Starting phenix.real_space_refine on Sun May 25 02:22:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xym_38778/05_2025/8xym_38778.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xym_38778/05_2025/8xym_38778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xym_38778/05_2025/8xym_38778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xym_38778/05_2025/8xym_38778.map" model { file = "/net/cci-nas-00/data/ceres_data/8xym_38778/05_2025/8xym_38778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xym_38778/05_2025/8xym_38778.cif" } resolution = 2.74 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= 0.028 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 114 5.16 5 C 16533 2.51 5 N 4280 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25979 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8443 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 57, 'TRANS': 1022} Chain breaks: 4 Chain: "B" Number of atoms: 8416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8416 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 56, 'TRANS': 1020} Chain breaks: 4 Chain: "C" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8434 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 57, 'TRANS': 1021} Chain breaks: 4 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: "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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 16.93, per 1000 atoms: 0.65 Number of scatterers: 25979 At special positions: 0 Unit cell: (155.94, 148.35, 169.05, 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 114 16.00 O 5052 8.00 N 4280 7.00 C 16533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 370 " " NAG A1308 " - " ASN A 705 " " NAG A1309 " - " ASN A 713 " " NAG A1310 " - " ASN A1094 " " NAG A1311 " - " ASN A1130 " " NAG A1312 " - " ASN A 30 " " NAG A1313 " - " ASN A1070 " " NAG B1301 " - " ASN B 30 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 149 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 370 " " NAG B1309 " - " ASN B 705 " " NAG B1310 " - " ASN B 713 " " NAG B1311 " - " ASN B1094 " " NAG C1301 " - " ASN C 30 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 705 " " NAG C1309 " - " ASN C 713 " " NAG C1310 " - " ASN C 797 " " NAG C1311 " - " ASN C1070 " " NAG C1312 " - " ASN C1094 " " NAG C1313 " - " ASN C1130 " " NAG C1314 " - " ASN C 165 " " NAG C1315 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 797 " " NAG F 1 " - " ASN B 122 " " NAG G 1 " - " ASN B 797 " " NAG H 1 " - " ASN C 122 " Time building additional restraints: 7.33 Conformation dependent library (CDL) restraints added in 3.6 seconds 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6052 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 48 sheets defined 25.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.696A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.666A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.995A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.640A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 748 through 751 removed outlier: 3.672A pdb=" N GLN A 751 " --> pdb=" O LEU A 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 751' Processing helix chain 'A' and resid 752 through 779 removed outlier: 3.835A pdb=" N CYS A 756 " --> pdb=" O TYR A 752 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 765 " --> pdb=" O ARG A 761 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 811 removed outlier: 4.132A pdb=" N LYS A 810 " --> pdb=" O LYS A 807 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG A 811 " --> pdb=" O PRO A 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 811' Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.634A pdb=" N GLY A 885 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 908 through 914 removed outlier: 4.190A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 937 Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.692A pdb=" N GLN A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.506A pdb=" N ILE A 976 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.602A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.643A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.523A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.509A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.569A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.554A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 748 through 751 removed outlier: 3.611A pdb=" N GLN B 751 " --> pdb=" O LEU B 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 751' Processing helix chain 'B' and resid 752 through 779 removed outlier: 4.137A pdb=" N CYS B 756 " --> pdb=" O TYR B 752 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 769 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 779 " --> pdb=" O GLN B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 811 removed outlier: 3.688A pdb=" N LYS B 810 " --> pdb=" O LYS B 807 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 811 " --> pdb=" O PRO B 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 807 through 811' Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.526A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 839 removed outlier: 3.574A pdb=" N ASP B 839 " --> pdb=" O ASP B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 851 Processing helix chain 'B' and resid 862 through 881 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 