Starting phenix.real_space_refine on Sat May 24 00:29:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f9y_50263/05_2025/9f9y_50263.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f9y_50263/05_2025/9f9y_50263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f9y_50263/05_2025/9f9y_50263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f9y_50263/05_2025/9f9y_50263.map" model { file = "/net/cci-nas-00/data/ceres_data/9f9y_50263/05_2025/9f9y_50263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f9y_50263/05_2025/9f9y_50263.cif" } resolution = 2.8 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= 0.000 sd= 0.019 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 108 5.16 5 C 15834 2.51 5 N 4050 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24810 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8004 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} Chain breaks: 6 Chain: "B" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8004 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} Chain breaks: 6 Chain: "C" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8004 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} 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: 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 13.51, per 1000 atoms: 0.54 Number of scatterers: 24810 At special positions: 0 Unit cell: (128.533, 129.993, 171.62, 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 108 16.00 O 4818 8.00 N 4050 7.00 C 15834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 276 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 500 " distance=2.03 Simple disulfide: pdb=" SG CYS A 455 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 713 " - pdb=" SG CYS A 735 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A1007 " - pdb=" SG CYS A1018 " distance=2.03 Simple disulfide: pdb=" SG CYS A1057 " - pdb=" SG CYS A1101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 276 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 500 " distance=2.03 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 463 " distance=2.03 Simple disulfide: pdb=" SG CYS B 513 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 637 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 713 " - pdb=" SG CYS B 735 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 724 " distance=2.03 Simple disulfide: pdb=" SG CYS B1007 " - pdb=" SG CYS B1018 " distance=2.03 Simple disulfide: pdb=" SG CYS B1057 " - pdb=" SG CYS B1101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 276 " distance=2.03 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 500 " distance=2.03 Simple disulfide: pdb=" SG CYS C 455 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 513 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 624 " distance=2.03 Simple disulfide: pdb=" SG CYS C 637 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 735 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 724 " distance=2.03 Simple disulfide: pdb=" SG CYS C1007 " - pdb=" SG CYS C1018 " distance=2.03 Simple disulfide: pdb=" SG CYS C1057 " - pdb=" SG CYS C1101 " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 49 " " NAG A1302 " - " ASN A 108 " " NAG A1303 " - " ASN A 140 " " NAG A1304 " - " ASN A 163 " " NAG A1305 " - " ASN A 209 " " NAG A1306 " - " ASN A 257 " " NAG A1307 " - " ASN A 306 " " NAG A1308 " - " ASN A 318 " " NAG A1309 " - " ASN A 591 " " NAG A1310 " - " ASN A 632 " " NAG A1311 " - " ASN A 684 " " NAG A1312 " - " ASN A1049 " " NAG A1313 " - " ASN A1109 " " NAG B1301 " - " ASN B 49 " " NAG B1302 " - " ASN B 108 " " NAG B1303 " - " ASN B 140 " " NAG B1304 " - " ASN B 163 " " NAG B1305 " - " ASN B 209 " " NAG B1306 " - " ASN B 257 " " NAG B1307 " - " ASN B 306 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 591 " " NAG B1310 " - " ASN B 632 " " NAG B1311 " - " ASN B 684 " " NAG B1312 " - " ASN B1049 " " NAG B1313 " - " ASN B1109 " " NAG C1301 " - " ASN C 49 " " NAG C1302 " - " ASN C 108 " " NAG C1303 " - " ASN C 140 " " NAG C1304 " - " ASN C 163 " " NAG C1305 " - " ASN C 209 " " NAG C1306 " - " ASN C 257 " " NAG C1307 " - " ASN C 306 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 591 " " NAG C1310 " - " ASN C 632 " " NAG C1311 " - " ASN C 684 " " NAG C1312 " - " ASN C1049 " " NAG C1313 " - " ASN C1109 " " NAG D 1 " - " ASN A 692 " " NAG E 1 " - " ASN A 776 " " NAG F 1 " - " ASN A1073 " " NAG G 1 " - " ASN B 692 " " NAG H 1 " - " ASN B 776 " " NAG I 1 " - " ASN B1073 " " NAG J 1 " - " ASN C 692 " " NAG K 1 " - " ASN C 776 " " NAG L 1 " - " ASN C1073 " Time building additional restraints: 5.88 Conformation dependent library (CDL) restraints added in 3.2 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 48 sheets defined 29.1% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.532A pdb=" N VAL A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.637A pdb=" N VAL A 342 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 removed outlier: 3.529A pdb=" N LEU A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A 363 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.233A pdb=" N SER A 383 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 477 through 480 Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 612 through 615 removed outlier: 6.611A pdb=" N SER A 615 " --> pdb=" O SER A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.584A pdb=" N ASP A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 801 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 841 through 860 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 872 through 884 Processing helix chain 'A' and resid 887 through 894 removed outlier: 4.079A pdb=" N LEU A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 916 removed outlier: 3.934A pdb=" N GLN A 910 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 911 " --> pdb=" O GLY A 907 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 940 removed outlier: 3.608A pdb=" N GLN A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 943 No H-bonds generated for 'chain 'A' and resid 941 through 943' Processing helix chain 'A' and resid 951 through 959 Processing helix chain 'A' and resid 960 through 1008 removed outlier: 4.711A pdb=" N VAL A 966 " --> pdb=" O PRO A 962 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 974 " --> pdb=" O ARG A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1122 removed outlier: 4.118A pdb=" N GLU A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 312 through 318 removed outlier: 3.536A pdb=" N VAL B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.633A pdb=" N VAL B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.533A pdb=" N LEU B 362 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN B 363 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.233A pdb=" N SER B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 477 through 480 Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.666A pdb=" N VAL B 610 " --> pdb=" O PRO B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 removed outlier: 6.454A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 712 through 719 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.589A pdb=" N ASP B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 801 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 841 through 860 Processing helix chain 'B' and resid 861 through 865 Processing helix chain 'B' and resid 872 through 884 Processing helix chain 'B' and resid 887 through 894 removed outlier: 4.085A pdb=" N LEU B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 916 removed outlier: 3.933A pdb=" N GLN B 910 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY B 911 " --> pdb=" O GLY B 907 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 940 removed outlier: 3.602A pdb=" N GLN B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 943 No H-bonds generated for 'chain 'B' and resid 941 through 943' Processing helix chain 'B' and resid 951 through 959 Processing helix chain 'B' and resid 960 through 1008 removed outlier: 4.730A pdb=" N VAL B 966 " --> pdb=" O PRO B 962 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN B 967 " --> pdb=" O GLU B 963 