Starting phenix.real_space_refine on Sat Jun 21 03:58:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5j_38937/06_2025/8y5j_38937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5j_38937/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y5j_38937/06_2025/8y5j_38937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5j_38937/06_2025/8y5j_38937.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5j_38937/06_2025/8y5j_38937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5j_38937/06_2025/8y5j_38937.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.31, per 1000 atoms: 0.63 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: 6.49 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 3.80 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: 11.10 Time building geometry restraints manager: 7.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 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 1139 or resid 1301 through 1308)) selection = chain 'B' selection = (chain 'C' and (resid 26 through 138 or resid 154 through 515 or resid 529 throu \ gh 1139 or resid 1301 through 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: 43.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 60.520 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.190 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A1101 HIS 0.002 0.001 HIS A1057 PHE 0.018 0.001 PHE C 905 TYR 0.022 0.001 TYR A 160 ARG 0.006 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 30) link_NAG-ASN : angle 3.64605 ( 90) link_BETA1-4 : bond 0.03452 ( 5) link_BETA1-4 : angle 7.10277 ( 15) hydrogen bonds : bond 0.18649 ( 943) hydrogen bonds : angle 8.05711 ( 2631) SS BOND : bond 0.00217 ( 37) SS BOND : angle 0.86527 ( 74) covalent geometry : bond 0.00368 (24720) covalent geometry : angle 0.61986 (33644) *********************** 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 : 3.141 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 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: 0.7461 (p90) REVERT: A 382 VAL cc_start: 0.9002 (t) cc_final: 0.8788 (p) 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 168 PHE cc_start: 0.7566 (t80) cc_final: 0.7325 (m-80) REVERT: B 171 VAL cc_start: 0.9578 (m) cc_final: 0.9229 (t) REVERT: B 201 PHE cc_start: 0.8806 (t80) cc_final: 0.8535 (t80) REVERT: B 265 TYR cc_start: 0.7214 (p90) cc_final: 0.6713 (p90) REVERT: B 696 MET cc_start: 0.8929 (ttp) cc_final: 0.8728 (ptm) REVERT: B 1134 ASN cc_start: 0.8523 (t0) cc_final: 0.8128 (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: 0.7311 (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: 0.8056 (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: 1.3329 time to fit residues: 405.2362 Evaluate side-chains 128 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 2.584 ------------------------------------------------------------------------------- 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 254 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 273 optimal weight: 0.0060 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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 321 GLN C 388 ASN C 612 GLN C 906 ASN C1004 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.075837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.051848 restraints weight = 89760.062| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.30 r_work: 0.2947 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 24792 Z= 0.170 Angle : 0.651 11.428 33823 Z= 0.332 Chirality : 0.046 0.353 3898 Planarity : 0.004 0.066 4298 Dihedral : 7.508 99.232 3972 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.76 % Favored : 93.11 % Rotamer: Outliers : 0.90 % Allowed : 7.32 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 2974 helix: 2.11 (0.20), residues: 700 sheet: -0.46 (0.21), residues: 558 loop : -1.80 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.005 0.001 HIS B 207 PHE 0.018 0.001 PHE C 938 TYR 0.026 0.001 TYR A 365 ARG 0.007 0.001 ARG C 497 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 30) link_NAG-ASN : angle 2.87855 ( 90) link_BETA1-4 : bond 0.01115 ( 5) link_BETA1-4 : angle 4.20838 ( 15) hydrogen bonds : bond 0.05266 ( 943) hydrogen bonds : angle 6.09574 ( 2631) SS BOND : bond 0.00303 ( 37) SS BOND : angle 1.29807 ( 74) covalent geometry : bond 0.00387 (24720) covalent geometry : angle 0.62613 (33644) *********************** 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 156 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 2.985 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 739 MET cc_start: 0.9287 (ttm) cc_final: 0.8657 (tmm) REVERT: A 917 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9181 (mp0) REVERT: A 987 GLU cc_start: 