909 through 915 removed outlier: 3.630A pdb=" N TYR B 913 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 937 Processing helix chain 'B' and resid 941 through 961 removed outlier: 3.566A pdb=" N GLN B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 removed outlier: 3.542A pdb=" N ILE B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.569A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.791A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.250A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.604A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 748 through 751 removed outlier: 3.725A pdb=" N GLN C 751 " --> pdb=" O LEU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 748 through 751' Processing helix chain 'C' and resid 752 through 779 removed outlier: 4.024A pdb=" N CYS C 756 " --> pdb=" O TYR C 752 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 757 " --> pdb=" O GLY C 753 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 811 removed outlier: 4.385A pdb=" N ARG C 811 " --> pdb=" O PRO C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 832 through 839 removed outlier: 3.505A pdb=" N ASP C 839 " --> pdb=" O ASP C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 851 Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 882 through 886 removed outlier: 3.568A pdb=" N GLY C 885 " --> pdb=" O TRP C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 906 Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.555A pdb=" N TYR C 913 " --> pdb=" O GLN C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 937 Processing helix chain 'C' and resid 941 through 961 removed outlier: 3.649A pdb=" N GLN C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 removed outlier: 3.602A pdb=" N ILE C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 1029 removed outlier: 5.507A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C1029 " --> pdb=" O MET C1025 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.698A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.196A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.413A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.916A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.906A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.755A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.658A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.337A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 598 removed outlier: 3.546A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.035A pdb=" N GLU A 654 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR A 692 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 724 removed outlier: 6.583A pdb=" N ALA A 709 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A1070 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU A1068 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A1046 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.725A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.637A pdb=" N ILE A 784 " --> pdb=" O ASN C 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1116 through 1121 removed outlier: 3.625A pdb=" N SER A1119 " --> pdb=" O ALA A1083 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA A1083 " --> pdb=" O SER A1119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1090 through 1093 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 29 removed outlier: 4.447A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.988A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.174A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 13.027A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.971A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.007A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.639A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.485A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 357 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.252A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 594 through 598 removed outlier: 3.969A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 Processing sheet with id=AD1, first strand: chain 'B' and resid 698 through 699 Processing sheet with id=AD2, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.746A pdb=" N SER B 707 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B1072 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 709 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN B1070 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.746A pdb=" N SER B 707 " --> pdb=" O THR B1072 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B1072 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 709 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN B1070 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR B1072 " --> pdb=" O SER B1093 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.596A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1116 through 1118 removed outlier: 3.792A pdb=" N ILE B1077 " --> pdb=" O HIS B1084 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.314A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.179A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.761A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.018A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.638A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.638A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.495A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.471A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 