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 974 " --> pdb=" O ARG B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1122 removed outlier: 4.119A pdb=" N GLU B1119 " --> pdb=" O PRO B1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.537A pdb=" N VAL C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 339 through 346 removed outlier: 3.638A pdb=" N VAL C 342 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 364 removed outlier: 3.528A pdb=" N LEU C 362 " --> pdb=" O PRO C 359 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN C 363 " --> pdb=" O THR C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.233A pdb=" N SER C 383 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 424 Processing helix chain 'C' and resid 477 through 480 Processing helix chain 'C' and resid 605 through 611 removed outlier: 3.659A pdb=" N VAL C 610 " --> pdb=" O PRO C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 6.454A pdb=" N SER C 615 " --> pdb=" O SER C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 712 through 719 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 730 through 732 No H-bonds generated for 'chain 'C' and resid 730 through 732' Processing helix chain 'C' and resid 733 through 758 removed outlier: 3.589A pdb=" N ASP C 750 " --> pdb=" O ALA C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 801 Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 841 through 860 Processing helix chain 'C' and resid 861 through 865 Processing helix chain 'C' and resid 872 through 884 Processing helix chain 'C' and resid 887 through 894 removed outlier: 4.092A pdb=" N LEU C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 916 removed outlier: 3.933A pdb=" N GLN C 910 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C 911 " --> pdb=" O GLY C 907 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 940 removed outlier: 3.603A pdb=" N GLN C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 943 No H-bonds generated for 'chain 'C' and resid 941 through 943' Processing helix chain 'C' and resid 951 through 959 Processing helix chain 'C' and resid 960 through 1008 removed outlier: 4.707A pdb=" N VAL C 966 " --> pdb=" O PRO C 962 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 974 " --> pdb=" O ARG C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1122 removed outlier: 4.117A pdb=" N GLU C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 8.020A pdb=" N ASN A 49 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR A 244 " --> pdb=" O ASN A 49 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N SER A 180 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N HIS A 182 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N LEU A 198 " --> pdb=" O HIS A 182 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 24 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 43 removed outlier: 4.031A pdb=" N ASP A 262 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.550A pdb=" N SER A 137 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 294 removed outlier: 4.299A pdb=" N VAL A 570 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN A 292 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY A 568 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY A 569 " --> pdb=" O GLN A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 303 removed outlier: 5.458A pdb=" N ASP A 549 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY A 541 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 329 through 333 removed outlier: 3.727A pdb=" N ASN A 369 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 351 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 337 removed outlier: 6.686A pdb=" N CYS A 336 " --> pdb=" O CYS A 500 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 449 Processing sheet with id=AB2, first strand: chain 'A' and resid 628 through 630 removed outlier: 6.024A pdb=" N GLU A 629 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR A 671 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 647 " --> pdb=" O PRO A 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 677 through 679 Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 690 removed outlier: 3.795A pdb=" N ALA A1053 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A1070 " --> pdb=" O ALA A1053 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 703 removed outlier: 6.974A pdb=" N GLY A1034 " --> pdb=" O SER A1030 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER A1030 " --> pdb=" O GLY A1034 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A1036 " --> pdb=" O PRO A1028 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A1038 " --> pdb=" O SER A1026 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A1026 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A1040 " --> pdb=" O LEU A1024 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 708 through 711 removed outlier: 4.464A pdb=" N LYS A 708 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 763 through 765 removed outlier: 5.848A pdb=" N ILE A 763 " --> pdb=" O ASN B 678 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 15 through 18 removed outlier: 8.031A pdb=" N ASN B 49 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR B 244 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 180 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N HIS B 182 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU B 198 " --> pdb=" O HIS B 182 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 24 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 35 through 43 removed outlier: 4.026A pdb=" N ASP B 262 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AC3, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.545A pdb=" N SER B 137 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 286 through 294 removed outlier: 4.307A pdb=" N VAL B 570 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASN B 292 " --> pdb=" O GLY B 568 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY B 568 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY B 569 " --> pdb=" O GLN B 588 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 300 through 303 removed outlier: 5.449A pdb=" N ASP B 549 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY B 541 " --> pdb=" O ASP B 549 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 329 through 333 removed outlier: 3.725A pdb=" N ASN B 369 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 351 " --> pdb=" O ALA B 410 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.689A pdb=" N CYS B 336 " --> pdb=" O CYS B 500 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 427 through 429 Processing sheet with id=AC9, first strand: chain 'B' and resid 448 through 449 Processing sheet with id=AD1, first strand: chain 'B' and resid 628 through 630 removed outlier: 6.028A pdb=" N GLU B 629 " --> pdb=" O ALA B 669 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR B 671 " --> pdb=" O GLU B 629 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 686 through 690 removed outlier: 3.834A pdb=" N ALA B1053 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B1070 " --> pdb=" O ALA B1053 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 693 through 703 removed outlier: 6.985A pdb=" N GLY B1034 " --> pdb=" O SER B1030 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER B1030 " --> pdb=" O GLY B1034 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1036 " --> pdb=" O PRO B1028 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B1038 " --> pdb=" O SER B1026 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER B1026 " --> pdb=" O LEU B1038 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B1040 " --> pdb=" O LEU B1024 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 711 removed outlier: 4.478A pdb=" N LYS B 708 " --> pdb=" O LEU B 836 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 763 through 765 removed outlier: 5.824A pdb=" N ILE B 763 " --> pdb=" O ASN C 678 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 15 through 18 removed outlier: 8.031A pdb=" N ASN C 49 " --> pdb=" O TYR C 244 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR C 244 