Starting phenix.real_space_refine on Fri Sep 19 08:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5j_38937/09_2025/8y5j_38937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5j_38937/09_2025/8y5j_38937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y5j_38937/09_2025/8y5j_38937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5j_38937/09_2025/8y5j_38937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y5j_38937/09_2025/8y5j_38937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5j_38937/09_2025/8y5j_38937.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.026 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 106 5.16 5 C 15427 2.51 5 N 3954 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24146 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7922 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 55, 'TRANS': 955} Chain breaks: 6 Chain: "B" Number of atoms: 7815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7815 Classifications: {'peptide': 996} Link IDs: {'PTRANS': 52, 'TRANS': 943} Chain breaks: 7 Chain: "C" Number of atoms: 7922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7922 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 55, 'TRANS': 955} Chain breaks: 6 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: "E" 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: "F" 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.75, per 1000 atoms: 0.24 Number of scatterers: 24146 At special positions: 0 Unit cell: (138.55, 135.15, 177.65, 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 106 16.00 O 4659 8.00 N 3954 7.00 C 15427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 648 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 737 " - pdb=" SG CYS A 759 " distance=2.03 Simple disulfide: pdb=" SG CYS A 742 " - pdb=" SG CYS A 748 " distance=2.03 Simple disulfide: pdb=" SG CYS A1031 " - pdb=" SG CYS A1042 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS B 737 " - pdb=" SG CYS B 759 " distance=2.03 Simple disulfide: pdb=" SG CYS B 742 " - pdb=" SG CYS B 748 " distance=2.03 Simple disulfide: pdb=" SG CYS B1031 " - pdb=" SG CYS B1042 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1125 " 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=2.03 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 524 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 487 " distance=2.03 Simple disulfide: pdb=" SG CYS C 537 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 661 " - pdb=" SG CYS C 670 " distance=2.03 Simple disulfide: pdb=" SG CYS C 737 " - pdb=" SG CYS C 759 " distance=2.03 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 748 " distance=2.03 Simple disulfide: pdb=" SG CYS C1031 " - pdb=" SG CYS C1042 " distance=2.03 Simple disulfide: pdb=" SG CYS C1081 " - pdb=" SG CYS C1125 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1301 " - " ASN A 615 " " NAG A1302 " - " ASN A 708 " " NAG A1303 " - " ASN A 716 " " NAG A1304 " - " ASN A1073 " " NAG A1305 " - " ASN A1097 " " NAG A1306 " - " ASN A1133 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 331 " " NAG A1310 " - " ASN A 354 " " NAG B1301 " - " ASN B 615 " " NAG B1302 " - " ASN B 708 " " NAG B1303 " - " ASN B 716 " " NAG B1304 " - " ASN B1073 " " NAG B1305 " - " ASN B1097 " " NAG B1306 " - " ASN B1133 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 331 " " NAG C1301 " - " ASN C 615 " " NAG C1302 " - " ASN C 708 " " NAG C1303 " - " ASN C 716 " " NAG C1304 " - " ASN C1073 " " NAG C1305 " - " ASN C1097 " " NAG C1306 " - " ASN C1133 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 282 " " NAG D 1 " - " ASN A 800 " " NAG E 1 " - " ASN B 800 " " NAG F 1 " - " ASN C 800 " " NAG G 1 " - " ASN C 354 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 979.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5654 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 42 sheets defined 25.8% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 removed outlier: 5.137A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.790A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 736 through 742 Processing helix chain 'A' and resid 745 through 753 Processing helix chain 'A' and resid 757 through 782 Processing helix chain 'A' and resid 810 through 814 removed outlier: 3.713A pdb=" N LYS A 813 " --> pdb=" O LYS A 810 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG A 814 " --> pdb=" O PRO A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 814' Processing helix chain 'A' and resid 815 through 825 Processing helix chain 'A' and resid 865 through 884 Processing helix chain 'A' and resid 885 through 889 removed outlier: 3.544A pdb=" N GLY A 888 " --> pdb=" O TRP A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 907 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.511A pdb=" N TYR A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 940 removed outlier: 4.126A pdb=" N GLN A 934 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 935 " --> pdb=" O GLY A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 removed outlier: 3.571A pdb=" N GLN A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 967 No H-bonds generated for 'chain 'A' and resid 965 through 967' Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.630A pdb=" N ILE A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1032 removed outlier: 4.579A pdb=" N VAL A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 5.097A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.537A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 Processing helix chain 'B' and resid 736 through 742 Processing helix chain 'B' and resid 745 through 754 removed outlier: 3.835A pdb=" N GLN B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 Processing helix chain 'B' and resid 810 through 814 removed outlier: 3.566A pdb=" N LYS B 813 " --> pdb=" O LYS B 810 