594 through 598 removed outlier: 4.237A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE8, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.817A pdb=" N SER C 707 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR C1072 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA C 709 " --> pdb=" O ASN C1070 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN C1070 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU C1068 " --> pdb=" O PRO C 711 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.817A pdb=" N SER C 707 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR C1072 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA C 709 " --> pdb=" O ASN C1070 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN C1070 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU C1068 " --> pdb=" O PRO C 711 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.528A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1077 through 1078 Processing sheet with id=AF3, first strand: chain 'C' and resid 1084 through 1086 1043 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.83 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8281 1.34 - 1.46: 6224 1.46 - 1.58: 11925 1.58 - 1.70: 0 1.70 - 1.82: 141 Bond restraints: 26571 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" C1 NAG A1313 " pdb=" O5 NAG A1313 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG A1312 " pdb=" O5 NAG A1312 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 ... (remaining 26566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 34634 1.35 - 2.70: 1282 2.70 - 4.05: 211 4.05 - 5.40: 33 5.40 - 6.75: 7 Bond angle restraints: 36167 Sorted by residual: angle pdb=" N VAL B1029 " pdb=" CA VAL B1029 " pdb=" C VAL B1029 " ideal model delta sigma weight residual 112.96 108.43 4.53 1.00e+00 1.00e+00 2.05e+01 angle pdb=" N GLY B1095 " pdb=" CA GLY B1095 " pdb=" C GLY B1095 " ideal model delta sigma weight residual 113.58 109.47 4.11 1.07e+00 8.73e-01 1.47e+01 angle pdb=" C ASP B 253 " pdb=" N SER B 254 " pdb=" CA SER B 254 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" N VAL B1124 " pdb=" CA VAL B1124 " pdb=" C VAL B1124 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 angle pdb=" CA CYS B 361 " pdb=" CB CYS B 361 " pdb=" SG CYS B 361 " ideal model delta sigma weight residual 114.40 120.50 -6.10 2.30e+00 1.89e-01 7.04e+00 ... (remaining 36162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 15038 17.03 - 34.07: 1186 34.07 - 51.10: 197 51.10 - 68.13: 55 68.13 - 85.17: 19 Dihedral angle restraints: 16495 sinusoidal: 7076 harmonic: 9419 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 144.12 -51.12 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 54.08 38.92 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 16492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4133 0.114 - 0.228: 96 0.228 - 0.341: 3 0.341 - 0.455: 0 0.455 - 0.569: 2 Chirality restraints: 4234 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A1094 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 30 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 4231 not shown) Planarity restraints: 4669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " 0.315 2.00e-02 2.50e+03 2.72e-01 9.22e+02 pdb=" C7 NAG C1301 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " 0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.296 2.00e-02 2.50e+03 2.51e-01 7.86e+02 pdb=" C7 NAG A1301 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.435 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.158 2.00e-02 2.50e+03 1.32e-01 2.19e+02 pdb=" C7 NAG F 2 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.219 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.012 2.00e-02 2.50e+03 ... (remaining 4666 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1835 2.74 - 3.28: 24753 3.28 - 3.82: 39345 3.82 - 4.36: 46322 4.36 - 4.90: 83721 Nonbonded interactions: 195976 Sorted by model distance: nonbonded pdb=" OG1 THR A1112 " pdb=" OD1 ASP A1114 " model vdw 2.197 3.040 nonbonded pdb=" O HIS B 245 " pdb=" OG1 THR B 259 " model vdw 2.202 3.040 nonbonded pdb=" O GLY A 876 " pdb=" OG SER A 880 " model vdw 2.218 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 691 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR B1112 " pdb=" OD1 ASP B1114 " model vdw 2.261 3.040 ... (remaining 195971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 676 or resid 685 through 1133 or resid 1303 thr \ ough 1313)) selection = (chain 'B' and (resid 17 through 676 or resid 685 through 1133 or resid 1301 thr \ ough 1311)) selection = (chain 'C' and (resid 17 through 1133 or resid 1303 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 7.080 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: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 64.740 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 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 0.047 26659 Z= 0.170 Angle : 0.623 19.513 36392 Z= 0.323 Chirality : 0.047 0.569 4234 Planarity : 0.007 0.272 4625 Dihedral : 12.493 85.167 10326 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.02 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3206 helix: 1.21 (0.21), residues: 696 sheet: 0.41 (0.20), residues: 674 loop : -2.03 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 