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER C 180 " --> pdb=" O PRO C 200 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N HIS C 182 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N LEU C 198 " --> pdb=" O HIS C 182 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 24 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 35 through 43 removed outlier: 4.029A pdb=" N ASP C 262 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AE1, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.551A pdb=" N SER C 137 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 286 through 294 removed outlier: 4.306A pdb=" N VAL C 570 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN C 292 " --> pdb=" O GLY C 568 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY C 568 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY C 569 " --> pdb=" O GLN C 588 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 300 through 303 removed outlier: 5.453A pdb=" N ASP C 549 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY C 541 " --> pdb=" O ASP C 549 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 329 through 333 removed outlier: 3.725A pdb=" N ASN C 369 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 351 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 336 through 337 removed outlier: 6.683A pdb=" N CYS C 336 " --> pdb=" O CYS C 500 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 427 through 429 Processing sheet with id=AE7, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AE8, first strand: chain 'C' and resid 628 through 630 removed outlier: 6.016A pdb=" N GLU C 629 " --> pdb=" O ALA C 669 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 671 " --> pdb=" O GLU C 629 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 645 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 686 through 690 removed outlier: 3.843A pdb=" N ALA C1053 " --> pdb=" O PHE C1070 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE C1070 " --> pdb=" O ALA C1053 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 693 through 703 removed outlier: 6.992A pdb=" N GLY C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER C1030 " --> pdb=" O GLY C1034 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C1036 " --> pdb=" O PRO C1028 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C1038 " --> pdb=" O SER C1026 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER C1026 " --> pdb=" O LEU C1038 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C1040 " --> pdb=" O LEU C1024 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 708 through 711 removed outlier: 4.477A pdb=" N LYS C 708 " --> pdb=" O LEU C 836 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1095 through 1097 1065 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.65 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7826 1.34 - 1.46: 6034 1.46 - 1.58: 11379 1.58 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 25374 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 33426 1.32 - 2.63: 868 2.63 - 3.95: 201 3.95 - 5.26: 20 5.26 - 6.58: 6 Bond angle restraints: 34521 Sorted by residual: angle pdb=" N ALA C 598 " pdb=" CA ALA C 598 " pdb=" C ALA C 598 " ideal model delta sigma weight residual 111.11 114.11 -3.00 1.20e+00 6.94e-01 6.27e+00 angle pdb=" N ALA B 598 " pdb=" CA ALA B 598 " pdb=" C ALA B 598 " ideal model delta sigma weight residual 111.11 114.04 -2.93 1.20e+00 6.94e-01 5.96e+00 angle pdb=" C SER A 596 " pdb=" N VAL A 597 " pdb=" CA VAL A 597 " ideal model delta sigma weight residual 120.46 123.48 -3.02 1.37e+00 5.33e-01 4.86e+00 angle pdb=" N PRO A 961 " pdb=" CA PRO A 961 " pdb=" C PRO A 961 " ideal model delta sigma weight residual 110.70 113.33 -2.63 1.22e+00 6.72e-01 4.66e+00 angle pdb=" N PRO C 961 " pdb=" CA PRO C 961 " pdb=" C PRO C 961 " ideal model delta sigma weight residual 110.70 113.32 -2.62 1.22e+00 6.72e-01 4.61e+00 ... (remaining 34516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15060 17.58 - 35.16: 610 35.16 - 52.73: 93 52.73 - 70.31: 45 70.31 - 87.89: 17 Dihedral angle restraints: 15825 sinusoidal: 6882 harmonic: 8943 Sorted by residual: dihedral pdb=" CA THR B 574 " pdb=" C THR B 574 " pdb=" N PRO B 575 " pdb=" CA PRO B 575 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR A 574 " pdb=" C THR A 574 " pdb=" N PRO A 575 " pdb=" CA PRO A 575 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR C 574 " pdb=" C THR C 574 " pdb=" N PRO C 575 " pdb=" CA PRO C 575 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 15822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2350 0.029 - 0.058: 1057 0.058 - 0.087: 319 0.087 - 0.116: 290 0.116 - 0.144: 64 Chirality restraints: 4080 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 4077 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 605 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO C 606 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 606 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 606 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 605 " 0.044 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO B 606 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 606 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 606 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 605 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 606 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " -0.022 5.00e-02 4.00e+02 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5759 2.79 - 3.32: 22578 3.32 - 3.84: 40041 3.84 - 4.37: 48421 4.37 - 4.90: 83598 Nonbonded interactions: 200397 Sorted by model distance: nonbonded pdb=" O GLN C 120 " pdb=" OG SER C 136 " model vdw 2.261 3.040 nonbonded pdb=" O GLN A 120 " pdb=" OG SER A 136 " model vdw 2.262 3.040 nonbonded pdb=" O GLN B 120 " pdb=" OG SER B 136 " model vdw 2.262 3.040 nonbonded pdb=" O TRP A 608 " pdb=" OG SER A 612 " model vdw 2.293 3.040 nonbonded pdb=" O PRO A1028 " pdb=" NE2 GLN A1029 " model vdw 2.306 3.120 ... (remaining 200392 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 54.390 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 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 0.036 25470 Z= 0.183 Angle : 0.527 6.576 34770 Z= 0.257 Chirality : 0.044 0.144 4080 Planarity : 0.003 0.068 4380 Dihedral : 10.390 87.887 9960 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.52 % Allowed : 4.04 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.15), residues: 3036 helix: 1.93 (0.20), residues: 732 sheet: 0.58 (0.18), residues: 735 loop : -0.63 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 861 HIS 0.003 0.000 HIS C1039 PHE 0.009 0.001 PHE C1096 TYR 0.017 0.001 TYR B1042 ARG 0.003 0.000 ARG C 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 48) link_NAG-ASN : angle 1.42102 ( 144) link_BETA1-4 : bond 0.00383 ( 9) link_BETA1-4 : angle 1.09721 ( 27) hydrogen bonds : bond 0.11190 ( 1065) hydrogen bonds : angle 6.07107 ( 2847) SS BOND : bond 0.00136 ( 39) SS BOND : angle 0.65276 ( 78) covalent geometry : bond 0.00402 (25374) covalent geometry : angle 0.51881 (34521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 2.669 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 101 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7780 (mm-40) REVERT: A 143 PHE cc_start: 0.8597 (t80) cc_final: 0.8361 (t80) REVERT: A 284 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8230 (mm-30) REVERT: A 326 TYR cc_start: 0.9066 (p90) cc_final: 0.8656 (p90) REVERT: A 349 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.6645 (p90) REVERT: A 416 LEU cc_start: 0.9207 (mt) cc_final: 0.8673 (tt) REVERT: A 600 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6629 (t-90) REVERT: A 715 MET cc_start: 0.9080 (tpp) cc_final: 0.8763 (tpt) REVERT: A 798 PHE cc_start: 0.8398 (t80) cc_final: 0.8071 (t80) REVERT: A 831 ASN cc_start: 0.8414 (m-40) cc_final: 0.8120 (m-40) REVERT: A 969 ASP cc_start: 0.8593 (t70) cc_final: 0.8293 (t0) REVERT: A 1120 LEU cc_start: 0.7590 (pp) cc_final: 0.7277 (pp) REVERT: B 101 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7765 (mm-40) REVERT: B 143 PHE cc_start: 0.8617 (t80) cc_final: 0.8254 (t80) REVERT: B 284 