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG B 814 " --> pdb=" O PRO B 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 814' Processing helix chain 'B' and resid 815 through 825 Processing helix chain 'B' and resid 865 through 884 Processing helix chain 'B' and resid 885 through 889 Processing helix chain 'B' and resid 896 through 907 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.590A pdb=" N TYR B 916 " --> pdb=" O GLN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 940 Processing helix chain 'B' and resid 944 through 964 removed outlier: 3.529A pdb=" N GLN B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 975 through 981 removed outlier: 3.569A pdb=" N ILE B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1032 removed outlier: 4.722A pdb=" N VAL B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1117 No H-bonds generated for 'chain 'B' and resid 1115 through 1117' Processing helix chain 'C' and resid 295 through 304 removed outlier: 5.124A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.010A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.972A pdb=" N GLU C 406 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 615 through 625 Processing helix chain 'C' and resid 736 through 742 Processing helix chain 'C' and resid 745 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 757 through 782 Processing helix chain 'C' and resid 810 through 814 removed outlier: 3.635A pdb=" N LYS C 813 " --> pdb=" O LYS C 810 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG C 814 " --> pdb=" O PRO C 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 810 through 814' Processing helix chain 'C' and resid 815 through 825 Processing helix chain 'C' and resid 865 through 884 Processing helix chain 'C' and resid 885 through 890 removed outlier: 3.513A pdb=" N GLY C 888 " --> pdb=" O TRP C 885 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY C 890 " --> pdb=" O PHE C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 911 through 918 removed outlier: 4.319A pdb=" N LEU C 915 " --> pdb=" O THR C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 940 Processing helix chain 'C' and resid 944 through 964 removed outlier: 3.620A pdb=" N GLN C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 967 No H-bonds generated for 'chain 'C' and resid 965 through 967' Processing helix chain 'C' and resid 975 through 981 Processing helix chain 'C' and resid 984 through 1032 Processing helix chain 'C' and resid 1115 through 1117 No H-bonds generated for 'chain 'C' and resid 1115 through 1117' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.554A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.617A pdb=" N ALA C 574 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 552 " --> pdb=" O ASP C 585 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY C 549 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.008A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.223A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.679A pdb=" N THR A 598 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 593 " --> pdb=" O GLN A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.805A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.688A pdb=" N GLY A 549 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 552 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 653 through 659 removed outlier: 6.177A pdb=" N GLU A 653 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N THR A 695 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N VAL A 655 " --> pdb=" O THR A 695 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 669 " --> pdb=" O ILE A 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.483A pdb=" N ALA A 712 " --> pdb=" O ASN A1073 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A1073 " --> pdb=" O ALA A 712 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU A1071 " --> pdb=" O PRO A 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1046 through 1049 removed outlier: 6.942A pdb=" N VAL A1064 " --> pdb=" O LEU A1048 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 732 through 735 removed outlier: 4.389A pdb=" N LYS A 732 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 removed outlier: 5.665A pdb=" N ILE A 787 " --> pdb=" O ASN C 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1080 through 1081 Processing sheet with id=AB6, first strand: chain 'A' and resid 1085 through 1089 removed outlier: 4.766A pdb=" N ALA A1086 " --> pdb=" O SER A1122 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A1122 " --> pdb=" O ALA A1086 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.529A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.900A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.375A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.883A pdb=" N VAL B 594 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN B 317 " --> pdb=" O GLY B 592 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY B 592 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY B 593 " --> pdb=" O GLN B 612 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 609 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 642 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.204A pdb=" N GLU B 324 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 549 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 374 through 379 removed outlier: 6.825A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 552 through 553 removed outlier: 3.585A pdb=" N THR B 552 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 564 through 565 removed outlier: 6.897A pdb=" N PHE B 564 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 653 through 659 removed outlier: 4.155A pdb=" N GLU B 653 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR B 695 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN B 657 " --> pdb=" O THR B 695 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.493A