882 HIS 0.004 0.001 HIS C1079 PHE 0.022 0.001 PHE B 902 TYR 0.030 0.001 TYR C 266 ARG 0.003 0.000 ARG A1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 44) link_NAG-ASN : angle 2.28091 ( 132) link_BETA1-4 : bond 0.02031 ( 5) link_BETA1-4 : angle 6.45834 ( 15) hydrogen bonds : bond 0.15358 ( 1006) hydrogen bonds : angle 6.84683 ( 2850) SS BOND : bond 0.00202 ( 39) SS BOND : angle 1.32773 ( 78) covalent geometry : bond 0.00352 (26571) covalent geometry : angle 0.59182 (36167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 3.110 Fit side-chains revert: symmetry clash REVERT: A 516 GLU cc_start: 0.8553 (pm20) cc_final: 0.8254 (pm20) REVERT: A 900 TYR cc_start: 0.7765 (t80) cc_final: 0.7317 (t80) REVERT: A 1107 GLU cc_start: 0.8862 (tt0) cc_final: 0.8481 (tm-30) REVERT: A 1134 TYR cc_start: 0.8813 (t80) cc_final: 0.8543 (t80) REVERT: B 984 GLU cc_start: 0.8355 (mp0) cc_final: 0.8059 (mp0) REVERT: B 998 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 1121 ASN cc_start: 0.8601 (t0) cc_final: 0.8068 (t0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 1.3569 time to fit residues: 201.0322 Evaluate side-chains 71 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 953 GLN B 146 HIS C1067 GLN ** C1079 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.066037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051012 restraints weight = 86633.959| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.56 r_work: 0.2848 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26659 Z= 0.192 Angle : 0.623 9.286 36392 Z= 0.325 Chirality : 0.046 0.328 4234 Planarity : 0.004 0.049 4625 Dihedral : 6.963 59.707 4507 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.58 % Favored : 92.39 % Rotamer: Outliers : 0.64 % Allowed : 4.42 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3206 helix: 1.25 (0.20), residues: 716 sheet: 0.25 (0.20), residues: 711 loop : -2.03 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 882 HIS 0.006 0.001 HIS C 146 PHE 0.024 0.001 PHE A 819 TYR 0.022 0.001 TYR C 266 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 44) link_NAG-ASN : angle 1.83928 ( 132) link_BETA1-4 : bond 0.00870 ( 5) link_BETA1-4 : angle 3.78195 ( 15) hydrogen bonds : bond 0.06538 ( 1006) hydrogen bonds : angle 5.48736 ( 2850) SS BOND : bond 0.00324 ( 39) SS BOND : angle 1.34897 ( 78) covalent geometry : bond 0.00451 (26571) covalent geometry : angle 0.60718 (36167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 3.204 Fit side-chains revert: symmetry clash REVERT: A 516 GLU cc_start: 0.8646 (pm20) cc_final: 0.8327 (pm20) REVERT: A 900 TYR cc_start: 0.7891 (t80) cc_final: 0.7454 (t80) REVERT: A 1107 GLU cc_start: 0.9085 (tt0) cc_final: 0.8589 (tm-30) REVERT: B 565 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7453 (p90) REVERT: B 900 TYR cc_start: 0.8108 (t80) cc_final: 0.7706 (t80) REVERT: B 984 GLU cc_start: 0.8535 (mp0) cc_final: 0.8302 (mp0) REVERT: B 998 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8412 (tm-30) REVERT: B 1121 ASN cc_start: 0.8573 (t0) cc_final: 0.7850 (t0) REVERT: C 986 GLU cc_start: 0.8277 (pm20) cc_final: 0.7897 (pm20) outliers start: 18 outliers final: 5 residues processed: 86 average time/residue: 1.2882 time to fit residues: 133.2760 Evaluate side-chains 73 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 398 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 95 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 193 optimal weight: 0.4980 chunk 232 optimal weight: 0.9990 chunk 288 optimal weight: 0.5980 chunk 316 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1079 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051429 restraints weight = 85798.264| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.58 r_work: 0.2849 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26659 Z= 0.151 Angle : 0.580 10.074 36392 Z= 0.302 Chirality : 0.045 0.278 4234 Planarity : 0.004 0.046 4625 Dihedral : 6.344 56.787 4507 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.02 % Favored : 92.95 % Rotamer: Outliers : 0.53 % Allowed : 7.17 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.94 (0.15), residues: 3206 helix: 1.46 (0.20), residues: 713 sheet: 0.28 (0.20), residues: 727 loop : -2.02 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 882 HIS 0.004 0.001 HIS A 66 PHE 0.019 0.001 PHE A 819 TYR 0.020 0.001 TYR C 266 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 44) link_NAG-ASN : angle 1.72515 ( 132) link_BETA1-4 : bond 0.00951 ( 5) link_BETA1-4 : angle 3.83321 ( 15) hydrogen bonds : bond 0.05749 ( 1006) hydrogen bonds : angle 5.18753 ( 2850) SS BOND : bond 0.00445 ( 39) SS BOND : angle 1.29778 ( 78) covalent geometry : bond 0.00348 (26571) covalent geometry : angle 0.56363 (36167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8245 (mt-10) REVERT: A 900 TYR cc_start: 0.7866 (t80) cc_final: 0.7436 (t80) REVERT: A 1107 GLU cc_start: 0.9085 (tt0) cc_final: 0.8596 (tm-30) REVERT: B 565 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7325 (p90) REVERT: B 900 TYR cc_start: 0.8160 (t80) cc_final: 0.7866 (t80) REVERT: B 984 GLU cc_start: 0.8590 (mp0) cc_final: 0.8321 (mp0) REVERT: B 998 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8397 (tm-30) REVERT: B 1121 ASN cc_start: 0.8565 (t0) cc_final: 0.7741 (t0) REVERT: C 153 MET cc_start: 0.9155 (mmm) cc_final: 0.8933 (mmm) outliers start: 15 outliers final: 7 residues processed: 85 