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8185 (mm-30) REVERT: B 326 TYR cc_start: 0.9066 (p90) cc_final: 0.8830 (p90) REVERT: B 349 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7437 (p90) REVERT: B 416 LEU cc_start: 0.9186 (mt) cc_final: 0.8603 (tt) REVERT: B 706 MET cc_start: 0.9645 (ptt) cc_final: 0.9416 (ptt) REVERT: B 831 ASN cc_start: 0.8439 (m-40) cc_final: 0.8145 (m-40) REVERT: B 969 ASP cc_start: 0.8691 (t70) cc_final: 0.8330 (t0) REVERT: B 1120 LEU cc_start: 0.7726 (pp) cc_final: 0.7397 (pp) REVERT: C 326 TYR cc_start: 0.9062 (p90) cc_final: 0.8733 (p90) REVERT: C 349 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.6763 (p90) REVERT: C 358 SER cc_start: 0.8430 (m) cc_final: 0.8031 (p) REVERT: C 730 GLN cc_start: 0.9020 (tt0) cc_final: 0.8809 (tt0) REVERT: C 798 PHE cc_start: 0.8478 (t80) cc_final: 0.8188 (t80) REVERT: C 831 ASN cc_start: 0.8460 (m-40) cc_final: 0.8145 (m-40) REVERT: C 969 ASP cc_start: 0.8641 (t70) cc_final: 0.8316 (t0) REVERT: C 1120 LEU cc_start: 0.7690 (pp) cc_final: 0.7367 (pp) outliers start: 14 outliers final: 6 residues processed: 271 average time/residue: 1.1637 time to fit residues: 374.5063 Evaluate side-chains 179 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 597 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0030 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 277 optimal weight: 10.0000 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 120 GLN A 139 ASN A 193 GLN A 494 HIS ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 GLN A 932 GLN A 985 GLN B 18 ASN B 120 GLN B 139 ASN B 494 HIS B 600 HIS B 665 GLN B 730 GLN B 932 GLN B 985 GLN C 18 ASN C 120 GLN C 139 ASN C 494 HIS C 600 HIS C 665 GLN C 730 GLN C 932 GLN C 985 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.114039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.069137 restraints weight = 46759.409| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.85 r_work: 0.2777 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25470 Z= 0.227 Angle : 0.566 11.198 34770 Z= 0.285 Chirality : 0.045 0.187 4080 Planarity : 0.004 0.072 4380 Dihedral : 6.698 59.632 4505 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.39 % Allowed : 7.27 % Favored : 91.35 % 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: 0.29 (0.15), residues: 3036 helix: 1.69 (0.20), residues: 735 sheet: 0.61 (0.19), residues: 717 loop : -0.73 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.005 0.001 HIS B 600 PHE 0.021 0.001 PHE C 143 TYR 0.018 0.001 TYR B1042 ARG 0.006 0.000 ARG A 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 48) link_NAG-ASN : angle 1.42679 ( 144) link_BETA1-4 : bond 0.00098 ( 9) link_BETA1-4 : angle 1.23166 ( 27) hydrogen bonds : bond 0.04422 ( 1065) hydrogen bonds : angle 5.26217 ( 2847) SS BOND : bond 0.00223 ( 39) SS BOND : angle 0.80651 ( 78) covalent geometry : bond 0.00541 (25374) covalent geometry : angle 0.55768 (34521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 2.718 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 101 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7578 (mm-40) REVERT: A 119 PHE cc_start: 0.8752 (m-80) cc_final: 0.8548 (m-80) REVERT: A 143 PHE cc_start: 0.8593 (t80) cc_final: 0.8355 (t80) REVERT: A 284 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8602 (mm-30) REVERT: A 326 TYR cc_start: 0.9121 (p90) cc_final: 0.8765 (p90) REVERT: A 345 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8253 (p0) REVERT: A 349 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6678 (p90) REVERT: A 416 LEU cc_start: 0.9200 (mt) cc_final: 0.8677 (tt) REVERT: A 427 MET cc_start: 0.7505 (mpp) cc_final: 0.7138 (mpp) REVERT: A 715 MET cc_start: 0.9144 (tpp) cc_final: 0.8934 (tpt) REVERT: A 798 PHE cc_start: 0.8577 (t80) cc_final: 0.8338 (t80) REVERT: A 831 ASN cc_start: 0.8416 (m-40) cc_final: 0.8173 (m-40) REVERT: A 969 ASP cc_start: 0.8798 (t70) cc_final: 0.8534 (t0) REVERT: B 101 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7519 (mm-40) REVERT: B 143 PHE cc_start: 0.8607 (t80) cc_final: 0.8095 (t80) REVERT: B 284 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8611 (mm-30) REVERT: B 326 TYR cc_start: 0.9134 (p90) cc_final: 0.8881 (p90) REVERT: B 345 ASN cc_start: 0.8569 (m110) cc_final: 0.8201 (p0) REVERT: B 346 PHE cc_start: 0.7509 (t80) cc_final: 0.7273 (t80) REVERT: B 349 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7404 (p90) REVERT: B 377 ILE cc_start: 0.8661 (tp) cc_final: 0.8445 (tp) REVERT: B 427 MET cc_start: 0.7491 (mpp) cc_final: 0.7196 (mpp) REVERT: B 831 ASN cc_start: 0.8430 (m-40) cc_final: 0.8115 (m-40) REVERT: B 969 ASP cc_start: 0.8818 (t70) cc_final: 0.8514 (t0) REVERT: C 309 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6617 (p0) REVERT: C 326 TYR cc_start: 0.9068 (p90) cc_final: 0.8763 (p90) REVERT: C 345 ASN cc_start: 0.8529 (m110) cc_final: 0.8160 (p0) REVERT: C 346 PHE cc_start: 0.7571 (t80) cc_final: 0.7314 (t80) REVERT: C 349 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.6841 (p90) REVERT: C 377 ILE cc_start: 0.8613 (tp) cc_final: 0.8399 (tp) REVERT: C 416 LEU cc_start: 0.9065 (mt) cc_final: 0.8453 (tt) REVERT: C 427 MET cc_start: 0.7523 (mpp) cc_final: 0.7172 (mpp) REVERT: C 621 ARG cc_start: 0.9037 (ttm-80) cc_final: 0.8576 (ttp-110) REVERT: C 798 PHE cc_start: 0.8608 (t80) cc_final: 0.8136 (m-80) REVERT: C 831 ASN cc_start: 0.8504 (m-40) cc_final: 0.8212 (m-40) REVERT: C 969 ASP cc_start: 0.8814 (t70) cc_final: 0.8534 (t0) outliers start: 37 outliers final: 15 residues processed: 205 average time/residue: 1.0833 time to fit residues: 265.4692 Evaluate side-chains 185 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 126 optimal weight: 0.6980 chunk 233 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 302 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 214 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 345 ASN A 600 HIS A 730 GLN A 985 GLN B 18 ASN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.115959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.071604 restraints weight = 46318.361| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.85 r_work: 0.2829 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25470 Z= 0.104 Angle : 0.506 10.335 34770 Z= 0.251 Chirality : 0.043 0.178 4080 Planarity : 0.003 0.071 4380 Dihedral : 5.707 59.935 4502 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.87 % Allowed : 7.38 % Favored : 90.75 % 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: 0.48 (0.15), residues: 3036 helix: 2.03 (0.20), residues: 711 sheet: 0.65 (0.19), residues: 657 loop : -0.57 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 52 HIS 0.003 0.000 HIS B 600 PHE 0.025 0.001 PHE C 143 TYR 0.016 0.001 TYR A1042 ARG 0.005 0.000 ARG A 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 48) link_NAG-ASN : angle 1.25069 ( 144) link_BETA1-4 : bond 0.00314 ( 9) link_BETA1-4 : angle 0.94314 ( 27) hydrogen bonds : bond 0.03583 ( 1065) hydrogen bonds : angle 5.02115 ( 2847) SS BOND : bond 0.00124 ( 39) SS BOND : angle 0.63868 ( 78) covalent geometry : bond 0.00236 (25374) covalent geometry : angle 0.49924 (34521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 2.680 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 41 ASP cc_start: 0.8861 (t0) cc_final: 0.8644 (t70) REVERT: A 101 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7660 (mm-40) REVERT: A 143 PHE cc_start: 0.8571 (t80) cc_final: 0.8278 (t80) REVERT: A 284 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8600 (mm-30) REVERT: A 326 TYR cc_start: 0.9128 (p90) cc_final: 0.8731 (p90) REVERT: A 349 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.6625 (p90) REVERT: A 416 LEU cc_start: 0.9192 (mt) cc_final: 0.8677 (tt) REVERT: A 427 MET cc_start: 0.7605 (mpp) cc_final: 0.7203 (mpp) REVERT: A 561 ASP cc_start: 0.8007 (t0) cc_final: 0.7649 (t0) REVERT: A 798 PHE cc_start: 0.8528 (t80) cc_final: 0.8322 (t80) REVERT: A 831 ASN cc_start: 0.8356 (m-40) cc_final: 0.8088 (m-40) REVERT: A 969 ASP cc_start: 0.8704 (t70) cc_final: 0.8431 (t0) REVERT: B 33 SER cc_start: 0.9352 (p) cc_final: 0.9136 (m) REVERT: B 41 ASP cc_start: 0.8855 (t0) cc_final: 0.8593 (t70) REVERT: B 101 