pdb=" N ALA B 712 " --> pdb=" O ASN B1073 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN B1073 " --> pdb=" O ALA B 712 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU B1071 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR B1066 " --> pdb=" O HIS B1047 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N HIS B1047 " --> pdb=" O TYR B1066 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.493A pdb=" N ALA B 712 " --> pdb=" O ASN B1073 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN B1073 " --> pdb=" O ALA B 712 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU B1071 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B1075 " --> pdb=" O SER B1096 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 732 through 735 removed outlier: 4.469A pdb=" N LYS B 732 " --> pdb=" O LEU B 860 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1119 through 1124 removed outlier: 4.704A pdb=" N ALA B1086 " --> pdb=" O SER B1122 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.262A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.776A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.792A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.632A pdb=" N THR C 598 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL C 594 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN C 317 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY C 592 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY C 593 " --> pdb=" O GLN C 612 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 609 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.856A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.513A pdb=" N GLN C 492 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.895A pdb=" N TYR C 488 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 653 through 659 removed outlier: 3.945A pdb=" N GLU C 653 " --> pdb=" O ILE C 691 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR C 695 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN C 657 " --> pdb=" O THR C 695 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 669 " --> pdb=" O ILE C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.584A pdb=" N THR C1075 " --> pdb=" O SER C1096 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 716 through 727 removed outlier: 5.766A pdb=" N TYR C1066 " --> pdb=" O HIS C1047 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N HIS C1047 " --> pdb=" O TYR C1066 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 732 through 735 removed outlier: 4.429A pdb=" N LYS C 732 " --> pdb=" O LEU C 860 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1119 through 1124 removed outlier: 3.504A pdb=" N SER C1122 " --> pdb=" O ALA C1086 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA C1086 " --> pdb=" O SER C1122 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2631 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: 5.23 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7573 1.34 - 1.46: 6001 1.46 - 1.59: 11014 1.59 - 1.71: 0 1.71 - 1.84: 132 Bond restraints: 24720 Sorted by residual: bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.11e+01 bond pdb=" CA LEU C 517 " pdb=" CB LEU C 517 " ideal model delta sigma weight residual 1.524 1.581 -0.058 1.62e-02 3.81e+03 1.26e+01 bond pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.13e-02 7.83e+03 9.17e+00 bond pdb=" N VAL B 332 " pdb=" CA VAL B 332 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.31e-02 5.83e+03 7.39e+00 ... (remaining 24715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 32811 1.82 - 3.64: 743 3.64 - 5.46: 76 5.46 - 7.28: 13 7.28 - 9.10: 1 Bond angle restraints: 33644 Sorted by residual: angle pdb=" N GLU C 298 " pdb=" CA GLU C 298 " pdb=" C GLU C 298 " ideal model delta sigma weight residual 113.18 106.87 6.31 1.33e+00 5.65e-01 2.25e+01 angle pdb=" N VAL A 569 " pdb=" CA VAL A 569 " pdb=" C VAL A 569 " ideal model delta sigma weight residual 112.29 108.07 4.22 9.40e-01 1.13e+00 2.02e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 113.42 108.31 5.11 1.17e+00 7.31e-01 1.90e+01 angle pdb=" C THR B 333 " pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 121.81 130.91 -9.10 2.16e+00 2.14e-01 1.77e+01 angle pdb=" N PHE B 375 " pdb=" CA PHE B 375 " pdb=" C PHE B 375 " ideal model delta sigma weight residual 109.80 102.78 7.02 1.70e+00 3.46e-01 1.70e+01 ... (remaining 33639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 14175 21.04 - 42.07: 803 42.07 - 63.11: 122 63.11 - 84.14: 42 84.14 - 105.18: 11 Dihedral angle restraints: 15153 sinusoidal: 6362 harmonic: 8791 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 487 " pdb=" CB CYS B 487 " ideal model delta sinusoidal sigma weight residual -86.00 -168.36 82.36 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 487 " pdb=" CB CYS C 487 " ideal model delta sinusoidal sigma weight residual 93.00 164.56 -71.56 1 1.00e+01 1.00e-02 6.56e+01 dihedral pdb=" CB CYS B 737 " pdb=" SG CYS B 737 " pdb=" SG CYS B 759 " pdb=" CB CYS B 759 " ideal model delta sinusoidal sigma weight residual -86.00 -36.22 -49.78 1 1.00e+01 1.00e-02 3.40e+01 ... (remaining 15150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 3874 0.135 - 0.269: 16 0.269 - 0.404: 4 0.404 - 0.539: 1 0.539 - 0.673: 3 Chirality restraints: 3898 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.21e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.78e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.05e+01 ... (remaining 3895 not shown) Planarity restraints: 4328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " 0.299 2.00e-02 2.50e+03 2.60e-01 8.47e+02 pdb=" C7 NAG A1310 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " -0.454 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.269 2.00e-02 2.50e+03 2.34e-01 6.84e+02 pdb=" C7 NAG G 1 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.005 