0.8969 (mp0) cc_final: 0.8679 (mp0) REVERT: B 170 TYR cc_start: 0.8603 (m-80) cc_final: 0.8331 (m-80) REVERT: B 201 PHE cc_start: 0.8505 (t80) cc_final: 0.8179 (t80) REVERT: B 238 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5415 (p90) REVERT: B 265 TYR cc_start: 0.6815 (p90) cc_final: 0.6214 (p90) REVERT: B 1134 ASN cc_start: 0.8480 (t0) cc_final: 0.7986 (t0) REVERT: C 138 ASP cc_start: 0.7389 (t0) cc_final: 0.7121 (m-30) REVERT: C 314 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8816 (tm-30) REVERT: C 456 PHE cc_start: 0.7832 (m-80) cc_final: 0.7617 (m-80) REVERT: C 515 GLU cc_start: 0.8761 (tp30) cc_final: 0.8524 (tp30) REVERT: C 857 LEU cc_start: 0.9161 (mt) cc_final: 0.8768 (pp) REVERT: C 1016 GLU cc_start: 0.9184 (tp30) cc_final: 0.8892 (tp30) outliers start: 24 outliers final: 9 residues processed: 152 average time/residue: 1.2868 time to fit residues: 230.3399 Evaluate side-chains 120 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 2.833 ------------------------------------------------------------------------------- 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 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 197 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 292 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 C 218 GLN C 964 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.073324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049212 restraints weight = 89717.683| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.28 r_work: 0.2863 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24792 Z= 0.259 Angle : 0.674 10.593 33823 Z= 0.345 Chirality : 0.047 0.341 3898 Planarity : 0.004 0.049 4298 Dihedral : 7.115 108.380 3968 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.40 % Favored : 92.47 % Rotamer: Outliers : 1.92 % Allowed : 9.73 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 2974 helix: 1.89 (0.20), residues: 699 sheet: -0.62 (0.20), residues: 598 loop : -1.92 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.005 0.001 HIS B 49 PHE 0.024 0.002 PHE C 905 TYR 0.020 0.002 TYR B1066 ARG 0.007 0.001 ARG C 982 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 30) link_NAG-ASN : angle 2.87713 ( 90) link_BETA1-4 : bond 0.01034 ( 5) link_BETA1-4 : angle 3.84861 ( 15) hydrogen bonds : bond 0.05803 ( 943) hydrogen bonds : angle 5.83138 ( 2631) SS BOND : bond 0.00361 ( 37) SS BOND : angle 1.31620 ( 74) covalent geometry : bond 0.00598 (24720) covalent geometry : angle 0.65138 (33644) *********************** 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 155 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 2.976 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: 0.8349 (OUTLIER) cc_final: 0.7799 (p90) REVERT: A 568 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7882 (mp) REVERT: A 987 GLU cc_start: 0.8945 (mp0) cc_final: 0.8639 (mp0) REVERT: A 1001 GLN cc_start: 0.9304 (tp40) cc_final: 0.9098 (tp40) REVERT: B 170 TYR cc_start: 0.8666 (m-80) cc_final: 0.8430 (m-80) REVERT: B 201 PHE cc_start: 0.8641 (t80) cc_final: 0.8197 (t80) REVERT: B 238 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.5420 (p90) REVERT: B 507 TYR cc_start: 0.5368 (m-80) cc_final: 0.4903 (t80) REVERT: B 1001 GLN cc_start: 0.9425 (mt0) cc_final: 0.9106 (tm-30) REVERT: C 138 ASP cc_start: 0.7473 (t0) cc_final: 0.7145 (m-30) REVERT: C 314 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8664 (tm-30) REVERT: C 456 PHE cc_start: 0.7926 (m-80) cc_final: 0.7689 (m-80) REVERT: C 515 GLU cc_start: 0.8678 (tp30) cc_final: 0.8374 (tp30) REVERT: C 857 LEU cc_start: 0.9279 (mt) cc_final: 0.8854 (pp) REVERT: C 982 ARG cc_start: 0.9039 (tpp80) cc_final: 0.8730 (tpp80) REVERT: C 1001 GLN cc_start: 0.9592 (tt0) cc_final: 0.9136 (tm-30) outliers start: 51 outliers final: 18 residues processed: 143 average time/residue: 1.1343 time to fit residues: 195.0557 Evaluate side-chains 117 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 2.773 ------------------------------------------------------------------------------- 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 160 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 203 ILE 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 1073 ASN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 386 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 133 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 210 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.075430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050746 restraints weight = 89553.531| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.41 r_work: 0.2910 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24792 Z= 0.119 Angle : 0.597 17.930 33823 Z= 0.301 