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7608 (mm-40) REVERT: B 143 PHE cc_start: 0.8613 (t80) cc_final: 0.8098 (t80) REVERT: B 284 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8595 (mm-30) REVERT: B 326 TYR cc_start: 0.9161 (p90) cc_final: 0.8874 (p90) REVERT: B 349 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7304 (p90) REVERT: B 365 LEU cc_start: 0.8816 (mt) cc_final: 0.8582 (mp) REVERT: B 416 LEU cc_start: 0.9002 (mt) cc_final: 0.8388 (tt) REVERT: B 427 MET cc_start: 0.7598 (mpp) cc_final: 0.7282 (mpp) REVERT: B 561 ASP cc_start: 0.8047 (t0) cc_final: 0.7785 (t0) REVERT: B 798 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: B 831 ASN cc_start: 0.8404 (m-40) cc_final: 0.8093 (m-40) REVERT: B 932 GLN cc_start: 0.8692 (tt0) cc_final: 0.8471 (tt0) REVERT: B 969 ASP cc_start: 0.8730 (t70) cc_final: 0.8443 (t0) REVERT: C 41 ASP cc_start: 0.8837 (t0) cc_final: 0.8604 (t70) REVERT: C 326 TYR cc_start: 0.9077 (p90) cc_final: 0.8740 (p90) REVERT: C 349 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.6829 (p90) REVERT: C 416 LEU cc_start: 0.9064 (mt) cc_final: 0.8469 (tt) REVERT: C 427 MET cc_start: 0.7578 (mpp) cc_final: 0.7208 (mpp) REVERT: C 621 ARG cc_start: 0.8998 (ttm-80) cc_final: 0.8573 (ttp-110) REVERT: C 748 GLU cc_start: 0.8933 (tt0) cc_final: 0.8618 (tt0) REVERT: C 798 PHE cc_start: 0.8557 (t80) cc_final: 0.8137 (m-80) REVERT: C 831 ASN cc_start: 0.8472 (m-40) cc_final: 0.8167 (m-40) REVERT: C 969 ASP cc_start: 0.8698 (t70) cc_final: 0.8400 (t0) outliers start: 50 outliers final: 15 residues processed: 217 average time/residue: 1.1391 time to fit residues: 303.2486 Evaluate side-chains 194 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 915 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 244 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 18 ASN C 600 HIS C 985 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.112605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.067831 restraints weight = 46645.437| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.82 r_work: 0.2751 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 25470 Z= 0.328 Angle : 0.610 11.129 34770 Z= 0.306 Chirality : 0.047 0.160 4080 Planarity : 0.004 0.075 4380 Dihedral : 5.645 57.357 4500 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.13 % Allowed : 7.64 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.15), residues: 3036 helix: 1.82 (0.20), residues: 693 sheet: 0.40 (0.18), residues: 738 loop : -0.73 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1077 HIS 0.020 0.001 HIS A 600 PHE 0.026 0.002 PHE B 346 TYR 0.020 0.002 TYR A1042 ARG 0.003 0.000 ARG A 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 48) link_NAG-ASN : angle 1.64656 ( 144) link_BETA1-4 : bond 0.00106 ( 9) link_BETA1-4 : angle 1.47597 ( 27) hydrogen bonds : bond 0.04860 ( 1065) hydrogen bonds : angle 5.29057 ( 2847) SS BOND : bond 0.00301 ( 39) SS BOND : angle 0.86164 ( 78) covalent geometry : bond 0.00781 (25374) covalent geometry : angle 0.60026 (34521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7607 (mm-40) REVERT: A 284 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8603 (mm-30) REVERT: A 309 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6785 (p0) REVERT: A 326 TYR cc_start: 0.9111 (p90) cc_final: 0.8737 (p90) REVERT: A 349 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.6757 (p90) REVERT: A 416 LEU cc_start: 0.9197 (mt) cc_final: 0.8645 (tt) REVERT: A 427 MET cc_start: 0.7700 (mpp) cc_final: 0.7343 (mpp) REVERT: A 798 PHE cc_start: 0.8578 (t80) cc_final: 0.8311 (t80) REVERT: A 831 ASN cc_start: 0.8445 (m-40) cc_final: 0.8196 (m-40) REVERT: A 969 ASP cc_start: 0.8827 (t70) cc_final: 0.8573 (t0) REVERT: B 101 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7506 (mm-40) REVERT: B 122 LYS cc_start: 0.8607 (tttt) cc_final: 0.8346 (pmtt) REVERT: B 143 PHE cc_start: 0.8503 (t80) cc_final: 0.7983 (t80) REVERT: B 284 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8650 (mm-30) REVERT: B 326 TYR cc_start: 0.9154 (p90) cc_final: 0.8861 (p90) REVERT: B 349 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7402 (p90) REVERT: B 416 LEU cc_start: 0.9080 (mt) cc_final: 0.8440 (tt) REVERT: B 427 MET cc_start: 0.7725 (mpp) cc_final: 0.7399 (mpp) REVERT: B 798 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: B 831 ASN cc_start: 0.8474 (m-40) cc_final: 0.8165 (m-40) REVERT: B 969 ASP cc_start: 0.8830 (t70) cc_final: 0.8526 (t0) REVERT: C 101 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7609 (mm-40) REVERT: C 326 TYR cc_start: 0.9084 (p90) cc_final: 0.8746 (p90) REVERT: C 349 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.6953 (p90) REVERT: C 416 LEU cc_start: 0.9101 (mt) cc_final: 0.8521 (tt) REVERT: C 427 MET cc_start: 0.7714 (mpp) cc_final: 0.7366 (mpp) REVERT: C 431 PHE cc_start: 0.8438 (m-80) cc_final: 0.8219 (m-80) REVERT: C 621 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8555 (ttp-110) REVERT: C 798 PHE cc_start: 0.8599 (t80) cc_final: 0.8088 (m-80) REVERT: C 831 ASN cc_start: 0.8505 (m-40) cc_final: 0.8225 (m-40) REVERT: C 969 ASP cc_start: 0.8823 (t70) cc_final: 0.8532 (t0) outliers start: 57 outliers final: 22 residues processed: 208 average time/residue: 0.9321 time to fit residues: 236.3908 Evaluate side-chains 193 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 190 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 276 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 239 optimal weight: 30.0000 chunk 219 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069898 restraints weight = 46714.816| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.84 r_work: 0.2789 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25470 Z= 0.158 Angle : 0.529 10.218 34770 Z= 0.265 Chirality : 0.044 0.171 4080 Planarity : 0.004 0.074 4380 Dihedral : 5.167 55.053 4500 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.06 % Allowed : 8.39 % Favored : 89.55 % 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: 0.32 (0.15), residues: 3036 helix: 1.84 (0.20), residues: 705 sheet: 0.47 (0.19), residues: 702 loop : -0.63 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 411 HIS 0.003 0.000 HIS C 600 PHE 0.030 0.001 PHE C 346 TYR 0.017 0.001 TYR A1042 ARG 0.003 0.000 ARG A 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 48) link_NAG-ASN : angle 1.38344 ( 144) link_BETA1-4 : bond 0.00238 ( 9) link_BETA1-4 : angle 1.08886 ( 27) hydrogen bonds : bond 0.03978 ( 1065) hydrogen bonds : angle 5.08692 ( 2847) SS BOND : bond 0.00161 ( 39) SS BOND : angle 0.68759 ( 78) covalent geometry : bond 0.00370 (25374) covalent geometry : angle 0.52120 (34521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 174 time to evaluate : 2.515 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 41 ASP cc_start: 0.8948 (t0) cc_final: 0.8685 (t70) REVERT: A 101 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7582 (mm-40) REVERT: A 116 VAL cc_start: 0.8234 (m) cc_final: 0.7933 (p) REVERT: A 284 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8604 (mm-30) REVERT: A 309 ASN cc_start: 0.7151 (OUTLIER) cc_final: 0.6900 (p0) REVERT: A 326 TYR cc_start: 0.9131 (p90) cc_final: 0.8775 (p90) REVERT: A 349 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.6780 (p90) REVERT: A 416 LEU cc_start: 0.9191 (mt) cc_final: 0.8674 (tt) REVERT: A 427 MET cc_start: 0.7730 (mpp) cc_final: 0.7360 (mpp) REVERT: A 431 PHE cc_start: 0.8452 (m-80) cc_final: 0.8239 (m-80) REVERT: A 561 ASP cc_start: 0.7951 (t0) cc_final: 0.7662 (t0) REVERT: A 621 ARG cc_start: 0.9013 (ttm-80) cc_final: 0.8612 (ttp-110) REVERT: A 798 PHE cc_start: 0.8559 (t80) cc_final: 0.8292 (t80) REVERT: A 831 ASN cc_start: 0.8401 (m-40) cc_final: 0.8120 (m-40) REVERT: A 969 ASP cc_start: 0.8797 (t70) cc_final: 0.8533 (t0) REVERT: A 1117 GLN cc_start: 0.8728 (tp40) cc_final: 0.8521 (tm-30) REVERT: B 41 ASP cc_start: 0.8898 (t0) cc_final: 0.8662 (t70) REVERT: B 67 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.6990 (p0) REVERT: B 101 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7574 (mm-40) REVERT: B 143 PHE cc_start: 0.8512 (t80) cc_final: 0.8013 (t80) REVERT: B 284 