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.404 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.122 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C7 NAG A1304 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.092 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.159 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.018 2.00e-02 2.50e+03 ... (remaining 4325 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2980 2.75 - 3.29: 23241 3.29 - 3.83: 38439 3.83 - 4.36: 44400 4.36 - 4.90: 78007 Nonbonded interactions: 187067 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS B 824 " pdb=" O LEU B 937 " model vdw 2.251 3.120 nonbonded pdb=" OH TYR C 755 " pdb=" OD1 ASP C 993 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR B 755 " pdb=" OD1 ASP B 993 " model vdw 2.270 3.040 nonbonded pdb=" O ALA C 878 " pdb=" OG1 THR C 882 " model vdw 2.274 3.040 ... (remaining 187062 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 138 or resid 154 through 515 or resid 529 throu \ gh 1308)) selection = chain 'B' selection = (chain 'C' and (resid 26 through 138 or resid 154 through 515 or resid 529 throu \ gh 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.730 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 0.058 24792 Z= 0.202 Angle : 0.665 18.528 33823 Z= 0.364 Chirality : 0.049 0.673 3898 Planarity : 0.007 0.260 4298 Dihedral : 13.624 105.176 9388 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.52 % Favored : 93.24 % Rotamer: Outliers : 0.08 % Allowed : 0.41 % Favored : 99.51 % 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: -0.78 (0.15), residues: 2974 helix: 2.34 (0.20), residues: 698 sheet: -0.67 (0.22), residues: 556 loop : -1.79 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 355 TYR 0.022 0.001 TYR A 160 PHE 0.018 0.001 PHE C 905 TRP 0.010 0.001 TRP A1101 HIS 0.002 0.001 HIS A1057 Details of bonding type rmsd covalent geometry : bond 0.00368 (24720) covalent geometry : angle 0.61986 (33644) SS BOND : bond 0.00217 ( 37) SS BOND : angle 0.86527 ( 74) hydrogen bonds : bond 0.18649 ( 943) hydrogen bonds : angle 8.05711 ( 2631) link_BETA1-4 : bond 0.03452 ( 5) link_BETA1-4 : angle 7.10277 ( 15) link_NAG-ASN : bond 0.00700 ( 30) link_NAG-ASN : angle 3.64605 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.9127 (tt) cc_final: 0.8908 (pp) REVERT: A 347 PHE cc_start: 0.8094 (m-10) cc_final: 0.7661 (m-10) REVERT: A 365 TYR cc_start: 0.7782 (p90) cc_final: 0.7458 (p90) REVERT: A 382 VAL cc_start: 0.9002 (t) cc_final: 0.8788 (p) REVERT: A 423 TYR cc_start: 0.7826 (t80) cc_final: 0.7433 (t80) REVERT: A 533 VAL cc_start: 0.8526 (m) cc_final: 0.8310 (p) REVERT: A 977 ASN cc_start: 0.9208 (t0) cc_final: 0.8881 (t0) REVERT: B 201 PHE cc_start: 0.8806 (t80) cc_final: 0.8532 (t80) REVERT: B 265 TYR cc_start: 0.7214 (p90) cc_final: 0.6713 (p90) REVERT: B 989 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8523 (mm-30) REVERT: B 1134 ASN cc_start: 0.8523 (t0) cc_final: 0.8127 (t0) REVERT: C 52 GLN cc_start: 0.9322 (tt0) cc_final: 0.9085 (tm-30) REVERT: C 138 ASP cc_start: 0.7552 (t0) cc_final: 0.7299 (m-30) REVERT: C 319 ARG cc_start: 0.8600 (ttp-110) cc_final: 0.8315 (ptm-80) REVERT: C 500 TYR cc_start: 0.8792 (m-10) cc_final: 0.8064 (m-10) REVERT: C 857 LEU cc_start: 0.9062 (mt) cc_final: 0.8713 (pp) outliers start: 2 outliers final: 3 residues processed: 260 average time/residue: 0.6047 time to fit residues: 182.0796 Evaluate side-chains 130 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 635 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.0870 chunk 298 optimal weight: 0.7980 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN A 612 GLN A 954 ASN B 271 GLN B 339 HIS B 612 GLN B 643 GLN B1004 GLN C 30 ASN C 218 GLN C 321 GLN C 388 ASN C 612 GLN C 906 ASN C 964 GLN C1004 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.075893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.051753 restraints weight = 90006.981| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.34 r_work: 0.2946 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 24792 Z= 0.169 Angle : 0.648 12.133 33823 Z= 0.329 Chirality : 0.046 0.355 3898 Planarity : 0.004 0.066 4298 Dihedral : 7.452 97.016 3972 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.79 % Favored : 93.07 % Rotamer: Outliers : 0.98 % Allowed : 7.20 % Favored : 91.82 % 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: -0.78 (0.15), residues: 2974 helix: 2.16 (0.20), residues: 693 sheet: -0.44 (0.21), residues: 558 loop : -1.79 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 497 TYR 0.027 0.001 TYR A 365 PHE 0.017 0.001 PHE C 938 TRP 0.013 0.002 TRP B 353 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00384 (24720) covalent geometry : angle 0.62293 (33644) SS BOND : bond 0.00576 ( 37) SS BOND : angle 1.28223 ( 74) hydrogen bonds : bond 0.05361 ( 943) hydrogen bonds : angle 6.08216 ( 2631) link_BETA1-4 : bond 0.01216 ( 5) link_BETA1-4 : angle 4.04687 ( 15) link_NAG-ASN : bond 0.00555 ( 30) link_NAG-ASN : angle 2.90631 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.6711 (m-10) cc_final: 0.6498 (m-10) REVERT: A 739 MET cc_start: 0.9286 (ttm) cc_final: 0.8677 (tmm) REVERT: A 917 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9185 (mp0) REVERT: A 987 GLU cc_start: 0.8832 (mp0) cc_final: 0.8584 (mp0) REVERT: B 201 PHE cc_start: 0.8500 (t80) cc_final: 0.8199 (t80) REVERT: B 238 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5402 (p90) REVERT: B 265 TYR cc_start: 0.6821 (p90) cc_final: 0.6212 (p90) REVERT: B 1134 ASN cc_start: 0.8483 (t0) cc_final: 0.7986 (t0) REVERT: C 52 GLN cc_start: 0.9455 (tt0) cc_final: 0.9207 (tm-30) REVERT: C 138 ASP cc_start: 0.7375 (t0) cc_final: 0.7100 (m-30) REVERT: C 314 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8804 (tm-30) REVERT: C 456 PHE cc_start: 0.7819 (m-80) cc_final: 0.7488 (m-10) REVERT: C 515 GLU cc_start: 