Chirality : 0.045 0.358 3898 Planarity : 0.004 0.056 4298 Dihedral : 7.020 117.569 3968 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.88 % Favored : 93.95 % Rotamer: Outliers : 1.36 % Allowed : 11.46 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 2974 helix: 2.07 (0.20), residues: 701 sheet: -0.58 (0.20), residues: 587 loop : -1.79 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 104 HIS 0.003 0.000 HIS A 445 PHE 0.028 0.001 PHE A1074 TYR 0.018 0.001 TYR B1066 ARG 0.010 0.000 ARG A 497 Details of bonding type rmsd link_NAG-ASN : bond 0.01015 ( 30) link_NAG-ASN : angle 3.58679 ( 90) link_BETA1-4 : bond 0.01079 ( 5) link_BETA1-4 : angle 3.40773 ( 15) hydrogen bonds : bond 0.04651 ( 943) hydrogen bonds : angle 5.47216 ( 2631) SS BOND : bond 0.00261 ( 37) SS BOND : angle 1.06574 ( 74) covalent geometry : bond 0.00253 (24720) covalent geometry : angle 0.56239 (33644) *********************** 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 144 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 3.985 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 126 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7817 (p) REVERT: A 281 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8670 (pp20) REVERT: A 568 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7880 (mp) REVERT: A 739 MET cc_start: 0.9030 (tmm) cc_final: 0.8764 (tmm) REVERT: A 987 GLU cc_start: 0.9020 (mp0) cc_final: 0.8738 (mp0) REVERT: A 1001 GLN cc_start: 0.9327 (tp40) cc_final: 0.9067 (tp40) REVERT: B 170 TYR cc_start: 0.8695 (m-80) cc_final: 0.8478 (m-80) REVERT: B 201 PHE cc_start: 0.8534 (t80) cc_final: 0.8216 (t80) REVERT: B 238 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5434 (p90) REVERT: B 507 TYR cc_start: 0.5213 (m-80) cc_final: 0.4850 (t80) REVERT: B 758 PHE cc_start: 0.7998 (m-80) cc_final: 0.7417 (m-80) REVERT: C 138 ASP cc_start: 0.7390 (t0) cc_final: 0.7057 (m-30) REVERT: C 456 PHE cc_start: 0.7847 (m-80) cc_final: 0.7625 (m-80) REVERT: C 515 GLU cc_start: 0.8761 (tp30) cc_final: 0.8443 (tp30) REVERT: C 982 ARG cc_start: 0.9048 (tpp80) cc_final: 0.8809 (tpp80) REVERT: C 984 ASP cc_start: 0.8678 (p0) cc_final: 0.8302 (p0) REVERT: C 987 GLU cc_start: 0.9582 (mp0) cc_final: 0.9320 (mp0) REVERT: C 1001 GLN cc_start: 0.9566 (tt0) cc_final: 0.9043 (tm-30) outliers start: 36 outliers final: 15 residues processed: 138 average time/residue: 1.2939 time to fit residues: 216.8973 Evaluate side-chains 115 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 281 GLU Chi-restraints excluded: chain A residue 334 ASN 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 B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 1073 ASN 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 1000 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 211 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 126 optimal weight: 0.0670 chunk 120 optimal weight: 7.9990 overall best weight: 2.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN B 954 ASN C 218 GLN C 954 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.072504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.048781 restraints weight = 90288.611| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.22 r_work: 0.2860 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 24792 Z= 0.251 Angle : 0.646 14.536 33823 Z= 0.325 Chirality : 0.045 0.348 3898 Planarity : 0.004 0.052 4298 Dihedral : 7.040 118.546 3968 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.46 % Favored : 92.40 % Rotamer: Outliers : 2.41 % Allowed : 11.46 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2974 helix: 1.92 (0.20), residues: 706 sheet: -0.74 (0.20), residues: 619 loop : -1.85 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 452 HIS 0.004 0.001 HIS B 207 PHE 0.025 0.001 PHE C 938 TYR 0.018 0.001 TYR B1066 ARG 0.003 0.000 ARG B1018 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 30) link_NAG-ASN : angle 3.60047 ( 90) link_BETA1-4 : bond 0.00934 ( 5) link_BETA1-4 : angle 3.34394 ( 15) hydrogen bonds : bond 0.05321 ( 943) hydrogen bonds : angle 5.57187 ( 2631) SS BOND : bond 0.00389 ( 37) SS BOND : angle 1.48374 ( 74) covalent geometry : bond 0.00580 (24720) covalent geometry : angle 0.61193 (33644) *********************** 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 160 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 96 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8588 (pp20) REVERT: A 368 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9350 (mm) REVERT: A 452 TRP cc_start: 0.9087 (m-10) cc_final: 0.8423 (m100) REVERT: A 568 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7972 (mp) REVERT: A 696 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8926 (ptp) REVERT: A 739 MET cc_start: 0.9141 (tmm) cc_final: 0.8782 (tmm) REVERT: A 987 GLU cc_start: 0.9024 (mp0) cc_final: 0.8715 (mp0) REVERT: A 1001 GLN cc_start: 0.9399 (tp40) cc_final: 0.9087 (tp40) REVERT: B 33 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8440 (m) REVERT: B 201 PHE cc_start: 0.8620 (t80) cc_final: 0.8300 (t80) REVERT: B 238 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5457 (p90) REVERT: B 1001 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8889 (mp10) REVERT: C 138 ASP cc_start: 0.7393 (t0) cc_final: 0.7139 (m-30) REVERT: C 456 PHE cc_start: 0.7943 (m-80) cc_final: 0.7681 (m-80) REVERT: C 515 GLU cc_start: 0.8764 (tp30) cc_final: 0.8457 (tp30) REVERT: C 1001 GLN cc_start: 0.9564 (tt0) cc_final: 0.9038 (tm-30) outliers start: 64 outliers final: 29 residues processed: 146 average time/residue: 0.9446 time to fit residues: 169.9971 Evaluate side-chains 125 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 281 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 417 ASN 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 598 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE 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 320 VAL Chi-restraints excluded: chain C residue 324 GLU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 43 optimal weight: 0.0070 chunk 299 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 275 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.073668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049899 restraints weight = 89173.464| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.25 r_work: 0.2894 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24792 Z= 0.132 Angle : 0.581 15.055 33823 Z= 0.294 Chirality : 0.044 0.351 3898 Planarity : 0.004 0.047 4298 Dihedral : 6.967 119.803 3968 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 1.85 % Allowed : 12.59 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 2974 helix: 2.04 (0.20), residues: 707 sheet: -0.58 (0.20), residues: 587 loop : -1.81 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 104 HIS 0.002 0.000 HIS B1087 PHE 0.017 0.001 PHE B 92 TYR 0.018 0.001 TYR B1066 ARG 0.004 0.000 ARG C 982 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 30) link_NAG-ASN : angle 3.42833 ( 90) link_BETA1-4 : bond 0.01024 ( 5) link_BETA1-4 : angle 3.08411 ( 15) hydrogen bonds : bond 0.04646 ( 943) hydrogen bonds : angle 5.34021 ( 2631) SS BOND : bond 0.00288 ( 37) SS BOND : angle 1.23770 ( 74) covalent geometry : bond 0.00298 (24720) covalent geometry : angle 0.54846 (33644) *********************** 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 149 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 2.833 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 126 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7780 (p) REVERT: A 281 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8659 (pp20) REVERT: A 368 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9339 (mm) REVERT: A 568 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7973 (mp) REVERT: A 696 MET cc_start: 0.9336 (ttp) cc_final: 0.8867 (ptp) REVERT: A 739 MET cc_start: 0.9134 (tmm) cc_final: 0.8738 (tmm) REVERT: A 987 GLU cc_start: 0.9059 (mp0) cc_final: 0.8696 (mp0) REVERT: A 1001 GLN cc_start: 0.9391 (tp40) cc_final: 0.9032 (tp40) REVERT: B 168 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: B 201 PHE cc_start: 0.8574 (t80) cc_final: 0.8266 (t80) REVERT: B 758 PHE cc_start: 0.7946 (m-80) cc_final: 0.7397 (m-80) REVERT: B 1001 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8931 (mp10) REVERT: C 138 ASP cc_start: 0.7363 (t0) cc_final: 0.7108 (m-30) REVERT: C 456 PHE cc_start: 0.7910 (m-80) cc_final: 0.7676 (m-80) REVERT: C 515 GLU cc_start: 0.8805 (tp30) cc_final: 0.8502 (tp30) REVERT: C 1001 GLN cc_start: 0.9571 (tt0) cc_final: 0.9047 (tm-30) outliers start: 49 outliers final: 29 residues processed: 142 average time/residue: 1.0464 time to fit residues: 182.1871 Evaluate side-chains 129 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 2.927 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 417 ASN 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 B residue 33 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 203 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 383 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 15 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 288 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 199 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.073828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050024 restraints weight = 89422.574| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 4.28 r_work: 0.2898 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24792 