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8627 (mm-30) REVERT: B 326 TYR cc_start: 0.9158 (p90) cc_final: 0.8865 (p90) REVERT: B 349 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7418 (p90) REVERT: B 416 LEU cc_start: 0.9091 (mt) cc_final: 0.8488 (tt) REVERT: B 427 MET cc_start: 0.7779 (mpp) cc_final: 0.7443 (mpp) REVERT: B 798 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: B 831 ASN cc_start: 0.8427 (m-40) cc_final: 0.8112 (m-40) REVERT: B 969 ASP cc_start: 0.8811 (t70) cc_final: 0.8520 (t0) REVERT: C 41 ASP cc_start: 0.8882 (t0) cc_final: 0.8657 (t70) REVERT: C 67 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7280 (p0) REVERT: C 101 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7655 (mm-40) REVERT: C 326 TYR cc_start: 0.9084 (p90) cc_final: 0.8754 (p90) REVERT: C 349 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.6898 (p90) REVERT: C 416 LEU cc_start: 0.9116 (mt) cc_final: 0.8543 (tt) REVERT: C 427 MET cc_start: 0.7682 (mpp) cc_final: 0.7317 (mpp) REVERT: C 621 ARG cc_start: 0.9009 (ttm-80) cc_final: 0.8535 (ttp-110) REVERT: C 798 PHE cc_start: 0.8585 (t80) cc_final: 0.8098 (m-80) REVERT: C 831 ASN cc_start: 0.8488 (m-40) cc_final: 0.8178 (m-40) REVERT: C 969 ASP cc_start: 0.8803 (t70) cc_final: 0.8495 (t0) REVERT: C 1117 GLN cc_start: 0.8715 (tp40) cc_final: 0.8492 (tm-30) outliers start: 55 outliers final: 22 residues processed: 207 average time/residue: 0.9720 time to fit residues: 243.8375 Evaluate side-chains 195 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 915 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 68 optimal weight: 0.0980 chunk 57 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 283 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.070771 restraints weight = 46538.948| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.85 r_work: 0.2816 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25470 Z= 0.115 Angle : 0.504 9.856 34770 Z= 0.251 Chirality : 0.043 0.156 4080 Planarity : 0.003 0.072 4380 Dihedral : 4.693 49.323 4498 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.87 % Allowed : 8.50 % Favored : 89.63 % 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: 0.48 (0.15), residues: 3036 helix: 2.21 (0.20), residues: 684 sheet: 0.58 (0.19), residues: 660 loop : -0.59 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 411 HIS 0.002 0.000 HIS C 600 PHE 0.029 0.001 PHE B 346 TYR 0.017 0.001 TYR A1042 ARG 0.002 0.000 ARG C 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 48) link_NAG-ASN : angle 1.32050 ( 144) link_BETA1-4 : bond 0.00298 ( 9) link_BETA1-4 : angle 1.01186 ( 27) hydrogen bonds : bond 0.03559 ( 1065) hydrogen bonds : angle 4.92073 ( 2847) SS BOND : bond 0.00135 ( 39) SS BOND : angle 0.65284 ( 78) covalent geometry : bond 0.00264 (25374) covalent geometry : angle 0.49728 (34521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 2.679 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 41 ASP cc_start: 0.8880 (t0) cc_final: 0.8614 (t70) REVERT: A 67 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7091 (p0) REVERT: A 87 ILE cc_start: 0.9290 (tp) cc_final: 0.8949 (pp) REVERT: A 101 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7575 (mm-40) REVERT: A 116 VAL cc_start: 0.8141 (m) cc_final: 0.7818 (p) REVERT: A 284 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8595 (mm-30) REVERT: A 326 TYR cc_start: 0.9117 (p90) cc_final: 0.8609 (p90) REVERT: A 349 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.6784 (p90) REVERT: A 416 LEU cc_start: 0.9181 (mt) cc_final: 0.8660 (tt) REVERT: A 427 MET cc_start: 0.7719 (mpp) cc_final: 0.7290 (mpp) REVERT: A 561 ASP cc_start: 0.7973 (t0) cc_final: 0.7645 (t0) REVERT: A 621 ARG cc_start: 0.8999 (ttm-80) cc_final: 0.8582 (ttp-110) REVERT: A 798 PHE cc_start: 0.8508 (t80) cc_final: 0.8301 (t80) REVERT: A 831 ASN cc_start: 0.8362 (m-40) cc_final: 0.8051 (m-40) REVERT: A 969 ASP cc_start: 0.8726 (t70) cc_final: 0.8469 (t0) REVERT: B 41 ASP cc_start: 0.8873 (t0) cc_final: 0.8636 (t70) REVERT: B 67 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.6980 (p0) REVERT: B 87 ILE cc_start: 0.9347 (tp) cc_final: 0.8907 (pp) REVERT: B 101 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7577 (mm-40) REVERT: B 116 VAL cc_start: 0.8088 (m) cc_final: 0.7803 (p) REVERT: B 143 PHE cc_start: 0.8510 (t80) cc_final: 0.8061 (t80) REVERT: B 284 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8605 (mm-30) REVERT: B 326 TYR cc_start: 0.9157 (p90) cc_final: 0.8844 (p90) REVERT: B 349 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7377 (p90) REVERT: B 365 LEU cc_start: 0.8812 (mt) cc_final: 0.8591 (mp) REVERT: B 416 LEU cc_start: 0.9122 (mt) cc_final: 0.8524 (tt) REVERT: B 427 MET cc_start: 0.7793 (mpp) cc_final: 0.7436 (mpp) REVERT: B 798 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 831 ASN cc_start: 0.8410 (m-40) cc_final: 0.8112 (m-40) REVERT: B 969 ASP cc_start: 0.8757 (t70) cc_final: 0.8473 (t0) REVERT: C 41 ASP cc_start: 0.8871 (t0) cc_final: 0.8634 (t70) REVERT: C 101 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7642 (mm-40) REVERT: C 116 VAL cc_start: 0.8135 (m) cc_final: 0.7815 (p) REVERT: C 326 TYR cc_start: 0.9096 (p90) cc_final: 0.8752 (p90) REVERT: C 349 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.6841 (p90) REVERT: C 416 LEU cc_start: 0.9175 (mt) cc_final: 0.8612 (tt) REVERT: C 427 MET cc_start: 0.7693 (mpp) cc_final: 0.7322 (mpp) REVERT: C 621 ARG cc_start: 0.8987 (ttm-80) cc_final: 0.8491 (ttp-110) REVERT: C 748 GLU cc_start: 0.8931 (tt0) cc_final: 0.8624 (tt0) REVERT: C 798 PHE cc_start: 0.8564 (t80) cc_final: 0.8119 (m-80) REVERT: C 831 ASN cc_start: 0.8469 (m-40) cc_final: 0.8149 (m-40) REVERT: C 969 ASP cc_start: 0.8724 (t70) cc_final: 0.8428 (t0) outliers start: 50 outliers final: 24 residues processed: 225 average time/residue: 1.0286 time to fit residues: 279.1268 Evaluate side-chains 206 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 257 optimal weight: 20.0000 chunk 211 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 262 optimal weight: 7.9990 chunk 269 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 289 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 600 HIS C 985 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.069787 restraints weight = 46672.624| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.83 r_work: 0.2787 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 25470 Z= 0.180 Angle : 0.538 10.283 34770 Z= 0.267 Chirality : 0.044 0.163 4080 Planarity : 0.004 0.072 4380 Dihedral : 4.657 47.495 4498 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.95 % Allowed : 9.36 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.15), residues: 3036 helix: 1.96 (0.20), residues: 702 sheet: 0.56 (0.19), residues: 702 loop : -0.61 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 52 HIS 0.004 0.001 HIS C 600 PHE 0.029 0.001 PHE C 346 TYR 0.019 0.001 TYR A 879 ARG 0.002 0.000 ARG C 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 48) link_NAG-ASN : angle 1.40901 ( 144) link_BETA1-4 : bond 0.00176 ( 9) link_BETA1-4 : angle 1.18618 ( 27) hydrogen bonds : bond 0.04002 ( 1065) hydrogen bonds : angle 4.98871 ( 2847) SS BOND : bond 0.00177 ( 39) SS BOND : angle 0.71147 ( 78) covalent geometry : bond 0.00427 (25374) covalent geometry : angle 0.53002 (34521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 2.725 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 41 ASP cc_start: 0.8911 (t0) cc_final: 0.8657 (t70) REVERT: A 67 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7045 (p0) REVERT: A 87 ILE cc_start: 0.9260 (tp) cc_final: 0.8964 (pp) REVERT: A 101 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7579 (mm-40) REVERT: A 116 VAL cc_start: 0.8195 (m) cc_final: 0.7863 (p) REVERT: A 284 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8616 (mm-30) REVERT: A 326 TYR cc_start: 0.9131 (p90) cc_final: 0.8720 (p90) REVERT: A 349 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.6765 (p90) REVERT: A 416 LEU cc_start: 0.9203 (mt) cc_final: 0.8670 (tt) REVERT: A 427 MET cc_start: 0.7754 (mpp) cc_final: 0.7414 (mpp) REVERT: A 621 ARG cc_start: 0.9013 (ttm-80) cc_final: 0.8610 (ttp-110) REVERT: A 798 PHE cc_start: 0.8568 (t80) cc_final: 0.8347 (t80) REVERT: A 831 ASN cc_start: 0.8374 (m-40) cc_final: 0.8093 (m-40) REVERT: A 969 ASP cc_start: 0.8779 (t70) cc_final: 0.8519 (t0) REVERT: A 980 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8780 (mt0) REVERT: A 1117 GLN cc_start: 0.8738 (tp40) cc_final: 0.8500 (tm-30) REVERT: B 41 ASP cc_start: 0.8887 (t0) cc_final: 0.8658 (t70) REVERT: B 87 ILE cc_start: 0.9351 (tp) cc_final: 0.8945 (pp) REVERT: B 101 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7573 (mm-40) REVERT: B 116 VAL cc_start: 0.8205 (m) cc_final: 0.7934 (p) REVERT: B 143 PHE cc_start: 0.8492 (t80) cc_final: 0.8198 (t80) REVERT: B 284 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8624 (mm-30) REVERT: B 326 TYR cc_start: 0.9168 (p90) cc_final: 0.8887 (p90) REVERT: B 349 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7367 (p90) REVERT: B 365 LEU cc_start: 0.8885 (mt) cc_final: 0.8656 (mp) REVERT: B 416 LEU cc_start: 0.9180 (mt) cc_final: 0.8603 (tt) REVERT: B 427 MET cc_start: 0.7799 (mpp) cc_final: 0.7457 (mpp) REVERT: B 798 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: B 831 ASN cc_start: 0.8417 (m-40) cc_final: 0.8121 (m-40) REVERT: C 41 ASP cc_start: 0.8902 (t0) cc_final: 0.8677 (t70) REVERT: C 101 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7641 (mm-40) REVERT: C 326 TYR cc_start: 0.9097 (p90) cc_final: 0.8751 (p90) REVERT: C 349 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.6873 (p90) REVERT: C 416 LEU cc_start: 0.9175 (mt) cc_final: 0.8624 (tt) REVERT: C 427 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7392 (mpp) REVERT: C 621 ARG cc_start: 0.9015 (ttm-80) cc_final: 0.8536 (ttp-110) REVERT: C 798 PHE cc_start: 0.8588 (t80) cc_final: 0.8106 (m-80) REVERT: C 831 ASN cc_start: 0.8468 (m-40) cc_final: 0.8162 (m-40) REVERT: C 969 ASP cc_start: 0.8796 (t70) cc_final: 0.8558 (t0) REVERT: C 1117 GLN cc_start: 0.8727 (tp40) cc_final: 0.8514 (tm-30) outliers start: 52 outliers final: 28 residues processed: 210 average time/residue: 0.9891 time to fit residues: 252.9298 Evaluate side-chains 207 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 254 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS C 600 HIS C 985 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.113962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.069426 restraints weight = 46668.469| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.83 r_work: 0.2781 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 25470 Z= 0.200 Angle : 0.549 10.181 34770 Z= 0.274 Chirality : 0.044 0.168 4080 Planarity : 0.004 0.072 4380 Dihedral : 4.648 49.239 4498 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.10 % Allowed : 9.55 % 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: 0.36 (0.15), residues: 3036 helix: 1.92 (0.20), residues: 702 sheet: 0.52 (0.19), residues: 702 loop : -0.63 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 52 HIS 0.004 0.001 HIS A 600 PHE 0.031 0.001 PHE A 346 TYR 0.018 0.001 TYR A 879 ARG 0.002 0.000 ARG B 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 48) link_NAG-ASN : angle 1.43529 ( 144) link_BETA1-4 : bond 0.00169 ( 9) link_BETA1-4 : angle 1.18278 ( 27) hydrogen bonds : bond 0.04085 ( 1065) hydrogen bonds : angle 5.01275 ( 2847) SS BOND : bond 0.00187 ( 39) SS BOND : angle 0.72942 ( 78) covalent geometry : bond 0.00477 (25374) covalent geometry : angle 0.54090 (34521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 2.508 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 41 ASP cc_start: 0.8952 (t0) cc_final: 0.8690 (t70) REVERT: A 67 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7104 (p0) REVERT: A 87 ILE cc_start: 0.9258 (tp) cc_final: 0.8961 (pp) REVERT: A 101 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7567 (mm-40) REVERT: A 116 VAL cc_start: 0.8213 (m) cc_final: 0.7874 (p) REVERT: A 284 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8632 (mm-30) REVERT: A 326 TYR cc_start: 0.9119 (p90) cc_final: 0.8701 (p90) REVERT: A 349 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.6772 (p90) REVERT: A 416 LEU cc_start: 0.9209 (mt) cc_final: 0.8683 (tt) REVERT: A 427 MET cc_start: 0.7742 (mpp) cc_final: 0.7409 (mpp) REVERT: A 621 ARG cc_start: 0.9036 (ttm-80) cc_final: 0.8629 (ttp-110) REVERT: A 798 PHE cc_start: 0.8575 (t80) cc_final: 0.8329 (t80) REVERT: A 831 ASN cc_start: 0.8385 (m-40) cc_final: 0.8092 (m-40) REVERT: A 969 ASP cc_start: 0.8805 (t70) cc_final: 0.8534 (t0) REVERT: B 41 ASP cc_start: 0.8886 (t0) cc_final: 0.8655 (t70) REVERT: B 67 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7026 (p0) REVERT: B 87 ILE cc_start: 0.9348 (tp) cc_final: 0.8951 (pp) REVERT: B 101 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7547 (mm-40) REVERT: B 116 VAL cc_start: 0.8206 (m) cc_final: 0.7950 (p) REVERT: B 284 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8631 (mm-30) REVERT: B 326 TYR cc_start: 0.9149 (p90) cc_final: 0.8762 (p90) REVERT: B 349 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7149 (p90) REVERT: B 416 LEU cc_start: 0.9194 (mt) cc_final: 0.8612 (tt) REVERT: B 427 MET cc_start: 0.7827 (mpp) cc_final: 0.7462 (mpp) REVERT: B 798 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: B 831 ASN cc_start: 0.8432 (m-40) cc_final: 0.8122 (m-40) REVERT: C 41 ASP cc_start: 0.8894 (t0) cc_final: 0.8664 (t70) REVERT: C 101 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7612 (mm-40) REVERT: C 326 TYR cc_start: 0.9096 (p90) cc_final: 0.8776 (p90) REVERT: C 349 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.6895 (p90) REVERT: C 416 LEU cc_start: 0.9180 (mt) cc_final: 0.8633 (tt) REVERT: C 427 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7398 (mpp) REVERT: C 621 ARG cc_start: 0.9025 (ttm-80) cc_final: 0.8540 (ttp-110) REVERT: C 798 PHE cc_start: 0.8586 (t80) cc_final: 0.8074 (m-80) REVERT: C 831 ASN cc_start: 0.8484 (m-40) cc_final: 0.8180 (m-40) REVERT: C 969 ASP cc_start: 0.8814 (t70) cc_final: 0.8516 (t0) outliers start: 56 outliers final: 29 residues processed: 205 average time/residue: 0.9630 time to fit residues: 241.4082 Evaluate side-chains 204 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Chi-restraints excluded: chain C residue 1116 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 82 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 281 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS C 600 HIS C 985 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.070355 restraints weight = 46613.904| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.84 r_work: 0.2802 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25470 Z= 0.148 Angle : 0.530 9.819 34770 Z= 0.263 Chirality : 0.043 0.178 4080 Planarity : 0.004 0.072 4380 Dihedral : 4.497 49.446 4498 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.76 % Allowed : 9.96 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.15), residues: 3036 helix: 2.01 (0.20), residues: 702 sheet: 0.48 (0.19), residues: 693 loop : -0.58 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.003 0.000 HIS B 600 PHE 0.031 0.001 PHE B 346 TYR 0.017 0.001 TYR A1042 ARG 0.002 0.000 ARG C 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 48) link_NAG-ASN : angle 1.35629 ( 144) link_BETA1-4 : bond 0.00221 ( 9) link_BETA1-4 : angle 1.05955 ( 27) hydrogen bonds : bond 0.03771 ( 1065) hydrogen bonds : angle 4.92873 ( 2847) SS BOND : bond 0.00155 ( 39) SS BOND : angle 0.69693 ( 78) covalent geometry : bond 0.00348 (25374) covalent geometry : angle 0.52248 (34521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 2.948 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 41 ASP cc_start: 0.8909 (t0) cc_final: 0.8652 (t70) REVERT: A 67 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7091 (p0) REVERT: A 87 ILE cc_start: 0.9228 (tp) cc_final: 0.8968 (pp) REVERT: A 101 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7571 (mm-40) REVERT: A 116 VAL cc_start: 0.8155 (m) cc_final: 0.7833 (p) REVERT: A 284 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 326 TYR cc_start: 0.9114 (p90) cc_final: 0.8684 (p90) REVERT: A 349 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.6691 (p90) REVERT: A 416 LEU