0.8747 (tp30) cc_final: 0.8504 (tp30) REVERT: C 857 LEU cc_start: 0.9157 (mt) cc_final: 0.8765 (pp) REVERT: C 1016 GLU cc_start: 0.9174 (tp30) cc_final: 0.8881 (tp30) outliers start: 26 outliers final: 10 residues processed: 155 average time/residue: 0.6029 time to fit residues: 108.4489 Evaluate side-chains 121 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 1000 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 278 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 210 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 343 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.074722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.050758 restraints weight = 89652.308| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.30 r_work: 0.2918 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24792 Z= 0.164 Angle : 0.598 9.971 33823 Z= 0.306 Chirality : 0.045 0.342 3898 Planarity : 0.004 0.064 4298 Dihedral : 6.939 109.372 3968 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.79 % Favored : 93.07 % Rotamer: Outliers : 1.32 % Allowed : 9.46 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.15), residues: 2974 helix: 2.13 (0.20), residues: 694 sheet: -0.47 (0.21), residues: 594 loop : -1.84 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 982 TYR 0.023 0.001 TYR C 500 PHE 0.019 0.001 PHE B 377 TRP 0.014 0.001 TRP C 452 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00373 (24720) covalent geometry : angle 0.57340 (33644) SS BOND : bond 0.00267 ( 37) SS BOND : angle 1.22407 ( 74) hydrogen bonds : bond 0.04948 ( 943) hydrogen bonds : angle 5.64975 ( 2631) link_BETA1-4 : bond 0.01135 ( 5) link_BETA1-4 : angle 3.87109 ( 15) link_NAG-ASN : bond 0.00439 ( 30) link_NAG-ASN : angle 2.79758 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8946 (t0) cc_final: 0.8680 (t0) REVERT: A 343 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6653 (p0) REVERT: A 987 GLU cc_start: 0.8888 (mp0) cc_final: 0.8555 (mp0) REVERT: B 201 PHE cc_start: 0.8573 (t80) cc_final: 0.8158 (t80) REVERT: B 238 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.5472 (p90) REVERT: B 265 TYR cc_start: 0.6880 (p90) cc_final: 0.6337 (p90) REVERT: B 377 PHE cc_start: 0.7260 (t80) cc_final: 0.7047 (t80) REVERT: B 507 TYR cc_start: 0.4885 (m-80) cc_final: 0.4478 (t80) REVERT: B 1134 ASN cc_start: 0.8585 (t0) cc_final: 0.7982 (t0) REVERT: C 52 GLN cc_start: 0.9459 (tt0) cc_final: 0.9222 (tm-30) REVERT: C 138 ASP cc_start: 0.7341 (t0) cc_final: 0.7034 (m-30) REVERT: C 456 PHE cc_start: 0.7883 (m-80) cc_final: 0.7546 (m-10) REVERT: C 515 GLU cc_start: 0.8743 (tp30) cc_final: 0.8426 (tp30) REVERT: C 857 LEU cc_start: 0.9218 (mt) cc_final: 0.8784 (pp) REVERT: C 982 ARG cc_start: 0.9010 (tpp80) cc_final: 0.8711 (tpp80) REVERT: C 1001 GLN cc_start: 0.9564 (tt0) cc_final: 0.9018 (tm-30) outliers start: 35 outliers final: 18 residues processed: 143 average time/residue: 0.6053 time to fit residues: 101.8297 Evaluate side-chains 120 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 987 GLU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1037 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 51 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B 954 ASN B 964 GLN C 218 GLN C 954 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047567 restraints weight = 90770.793| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.21 r_work: 0.2826 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 24792 Z= 0.386 Angle : 0.771 15.795 33823 Z= 0.392 Chirality : 0.049 0.353 3898 Planarity : 0.005 0.049 4298 Dihedral : 7.375 113.884 3968 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.41 % Favored : 91.43 % Rotamer: Outliers : 2.49 % Allowed : 11.27 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.15), residues: 2974 helix: 1.69 (0.20), residues: 705 sheet: -0.71 (0.20), residues: 599 loop : -2.02 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 497 TYR 0.025 0.002 TYR B 170 PHE 0.023 0.002 PHE C 905 TRP 0.019 0.002 TRP C 452 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00892 (24720) covalent geometry : angle 0.74264 (33644) SS BOND : bond 0.00446 ( 37) SS BOND : angle 1.59298 ( 74) hydrogen bonds : bond 0.06345 ( 943) hydrogen bonds : angle 5.94801 ( 2631) link_BETA1-4 : bond 0.00978 ( 5) link_BETA1-4 : angle 3.66773 ( 15) link_NAG-ASN : bond 0.00819 ( 30) link_NAG-ASN : angle 3.59720 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 103 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7740 (p90) REVERT: A 281 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8517 (pp20) REVERT: A 368 LEU cc_start: 0.9549 (mm) cc_final: 0.9331 (mm) REVERT: A 392 PHE cc_start: 0.6903 (m-80) cc_final: 0.6639 (m-80) REVERT: A 452 TRP cc_start: 0.9067 (m-10) cc_final: 0.8441 (m100) REVERT: A 568 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8027 (mp) REVERT: A 739 MET cc_start: 0.9043 (tmm) cc_final: 0.8826 (tmm) REVERT: A 987 GLU cc_start: 0.8959 (mp0) cc_final: 0.8668 (mp0) REVERT: B 201 PHE cc_start: 0.8691 (t80) cc_final: 0.8338 (t80) REVERT: B 238 PHE cc_start: 0.6314 (OUTLIER) cc_final: 0.5524 (p90) REVERT: B 899 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.8940 (mtm) REVERT: B 1001 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8904 (mp10) REVERT: C 138 ASP cc_start: 0.7455 (t0) cc_final: 0.7182 (m-30) REVERT: C 314 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8732 (tm-30) REVERT: C 456 PHE cc_start: 0.7907 (m-80) cc_final: 0.7634 (m-80) REVERT: C 515 GLU cc_start: 0.8686 (tp30) cc_final: 0.8385 (tp30) REVERT: C 857 LEU cc_start: 0.9360 (mt) cc_final: 0.8926 (pp) REVERT: C 984 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8553 (p0) REVERT: C 1001 GLN cc_start: 0.9578 (tt0) cc_final: 0.9065 (tm-30) outliers start: 66 outliers final: 23 residues processed: 149 average time/residue: 0.5074 time to fit residues: 91.1426 Evaluate side-chains 