Z= 0.128 Angle : 0.574 13.847 33823 Z= 0.289 Chirality : 0.044 0.347 3898 Planarity : 0.004 0.090 4298 Dihedral : 6.923 119.096 3968 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.72 % Favored : 93.14 % Rotamer: Outliers : 1.81 % Allowed : 13.12 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 2974 helix: 2.11 (0.20), residues: 701 sheet: -0.56 (0.20), residues: 599 loop : -1.77 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 104 HIS 0.002 0.000 HIS B1087 PHE 0.047 0.001 PHE A 392 TYR 0.017 0.001 TYR B1066 ARG 0.005 0.000 ARG C 982 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 30) link_NAG-ASN : angle 3.29584 ( 90) link_BETA1-4 : bond 0.00979 ( 5) link_BETA1-4 : angle 2.99797 ( 15) hydrogen bonds : bond 0.04472 ( 943) hydrogen bonds : angle 5.24563 ( 2631) SS BOND : bond 0.00260 ( 37) SS BOND : angle 1.08215 ( 74) covalent geometry : bond 0.00288 (24720) covalent geometry : angle 0.54379 (33644) *********************** 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 144 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 3.255 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 314 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8781 (tm-30) REVERT: A 368 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9330 (mm) REVERT: A 568 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 696 MET cc_start: 0.9333 (ttp) cc_final: 0.8844 (ptp) REVERT: A 739 MET cc_start: 0.9170 (tmm) cc_final: 0.8833 (tmm) REVERT: A 987 GLU cc_start: 0.9124 (mp0) cc_final: 0.8764 (mp0) REVERT: A 1001 GLN cc_start: 0.9400 (tp40) cc_final: 0.9043 (tp40) REVERT: B 168 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: B 201 PHE cc_start: 0.8575 (t80) cc_final: 0.8296 (t80) REVERT: B 758 PHE cc_start: 0.7953 (m-80) cc_final: 0.7472 (m-80) REVERT: B 894 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8745 (pt0) REVERT: B 1001 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8918 (mp10) REVERT: C 456 PHE cc_start: 0.7909 (m-80) cc_final: 0.7670 (m-80) REVERT: C 515 GLU cc_start: 0.8836 (tp30) cc_final: 0.8550 (tp30) REVERT: C 1001 GLN cc_start: 0.9576 (tt0) cc_final: 0.9057 (tm-30) outliers start: 48 outliers final: 28 residues processed: 139 average time/residue: 1.4012 time to fit residues: 238.0249 Evaluate side-chains 124 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 3.660 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 417 ASN 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 598 THR Chi-restraints excluded: chain A residue 1004 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 203 ILE 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 894 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 114 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 235 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.074553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050864 restraints weight = 88721.125| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.26 r_work: 0.2924 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24792 Z= 0.107 Angle : 0.558 12.899 33823 Z= 0.283 Chirality : 0.044 0.345 3898 Planarity : 0.004 0.088 4298 Dihedral : 6.734 117.730 3968 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.02 % Favored : 93.81 % Rotamer: Outliers : 1.73 % Allowed : 13.20 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2974 helix: 2.08 (0.20), residues: 707 sheet: -0.48 (0.20), residues: 594 loop : -1.74 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 104 HIS 0.003 0.000 HIS B 339 PHE 0.022 0.001 PHE B 564 TYR 0.018 0.001 TYR B1066 ARG 0.003 0.000 ARG C 982 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 30) link_NAG-ASN : angle 3.12960 ( 90) link_BETA1-4 : bond 0.01011 ( 5) link_BETA1-4 : angle 2.86807 ( 15) hydrogen bonds : bond 0.04091 ( 943) hydrogen bonds : angle 5.09889 ( 2631) SS BOND : bond 0.00238 ( 37) SS BOND : angle 0.92243 ( 74) covalent geometry : bond 0.00234 (24720) covalent geometry : angle 0.53047 (33644) *********************** 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 150 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 2.681 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: 0.9012 (t0) cc_final: 0.8580 (t0) REVERT: A 281 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8640 (pp20) REVERT: A 314 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8772 (tm-30) REVERT: A 368 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9318 (mm) REVERT: A 568 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7981 (mp) REVERT: A 696 MET cc_start: 0.9300 (ttp) cc_final: 0.8792 (ptp) REVERT: A 739 MET cc_start: 0.9174 (tmm) cc_final: 0.8838 (tmm) REVERT: A 987 GLU cc_start: 0.9159 (mp0) cc_final: 0.8780 (mp0) REVERT: A 1001 GLN cc_start: 0.9390 (tp40) cc_final: 0.9015 (tp40) REVERT: B 168 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: B 201 PHE cc_start: 0.8554 (t80) cc_final: 0.8322 (t80) REVERT: B 868 MET cc_start: 0.9189 (mtt) cc_final: 0.8844 (mtt) REVERT: B 1001 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8916 (mp10) REVERT: C 456 PHE cc_start: 0.7948 (m-80) cc_final: 0.7690 (m-80) REVERT: C 515 GLU cc_start: 0.8858 (tp30) cc_final: 0.8513 (tp30) REVERT: C 1001 GLN cc_start: 0.9578 (tt0) cc_final: 0.9034 (tm-30) outliers start: 46 outliers final: 27 residues processed: 147 average time/residue: 1.0619 time to fit residues: 189.4162 Evaluate side-chains 123 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 3.260 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 483 LYS 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 B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 203 ILE 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 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 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 290 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 269 optimal weight: 0.0370 chunk 2 optimal weight: 6.9990 chunk 281 optimal weight: 0.7980 chunk 252 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 265 optimal weight: 6.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.074669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051004 restraints weight = 89417.530| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.24 r_work: 0.2933 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24792 Z= 0.109 Angle : 0.570 11.883 33823 Z= 0.285 Chirality : 0.044 0.314 3898 Planarity : 0.004 0.080 4298 Dihedral : 7.511 122.800 3968 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.39 % Favored : 93.44 % Rotamer: Outliers : 1.51 % Allowed : 13.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 2974 helix: 2.11 (0.20), residues: 703 sheet: -0.45 (0.20), residues: 604 loop : -1.70 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 104 HIS 0.002 0.000 HIS B 339 PHE 0.027 0.001 PHE C 938 TYR 0.017 0.001 TYR B1066 ARG 0.004 0.000 ARG C 982 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 30) link_NAG-ASN : angle 3.07125 ( 90) link_BETA1-4 : bond 0.00985 ( 5) link_BETA1-4 : angle 2.83859 ( 15) hydrogen bonds : bond 0.04069 ( 943) hydrogen bonds : angle 5.06378 ( 2631) SS BOND : bond 0.00246 ( 37) SS BOND : angle 1.06415 ( 74) covalent geometry : bond 0.00243 (24720) covalent geometry : angle 0.54336 (33644) *********************** 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 132 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 2.664 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 281 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8612 (pp20) REVERT: A 314 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8738 (tm-30) REVERT: A 568 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 696 MET cc_start: 0.9297 (ttp) cc_final: 0.8781 (ptp) REVERT: A 739 MET cc_start: 0.9163 (tmm) cc_final: 0.8810 (tmm) REVERT: A 987 GLU cc_start: 0.9173 (mp0) cc_final: 0.8797 (mp0) REVERT: A 1001 GLN cc_start: 0.9394 (tp40) cc_final: 0.9019 (tp40) REVERT: B 168 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: B 201 PHE cc_start: 0.8550 (t80) cc_final: 0.8331 (t80) REVERT: B 739 MET cc_start: 0.9257 (tpp) cc_final: 0.9051 (ttp) REVERT: B 1001 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8899 (mp10) REVERT: C 456 PHE cc_start: 0.7952 (m-80) cc_final: 0.7717 (m-80) REVERT: C 515 GLU cc_start: 0.8858 (tp30) cc_final: 0.8521 (tp30) REVERT: C 982 ARG cc_start: 0.9171 (tpp80) cc_final: 0.8919 (tpp80) REVERT: C 1001 GLN cc_start: 0.9576 (tt0) cc_final: 0.9041 (tm-30) outliers start: 40 outliers final: 30 residues processed: 128 average time/residue: 1.1982 time to fit residues: 190.5726 Evaluate side-chains 124 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 3.307 ------------------------------------------------------------------------------- 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 227 VAL 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 391 CYS Chi-restraints excluded: chain A residue 395 VAL 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 598 THR 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 133 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 203 ILE 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 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 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 119 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 170 optimal weight: 0.0010 chunk 58 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 167 optimal weight: 0.0870 chunk 269 optimal weight: 0.0030 