cc_start: 0.9208 (mt) cc_final: 0.8685 (tt) REVERT: A 427 MET cc_start: 0.7713 (mpp) cc_final: 0.7351 (mpp) REVERT: A 621 ARG cc_start: 0.9012 (ttm-80) cc_final: 0.8602 (ttp-110) REVERT: A 798 PHE cc_start: 0.8564 (t80) cc_final: 0.8329 (t80) REVERT: A 831 ASN cc_start: 0.8366 (m-40) cc_final: 0.8071 (m-40) REVERT: A 969 ASP cc_start: 0.8781 (t70) cc_final: 0.8522 (t0) REVERT: B 41 ASP cc_start: 0.8891 (t0) cc_final: 0.8659 (t70) REVERT: B 67 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7039 (p0) REVERT: B 87 ILE cc_start: 0.9328 (tp) cc_final: 0.8953 (pp) REVERT: B 101 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7556 (mm-40) REVERT: B 116 VAL cc_start: 0.8167 (m) cc_final: 0.7913 (p) REVERT: B 284 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8622 (mm-30) REVERT: B 326 TYR cc_start: 0.9152 (p90) cc_final: 0.8719 (p90) REVERT: B 349 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7206 (p90) REVERT: B 365 LEU cc_start: 0.8860 (mt) cc_final: 0.8631 (mp) REVERT: B 416 LEU cc_start: 0.9184 (mt) cc_final: 0.8623 (tt) REVERT: B 427 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7438 (mpp) REVERT: B 798 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: B 831 ASN cc_start: 0.8410 (m-40) cc_final: 0.8122 (m-40) REVERT: C 41 ASP cc_start: 0.8899 (t0) cc_final: 0.8682 (t70) REVERT: C 101 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7621 (mm-40) REVERT: C 116 VAL cc_start: 0.8139 (m) cc_final: 0.7801 (p) REVERT: C 326 TYR cc_start: 0.9086 (p90) cc_final: 0.8634 (p90) REVERT: C 349 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.6850 (p90) REVERT: C 416 LEU cc_start: 0.9182 (mt) cc_final: 0.8646 (tt) REVERT: C 427 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7341 (mpp) REVERT: C 621 ARG cc_start: 0.9019 (ttm-80) cc_final: 0.8530 (ttp-110) REVERT: C 798 PHE cc_start: 0.8579 (t80) cc_final: 0.8072 (m-80) REVERT: C 831 ASN cc_start: 0.8469 (m-40) cc_final: 0.8154 (m-40) REVERT: C 969 ASP cc_start: 0.8783 (t70) cc_final: 0.8485 (t0) REVERT: C 1117 GLN cc_start: 0.8718 (tp40) cc_final: 0.8502 (tm-30) outliers start: 47 outliers final: 26 residues processed: 205 average time/residue: 0.9957 time to fit residues: 248.6141 Evaluate side-chains 201 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Chi-restraints excluded: chain C residue 1116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 112 optimal weight: 8.9990 chunk 300 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS B 985 GLN C 600 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.115145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.070889 restraints weight = 46420.214| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.84 r_work: 0.2811 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25470 Z= 0.131 Angle : 0.528 9.820 34770 Z= 0.263 Chirality : 0.043 0.190 4080 Planarity : 0.003 0.072 4380 Dihedral : 4.344 49.812 4496 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.65 % Allowed : 10.15 % Favored : 88.20 % 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: 0.44 (0.15), residues: 3036 helix: 2.05 (0.20), residues: 702 sheet: 0.47 (0.19), residues: 690 loop : -0.56 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.003 0.000 HIS B 600 PHE 0.033 0.001 PHE B 346 TYR 0.017 0.001 TYR A 355 ARG 0.002 0.000 ARG C 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 48) link_NAG-ASN : angle 1.32558 ( 144) link_BETA1-4 : bond 0.00279 ( 9) link_BETA1-4 : angle 1.05228 ( 27) hydrogen bonds : bond 0.03625 ( 1065) hydrogen bonds : angle 4.86605 ( 2847) SS BOND : bond 0.00141 ( 39) SS BOND : angle 0.68763 ( 78) covalent geometry : bond 0.00307 (25374) covalent geometry : angle 0.52061 (34521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 2.738 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 41 ASP cc_start: 0.8892 (t0) cc_final: 0.8628 (t70) REVERT: A 67 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7022 (p0) REVERT: A 87 ILE cc_start: 0.9200 (tp) cc_final: 0.8976 (pp) REVERT: A 101 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7543 (mm-40) REVERT: A 284 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8611 (mm-30) REVERT: A 326 TYR cc_start: 0.9104 (p90) cc_final: 0.8668 (p90) REVERT: A 349 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.6683 (p90) REVERT: A 416 LEU cc_start: 0.9232 (mt) cc_final: 0.8718 (tt) REVERT: A 427 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7274 (mpp) REVERT: A 621 ARG cc_start: 0.9000 (ttm-80) cc_final: 0.8577 (ttp-110) REVERT: A 798 PHE cc_start: 0.8559 (t80) cc_final: 0.8313 (t80) REVERT: A 831 ASN cc_start: 0.8343 (m-40) cc_final: 0.8055 (m-40) REVERT: A 969 ASP cc_start: 0.8759 (t70) cc_final: 0.8506 (t0) REVERT: B 41 ASP cc_start: 0.8890 (t0) cc_final: 0.8657 (t70) REVERT: B 67 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7037 (p0) REVERT: B 87 ILE cc_start: 0.9336 (tp) cc_final: 0.8959 (pp) REVERT: B 101 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7561 (mm-40) REVERT: B 116 VAL cc_start: 0.8184 (m) cc_final: 0.7952 (p) REVERT: B 284 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8608 (mm-30) REVERT: B 326 TYR cc_start: 0.9141 (p90) cc_final: 0.8651 (p90) REVERT: B 349 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7103 (p90) REVERT: B 365 LEU cc_start: 0.8858 (mt) cc_final: 0.8634 (mp) REVERT: B 416 LEU cc_start: 0.9179 (mt) cc_final: 0.8623 (tt) REVERT: B 427 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7384 (mpp) REVERT: B 798 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 831 ASN cc_start: 0.8385 (m-40) cc_final: 0.8099 (m-40) REVERT: C 41 ASP cc_start: 0.8892 (t0) cc_final: 0.8651 (t70) REVERT: C 101 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7638 (mm-40) REVERT: C 116 VAL cc_start: 0.8111 (m) cc_final: 0.7771 (p) REVERT: C 326 TYR cc_start: 0.9113 (p90) cc_final: 0.8727 (p90) REVERT: C 349 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.6824 (p90) REVERT: C 416 LEU cc_start: 0.9175 (mt) cc_final: 0.8639 (tt) REVERT: C 427 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7384 (mpp) REVERT: C 621 ARG cc_start: 0.9026 (ttm-80) cc_final: 0.8539 (ttp-110) REVERT: C 798 PHE cc_start: 0.8577 (t80) cc_final: 0.8083 (m-80) REVERT: C 831 ASN cc_start: 0.8425 (m-40) cc_final: 0.8123 (m-40) REVERT: C 969 ASP cc_start: 0.8752 (t70) cc_final: 0.8521 (t0) REVERT: C 1117 GLN cc_start: 0.8724 (tp40) cc_final: 0.8516 (tm-30) outliers start: 44 outliers final: 26 residues processed: 199 average time/residue: 0.9680 time to fit residues: 235.2332 Evaluate side-chains 206 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 915 SER Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 915 SER Chi-restraints excluded: chain C residue 1111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 178 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 292 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 985 GLN B 600 HIS C 600 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.069744 restraints weight = 46691.440| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.83 r_work: 0.2786 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25470 Z= 0.188 Angle : 0.555 9.766 34770 Z= 0.276 Chirality : 0.044 0.181 4080 Planarity : 0.004 0.072 4380 Dihedral : 4.445 51.421 4496 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.57 % Allowed : 10.30 % Favored : 88.13 % 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: 0.39 (0.15), residues: 3036 helix: 1.94 (0.20), residues: 702 sheet: 0.50 (0.18), residues: 702 loop : -0.60 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.004 0.001 HIS C 600 PHE 0.031 0.001 PHE B 346 TYR 0.018 0.001 TYR A1042 ARG 0.002 0.000 ARG C 970 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 48) link_NAG-ASN : angle 1.40353 ( 144) link_BETA1-4 : bond 0.00168 ( 9) link_BETA1-4 : angle 1.17467 ( 27) hydrogen bonds : bond 0.03991 ( 1065) hydrogen bonds : angle 4.96391 ( 2847) SS BOND : bond 0.00176 ( 39) SS BOND : angle 0.72422 ( 78) covalent geometry : bond 0.00447 (25374) covalent geometry : angle 0.54709 (34521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17706.69 seconds wall clock time: 305 minutes 14.97 seconds (18314.97 seconds total)