128 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 984 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 277 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN B 912 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.073871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.049425 restraints weight = 88970.948| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.30 r_work: 0.2881 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24792 Z= 0.145 Angle : 0.602 14.324 33823 Z= 0.306 Chirality : 0.045 0.360 3898 Planarity : 0.004 0.051 4298 Dihedral : 7.094 118.545 3968 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.76 % Favored : 93.11 % Rotamer: Outliers : 1.73 % Allowed : 12.22 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.15), residues: 2974 helix: 2.05 (0.20), residues: 700 sheet: -0.75 (0.20), residues: 595 loop : -1.90 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 497 TYR 0.018 0.001 TYR B1066 PHE 0.015 0.001 PHE A1074 TRP 0.020 0.001 TRP B 104 HIS 0.002 0.000 HIS B1087 Details of bonding type rmsd covalent geometry : bond 0.00328 (24720) covalent geometry : angle 0.56744 (33644) SS BOND : bond 0.00317 ( 37) SS BOND : angle 1.40812 ( 74) hydrogen bonds : bond 0.04975 ( 943) hydrogen bonds : angle 5.48652 ( 2631) link_BETA1-4 : bond 0.01042 ( 5) link_BETA1-4 : angle 3.19381 ( 15) link_NAG-ASN : bond 0.00705 ( 30) link_NAG-ASN : angle 3.56167 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9026 (t0) cc_final: 0.8599 (t0) REVERT: A 281 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8594 (pp20) REVERT: A 357 ARG cc_start: 0.8011 (tmm-80) cc_final: 0.7793 (tmm-80) REVERT: A 368 LEU cc_start: 0.9527 (mm) cc_final: 0.9298 (mm) REVERT: A 568 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 739 MET cc_start: 0.9106 (tmm) cc_final: 0.8832 (tmm) REVERT: A 987 GLU cc_start: 0.8987 (mp0) cc_final: 0.8574 (mp0) REVERT: B 201 PHE cc_start: 0.8626 (t80) cc_final: 0.8272 (t80) REVERT: B 369 TYR cc_start: 0.6863 (m-10) cc_final: 0.6611 (m-10) REVERT: B 758 PHE cc_start: 0.7966 (m-80) cc_final: 0.7376 (m-80) REVERT: B 877 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9137 (tm) REVERT: B 1001 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8917 (mp10) REVERT: C 138 ASP cc_start: 0.7371 (t0) cc_final: 0.7094 (m-30) REVERT: C 456 PHE cc_start: 0.7911 (m-80) cc_final: 0.7656 (m-80) REVERT: C 515 GLU cc_start: 0.8783 (tp30) cc_final: 0.8472 (tp30) REVERT: C 982 ARG cc_start: 0.9010 (tpp80) cc_final: 0.8791 (tpp80) REVERT: C 987 GLU cc_start: 0.9587 (mm-30) cc_final: 0.9287 (mp0) REVERT: C 1001 GLN cc_start: 0.9593 (tt0) cc_final: 0.9064 (tm-30) outliers start: 46 outliers final: 24 residues processed: 139 average time/residue: 0.4912 time to fit residues: 82.2851 Evaluate side-chains 127 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1004 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1000 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 88 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 234 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 216 optimal weight: 0.4980 chunk 23 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.073913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050209 restraints weight = 88887.972| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 4.25 r_work: 0.2904 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24792 Z= 0.120 Angle : 0.579 13.724 33823 Z= 0.292 Chirality : 0.044 0.350 3898 Planarity : 0.004 0.042 4298 Dihedral : 6.967 120.951 3968 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.89 % Favored : 92.97 % Rotamer: Outliers : 1.66 % Allowed : 13.01 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 2974 helix: 2.10 (0.20), residues: 707 sheet: -0.59 (0.20), residues: 600 loop : -1.86 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 982 TYR 0.020 0.001 TYR B 170 PHE 0.024 0.001 PHE C 938 TRP 0.020 0.001 TRP B 104 HIS 0.002 0.000 HIS B1087 Details of bonding type rmsd covalent geometry : bond 0.00270 (24720) covalent geometry : angle 0.54802 (33644) SS BOND : bond 0.00290 ( 37) SS BOND : angle 1.13501 ( 74) hydrogen bonds : bond 0.04500 ( 943) hydrogen bonds : angle 5.28842 ( 2631) link_BETA1-4 : bond 0.01032 ( 5) link_BETA1-4 : angle 3.03201 ( 15) link_NAG-ASN : bond 0.00656 ( 30) link_NAG-ASN : angle 3.31085 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9015 (t0) cc_final: 0.8581 (t0) REVERT: A 314 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8795 (tm-30) REVERT: A 368 LEU cc_start: 0.9508 (mm) cc_final: 0.9277 (mm) REVERT: A 392 PHE cc_start: 0.7497 (m-80) cc_final: 0.7212 (m-80) REVERT: A 568 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7910 (mp) REVERT: A 739 MET cc_start: 0.9134 (tmm) cc_final: 0.8809 (tmm) REVERT: A 987 GLU cc_start: 0.9006 (mp0) cc_final: 0.8596 (mp0) REVERT: B 201 PHE cc_start: 0.8627 (t80) cc_final: 0.8411 (t80) REVERT: B 758 PHE cc_start: 0.7843 (m-80) cc_final: 0.7349 (m-80) REVERT: B 1001 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8931 (mp10) REVERT: C 138 ASP cc_start: 0.7354 (t0) cc_final: 0.7100 (m-30) REVERT: C 456 PHE cc_start: 0.7885 (m-80) cc_final: 0.7546 (m-10) REVERT: C 515 GLU cc_start: 0.8828 (tp30) cc_final: 0.8523 (tp30) REVERT: C 984 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8442 (p0) REVERT: C 1001 GLN cc_start: 0.9596 (tt0) cc_final: 0.9063 (tm-30) outliers start: 44 outliers final: 22 residues processed: 144 average time/residue: 0.5050 time to fit residues: 87.9307 Evaluate side-chains 118 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1004 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain C residue 1000 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 25 optimal weight: 8.9990 chunk 168 optimal weight: 0.0670 chunk 136 optimal weight: 40.0000 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.073739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050215 