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.2178 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.074073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050333 restraints weight = 90546.619| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.30 r_work: 0.2901 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24792 Z= 0.131 Angle : 0.579 11.246 33823 Z= 0.290 Chirality : 0.044 0.306 3898 Planarity : 0.004 0.080 4298 Dihedral : 7.448 120.498 3968 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.42 % Favored : 93.41 % Rotamer: Outliers : 1.43 % Allowed : 13.91 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 2974 helix: 2.06 (0.20), residues: 709 sheet: -0.51 (0.20), residues: 609 loop : -1.70 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 452 HIS 0.001 0.000 HIS B1087 PHE 0.065 0.001 PHE A 392 TYR 0.024 0.001 TYR B 635 ARG 0.004 0.000 ARG A1018 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 30) link_NAG-ASN : angle 2.90425 ( 90) link_BETA1-4 : bond 0.00935 ( 5) link_BETA1-4 : angle 2.83396 ( 15) hydrogen bonds : bond 0.04209 ( 943) hydrogen bonds : angle 5.07868 ( 2631) SS BOND : bond 0.00217 ( 37) SS BOND : angle 1.05100 ( 74) covalent geometry : bond 0.00302 (24720) covalent geometry : angle 0.55526 (33644) ********************** 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 133 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 2.697 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 281 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8635 (pp20) REVERT: A 568 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7996 (mp) REVERT: A 696 MET cc_start: 0.9317 (ttp) cc_final: 0.8856 (ptp) REVERT: A 739 MET cc_start: 0.9170 (tmm) cc_final: 0.8804 (tmm) REVERT: A 987 GLU cc_start: 0.9167 (mp0) cc_final: 0.8793 (mp0) REVERT: A 1001 GLN cc_start: 0.9405 (tp40) cc_final: 0.9031 (tp40) REVERT: B 168 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: B 201 PHE cc_start: 0.8598 (t80) cc_final: 0.8384 (t80) REVERT: B 1001 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8944 (mp10) REVERT: C 456 PHE cc_start: 0.7945 (m-80) cc_final: 0.7682 (m-80) REVERT: C 515 GLU cc_start: 0.8894 (tp30) cc_final: 0.8551 (tp30) REVERT: C 993 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.9003 (t0) REVERT: C 1001 GLN cc_start: 0.9584 (tt0) cc_final: 0.9047 (tm-30) outliers start: 38 outliers final: 30 residues processed: 130 average time/residue: 0.9486 time to fit residues: 152.6682 Evaluate side-chains 127 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 2.653 ------------------------------------------------------------------------------- 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 281 GLU 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 483 LYS 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 598 THR 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 133 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 203 ILE 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 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 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 993 ASP 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 28 optimal weight: 8.9990 chunk 235 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 109 optimal weight: 0.2980 chunk 202 optimal weight: 0.0570 chunk 72 optimal weight: 0.0570 chunk 25 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 172 optimal weight: 0.1980 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051247 restraints weight = 90530.441| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.32 r_work: 0.2929 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24792 Z= 0.101 Angle : 0.568 12.414 33823 Z= 0.283 Chirality : 0.044 0.325 3898 Planarity : 0.004 0.079 4298 Dihedral : 7.168 117.694 3968 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.29 % Favored : 93.54 % Rotamer: Outliers : 1.09 % Allowed : 14.37 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 2974 helix: 2.15 (0.21), residues: 702 sheet: -0.38 (0.20), residues: 598 loop : -1.65 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 104 HIS 0.002 0.000 HIS B 339 PHE 0.030 0.001 PHE C 938 TYR 0.017 0.001 TYR B1066 ARG 0.006 0.000 ARG A1018 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 30) link_NAG-ASN : angle 2.78233 ( 90) link_BETA1-4 : bond 0.00979 ( 5) link_BETA1-4 : angle 2.71130 ( 15) hydrogen bonds : bond 0.03714 ( 943) hydrogen bonds : angle 4.94418 ( 2631) SS BOND : bond 0.00201 ( 37) SS BOND : angle 0.82767 ( 74) covalent geometry : bond 0.00218 (24720) covalent geometry : angle 0.54649 (33644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16015.94 seconds wall clock time: 285 minutes 30.66 seconds (17130.66 seconds total)