7911 (mmm) cc_final: 0.7609 (mmm) REVERT: A 380 TYR cc_start: 0.8972 (m-10) cc_final: 0.8733 (m-10) REVERT: A 508 TYR cc_start: 0.7673 (m-10) cc_final: 0.7417 (m-10) REVERT: A 661 GLU cc_start: 0.7298 (pp20) cc_final: 0.6789 (pp20) REVERT: A 774 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8524 (mm-40) REVERT: B 200 TYR cc_start: 0.7970 (m-80) cc_final: 0.7763 (m-10) REVERT: B 265 TYR cc_start: 0.8116 (p90) cc_final: 0.7447 (p90) REVERT: B 342 PHE cc_start: 0.8046 (m-80) cc_final: 0.7304 (m-80) REVERT: B 396 TYR cc_start: 0.8814 (m-80) cc_final: 0.8452 (m-80) REVERT: B 418 ILE cc_start: 0.2729 (OUTLIER) cc_final: 0.2457 (mp) REVERT: B 436 TRP cc_start: 0.8375 (p-90) cc_final: 0.8094 (p-90) REVERT: B 983 ARG cc_start: 0.8615 (ttp80) cc_final: 0.7930 (ttp-110) REVERT: C 84 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8210 (mm) REVERT: C 421 TYR cc_start: 0.8221 (m-10) cc_final: 0.7930 (m-10) REVERT: C 568 ASP cc_start: 0.8508 (p0) cc_final: 0.8200 (p0) REVERT: C 767 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8419 (mm) REVERT: C 979 ASP cc_start: 0.8845 (m-30) cc_final: 0.8543 (m-30) outliers start: 36 outliers final: 30 residues processed: 177 average time/residue: 0.1497 time to fit residues: 45.1861 Evaluate side-chains 179 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 495 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 130 VAL Chi-restraints excluded: chain B residue 238 PHE 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 662 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 84 LEU 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 938 LEU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8985 > 50: distance: 35 - 37: 8.216 distance: 37 - 38: 5.059 distance: 37 - 200: 7.285 distance: 38 - 39: 13.341 distance: 38 - 41: 11.595 distance: 39 - 40: 15.129 distance: 39 - 44: 17.181 distance: 40 - 197: 16.071 distance: 41 - 42: 11.168 distance: 41 - 43: 14.126 distance: 44 - 45: 17.361 distance: 45 - 46: 12.586 distance: 45 - 48: 19.465 distance: 46 - 47: 41.605 distance: 46 - 52: 26.091 distance: 48 - 49: 14.042 distance: 49 - 50: 28.208 distance: 49 - 51: 9.725 distance: 52 - 53: 17.551 distance: 52 - 184: 16.458 distance: 53 - 54: 25.904 distance: 53 - 56: 33.567 distance: 54 - 55: 39.246 distance: 54 - 59: 11.223 distance: 55 - 181: 31.613 distance: 56 - 57: 43.118 distance: 56 - 58: 23.260 distance: 59 - 60: 13.652 distance: 60 - 61: 11.842 distance: 60 - 63: 16.995 distance: 61 - 62: 34.420 distance: 61 - 68: 33.910 distance: 63 - 64: 20.503 distance: 64 - 65: 22.504 distance: 65 - 66: 18.500 distance: 65 - 67: 25.568 distance: 68 - 69: 20.415 distance: 69 - 70: 23.577 distance: 69 - 72: 12.388 distance: 70 - 71: 17.743 distance: 70 - 74: 36.687 distance: 72 - 73: 5.935 distance: 74 - 75: 23.030 distance: 75 - 76: 15.632 distance: 75 - 78: 7.312 distance: 76 - 77: 19.019 distance: 76 - 82: 21.920 distance: 78 - 79: 17.552 distance: 79 - 80: 23.785 distance: 79 - 81: 18.738 distance: 82 - 83: 14.024 distance: 83 - 84: 13.512 distance: 83 - 86: 7.618 distance: 84 - 85: 31.511 distance: 84 - 91: 14.105 distance: 86 - 87: 13.026 distance: 87 - 88: 13.744 distance: 88 - 89: 8.392 distance: 89 - 90: 16.268 distance: 91 - 92: 19.559 distance: 92 - 93: 16.322 distance: 92 - 95: 11.596 distance: 93 - 94: 31.125 distance: 93 - 100: 19.860 distance: 95 - 96: 14.435 distance: 96 - 97: 25.953 distance: 97 - 98: 12.820 distance: 98 - 99: 15.088 distance: 100 - 101: 15.378 distance: 101 - 102: 27.570 distance: 101 - 104: 21.230 distance: 102 - 103: 29.061 distance: 102 - 111: 22.309 distance: 104 - 105: 27.893 distance: 105 - 106: 4.409 distance: 105 - 107: 31.698 distance: 106 - 108: 9.026 distance: 107 - 109: 16.742 distance: 108 - 110: 32.771 distance: 109 - 110: 18.675 distance: 111 - 112: 14.557 distance: 112 - 115: 40.377 distance: 113 - 114: 56.827 distance: 113 - 119: 34.096 distance: 115 - 116: 41.451 distance: 116 - 117: 10.855 distance: 116 - 118: 57.585