restraints weight = 89005.752| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.21 r_work: 0.2903 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24792 Z= 0.127 Angle : 0.568 11.892 33823 Z= 0.287 Chirality : 0.044 0.346 3898 Planarity : 0.004 0.089 4298 Dihedral : 6.842 119.016 3968 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.52 % Favored : 93.31 % Rotamer: Outliers : 1.73 % Allowed : 13.54 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.15), residues: 2974 helix: 2.19 (0.20), residues: 701 sheet: -0.53 (0.20), residues: 597 loop : -1.81 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 982 TYR 0.017 0.001 TYR B1066 PHE 0.030 0.001 PHE B 377 TRP 0.022 0.001 TRP B 104 HIS 0.001 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00290 (24720) covalent geometry : angle 0.53955 (33644) SS BOND : bond 0.00269 ( 37) SS BOND : angle 1.06927 ( 74) hydrogen bonds : bond 0.04432 ( 943) hydrogen bonds : angle 5.21243 ( 2631) link_BETA1-4 : bond 0.00982 ( 5) link_BETA1-4 : angle 2.96159 ( 15) link_NAG-ASN : bond 0.00589 ( 30) link_NAG-ASN : angle 3.14147 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9014 (t0) cc_final: 0.8573 (t0) REVERT: A 281 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8602 (pp20) REVERT: A 314 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8804 (tm-30) REVERT: A 357 ARG cc_start: 0.8070 (tmm-80) cc_final: 0.7843 (tmm-80) REVERT: A 368 LEU cc_start: 0.9493 (mm) cc_final: 0.9262 (mm) REVERT: A 392 PHE cc_start: 0.7462 (m-80) cc_final: 0.6934 (m-80) REVERT: A 568 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 696 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8640 (ptp) REVERT: A 739 MET cc_start: 0.9166 (tmm) cc_final: 0.8773 (tmm) REVERT: A 987 GLU cc_start: 0.9093 (mp0) cc_final: 0.8691 (mp0) REVERT: B 758 PHE cc_start: 0.7910 (m-80) cc_final: 0.7499 (m-80) REVERT: B 868 MET cc_start: 0.9202 (mtt) cc_final: 0.8791 (mtt) REVERT: B 1001 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8908 (mp10) REVERT: C 456 PHE cc_start: 0.7921 (m-80) cc_final: 0.7683 (m-80) REVERT: C 515 GLU cc_start: 0.8855 (tp30) cc_final: 0.8564 (tp30) REVERT: C 987 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9447 (mp0) REVERT: C 1001 GLN cc_start: 0.9602 (tt0) cc_final: 0.9050 (tm-30) outliers start: 46 outliers final: 26 residues processed: 138 average time/residue: 0.4735 time to fit residues: 79.6624 Evaluate side-chains 127 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1004 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1000 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 201 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 300 optimal weight: 5.9990 chunk 223 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 185 optimal weight: 0.0270 chunk 246 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.073656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049963 restraints weight = 89972.031| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.25 r_work: 0.2886 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24792 Z= 0.138 Angle : 0.577 10.953 33823 Z= 0.290 Chirality : 0.044 0.344 3898 Planarity : 0.004 0.086 4298 Dihedral : 6.757 118.203 3968 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.79 % Favored : 93.07 % Rotamer: Outliers : 1.47 % Allowed : 13.88 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.15), residues: 2974 helix: 2.11 (0.20), residues: 708 sheet: -0.58 (0.20), residues: 609 loop : -1.79 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 982 TYR 0.021 0.001 TYR B 170 PHE 0.027 0.001 PHE C 938 TRP 0.021 0.001 TRP C 452 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00316 (24720) covalent geometry : angle 0.55157 (33644) SS BOND : bond 0.00259 ( 37) SS BOND : angle 1.05688 ( 74) hydrogen bonds : bond 0.04452 ( 943) hydrogen bonds : angle 5.19092 ( 2631) link_BETA1-4 : bond 0.00969 ( 5) link_BETA1-4 : angle 2.90894 ( 15) link_NAG-ASN : bond 0.00561 ( 30) link_NAG-ASN : angle 3.02572 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9020 (t0) cc_final: 0.8580 (t0) REVERT: A 281 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8616 (pp20) REVERT: A 314 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8791 (tm-30) REVERT: A 357 ARG cc_start: 0.8101 (tmm-80) cc_final: 0.7852 (tmm-80) REVERT: A 368 LEU cc_start: 0.9492 (mm) cc_final: 0.9252 (mm) REVERT: A 568 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 696 MET cc_start: 0.9333 (ttp) cc_final: 0.8811 (ptp) REVERT: A 739 MET cc_start: 0.9145 (tmm) cc_final: 0.8737 (tmm) REVERT: A 987 GLU cc_start: 0.9117 (mp0) cc_final: 0.8717 (mp0) REVERT: B 1001 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8934 (mp10) REVERT: C 456 PHE cc_start: 0.7905 (m-80) cc_final: 0.7656 (m-80) REVERT: C 515 GLU cc_start: 0.8865 (tp30) cc_final: 0.8565 (tp30) REVERT: C 987 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9440 (mp0) REVERT: C 1001 GLN cc_start: 0.9606 (tt0) cc_final: 0.9063 (tm-30) outliers start: 39 outliers final: 26 residues processed: 132 average time/residue: 0.5606 time to fit residues: 88.2021 Evaluate side-chains 123 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1000 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 177 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 GLN A 948 GLN B 912 GLN C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.047694 restraints weight = 92071.500| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 4.25 r_work: 0.2820 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 24792 Z= 0.288 Angle : 0.687 11.195 33823 Z= 0.349 Chirality : 0.047 0.349 3898 Planarity : 0.004 0.080 4298 Dihedral : 7.109 116.790 3968 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.20 % Favored : 91.66 % Rotamer: Outliers : 1.62 % Allowed : 13.69 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.15), residues: 2974 helix: 1.85 (0.20), residues: 710 sheet: -0.69 (0.20), residues: 618 loop : -1.94 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 982 TYR 0.020 0.002 TYR A 903 PHE 0.032 0.002 PHE B 377 TRP 0.028 0.002 TRP C 452 HIS 0.007 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00671 (24720) covalent geometry : angle 0.66365 (33644) SS BOND : bond 0.00353 ( 37) SS BOND : angle 1.42014 ( 74) hydrogen bonds : bond 0.05788 ( 943) hydrogen bonds : angle 5.56313 ( 2631) link_BETA1-4 : bond 0.00902 ( 5) link_BETA1-4 : angle 3.05852 ( 15) link_NAG-ASN : bond 0.00525 ( 30) link_NAG-ASN : angle 3.07699 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9065 (t0) cc_final: 0.8608 (t0) REVERT: A 281 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8580 (pp20) REVERT: A 314 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8687 (tm-30) REVERT: A 357 ARG cc_start: 0.8241 (tmm-80) cc_final: 0.7969 (tmm-80) REVERT: A 368 LEU cc_start: 0.9509 (mm) cc_final: 0.9297 (mm) REVERT: A 568 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8018 (mp) REVERT: A 696 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.9011 (ptp) REVERT: A 739 MET cc_start: 0.9199 (tmm) cc_final: 0.8819 (tmm) REVERT: A 987 GLU cc_start: 0.9107 (mp0) cc_final: 0.8691 (mp0) REVERT: B 33 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8350 (m) REVERT: B 1001 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8965 (mp10) REVERT: C 456 PHE cc_start: 0.7899 (m-80) cc_final: 0.7597 (m-80) REVERT: C 515 GLU cc_start: 0.8827 (tp30) cc_final: 0.8505 (tp30) REVERT: C 1001 GLN cc_start: 0.9604 (tt0) cc_final: 0.9089 (tm-30) outliers start: 43 outliers final: 31 residues processed: 125 average time/residue: 0.5112 time to fit residues: 77.0260 Evaluate side-chains 128 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 975 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 248 optimal weight: 0.0050 chunk 12 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 4 optimal weight: 0.0000 chunk 18 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN B 912 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.073515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049740 restraints weight = 90169.605| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.29 r_work: 0.2891 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24792 Z= 0.113 Angle : 0.589 10.443 33823 Z= 0.297 Chirality : 0.044 0.350 3898 Planarity : 0.004 0.086 4298 Dihedral : 6.739 117.133 3968 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 1.13 % Allowed : 14.44 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.15), residues: 2974 helix: 1.98 (0.20), residues: 714 sheet: -0.56 (0.20), residues: 597 loop : -1.80 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 982 TYR 0.021 0.001 TYR B 170 PHE 0.028 0.001 PHE C 938 TRP 0.026 0.001 TRP B 104 HIS 0.003 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00248 (24720) covalent geometry : angle 0.56505 (33644) SS BOND : bond 0.00250 ( 37) SS BOND : angle 1.04619 ( 74) hydrogen bonds : bond 0.04391 ( 943) hydrogen bonds : angle 5.17284 ( 2631) link_BETA1-4 : bond 0.01017 ( 5) link_BETA1-4 : angle 2.75926 ( 15) link_NAG-ASN : bond 0.00614 ( 30) link_NAG-ASN : angle 2.95763 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5948 Ramachandran restraints generated. 2974 Oldfield, 0 Emsley, 2974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9022 (t0) cc_final: 0.8562 (t0) REVERT: A 314 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8692 (tm-30) REVERT: A 368 LEU cc_start: 0.9513 (mm) cc_final: 0.9281 (mm) REVERT: A 696 MET cc_start: 0.9305 (ttp) cc_final: 0.8892 (ptp) REVERT: A 739 MET cc_start: 0.9180 (tmm) cc_final: 0.8764 (tmm) REVERT: A 987 GLU cc_start: 0.9133 (mp0) cc_final: 0.8710 (mp0) REVERT: B 1001 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8960 (mp10) REVERT: C 456 PHE cc_start: 0.7935 (m-80) cc_final: 0.7683 (m-80) REVERT: C 515 GLU cc_start: 0.8873 (tp30) cc_final: 0.8573 (tp30) REVERT: C 987 GLU cc_start: 0.9428 (mp0) cc_final: 0.9177 (mp0) REVERT: C 1001 GLN cc_start: 0.9613 (tt0) cc_final: 0.9071 (tm-30) outliers start: 30 outliers final: 27 residues processed: 129 average time/residue: 0.5433 time to fit residues: 84.5029 Evaluate side-chains 119 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1073 ASN Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1000 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 262 optimal weight: 0.8980 chunk 172 optimal weight: 0.4980 chunk 194 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 ASN B 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.073101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049337 restraints weight = 90828.554| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 4.30 r_work: 0.2878 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24792 Z= 0.126 Angle : 0.589 9.934 33823 Z= 0.297 Chirality : 0.044 0.305 3898 Planarity : 0.004 0.078 4298 Dihedral : 7.526 124.504 3968 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.72 % Favored : 93.14 % Rotamer: Outliers : 1.09 % Allowed : 14.67 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.15), residues: 2974 helix: 2.00 (0.20), residues: 714 sheet: -0.50 (0.20), residues: 616 loop : -1.80 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 982 TYR 0.017 0.001 TYR B1066 PHE 0.033 0.001 PHE B 377 TRP 0.026 0.001 TRP B 104 HIS 0.005 0.000 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00287 (24720) covalent geometry : angle 0.56584 (33644) SS BOND : bond 0.00241 ( 37) SS BOND : angle 1.13080 ( 74) hydrogen bonds : bond 0.04372 ( 943) hydrogen bonds : angle 5.10276 ( 2631) link_BETA1-4 : bond 0.00957 ( 5) link_BETA1-4 : angle 2.78265 ( 15) link_NAG-ASN : bond 0.00518 ( 30) link_NAG-ASN : angle 2.89939 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7643.55 seconds wall clock time: 131 minutes 18.09 seconds (7878.09 seconds total)