average time/residue: 1.3106 time to fit residues: 133.8613 Evaluate side-chains 71 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain C residue 398 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 84 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 249 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.065575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.050525 restraints weight = 86547.163| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.58 r_work: 0.2818 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26659 Z= 0.193 Angle : 0.601 10.122 36392 Z= 0.314 Chirality : 0.046 0.278 4234 Planarity : 0.004 0.049 4625 Dihedral : 6.193 57.853 4507 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.80 % Favored : 92.17 % Rotamer: Outliers : 0.81 % Allowed : 8.12 % Favored : 91.06 % 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: -0.95 (0.15), residues: 3206 helix: 1.41 (0.20), residues: 716 sheet: 0.24 (0.20), residues: 752 loop : -2.04 (0.13), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 152 HIS 0.004 0.001 HIS B1079 PHE 0.016 0.001 PHE B 902 TYR 0.021 0.001 TYR A1134 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 44) link_NAG-ASN : angle 1.77818 ( 132) link_BETA1-4 : bond 0.00807 ( 5) link_BETA1-4 : angle 3.70497 ( 15) hydrogen bonds : bond 0.06114 ( 1006) hydrogen bonds : angle 5.18756 ( 2850) SS BOND : bond 0.00326 ( 39) SS BOND : angle 1.31219 ( 78) covalent geometry : bond 0.00457 (26571) covalent geometry : angle 0.58555 (36167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 776 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8340 (mt-10) REVERT: A 900 TYR cc_start: 0.7917 (t80) cc_final: 0.7462 (t80) REVERT: A 1107 GLU cc_start: 0.9127 (tt0) cc_final: 0.8622 (tm-30) REVERT: B 565 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7329 (p90) REVERT: B 900 TYR cc_start: 0.8194 (t80) cc_final: 0.7900 (t80) REVERT: B 984 GLU cc_start: 0.8608 (mp0) cc_final: 0.8325 (mp0) REVERT: B 998 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 1121 ASN cc_start: 0.8579 (t0) cc_final: 0.7743 (t0) REVERT: C 319 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6624 (ptt90) REVERT: C 986 GLU cc_start: 0.8252 (pm20) cc_final: 0.7753 (pm20) outliers start: 23 outliers final: 13 residues processed: 83 average time/residue: 1.1535 time to fit residues: 117.0920 Evaluate side-chains 76 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 586 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 250 optimal weight: 0.0570 chunk 160 optimal weight: 0.8980 chunk 262 optimal weight: 5.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN C 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.066954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051937 restraints weight = 85472.579| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.57 r_work: 0.2860 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26659 Z= 0.119 Angle : 0.552 10.129 36392 Z= 0.286 Chirality : 0.044 0.279 4234 Planarity : 0.004 0.045 4625 Dihedral : 5.786 56.798 4507 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.58 % Favored : 93.39 % Rotamer: Outliers : 0.95 % Allowed : 8.94 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3206 helix: 1.60 (0.20), residues: 713 sheet: 0.31 (0.20), residues: 701 loop : -1.94 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 152 HIS 0.003 0.001 HIS B 66 PHE 0.014 0.001 PHE A 819 TYR 0.015 0.001 TYR A 265 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 44) link_NAG-ASN : angle 1.67240 ( 132) link_BETA1-4 : bond 0.00936 ( 5) link_BETA1-4 : angle 3.67609 ( 15) hydrogen bonds : bond 0.05130 ( 1006) hydrogen bonds : angle 5.00105 ( 2850) SS BOND : bond 0.00342 ( 39) SS BOND : angle 1.22993 ( 78) covalent geometry : bond 0.00262 (26571) covalent geometry : angle 0.53597 (36167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 3.229 Fit side-chains revert: symmetry clash REVERT: A 776 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8248 (mt-10) REVERT: A 900 TYR cc_start: 0.7899 (t80) cc_final: 0.7473 (t80) REVERT: A 1107 GLU cc_start: 0.9114 (tt0) cc_final: 0.8625 (tm-30) REVERT: B 565 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7263 (p90) REVERT: B 646 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8757 (ttp80) REVERT: B 900 TYR cc_start: 0.8170 (t80) cc_final: 0.7884 (t80) REVERT: B 984 GLU cc_start: 0.8594 (mp0) cc_final: 0.8309 (mp0) REVERT: B 998 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8360 (tm-30) REVERT: B 1121 ASN cc_start: 0.8576 (t0) cc_final: 0.7701 (t0) REVERT: C 153 MET cc_start: 0.9150 (mmm) cc_final: 0.8947 (mmm) REVERT: C 319 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6531 (ptt90) REVERT: C 782 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8617 (mmmm) REVERT: C 986 GLU cc_start: 0.8201 (pm20) cc_final: 0.7726 (pm20) outliers start: 27 outliers final: 8 residues processed: 94 average time/residue: 1.3042 time to fit residues: 147.0089 Evaluate side-chains 76 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 94 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 313 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 253 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051722 restraints weight = 85820.850| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.61 r_work: 0.2853 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26659 Z= 0.130 Angle : 0.550 9.669 36392 Z= 0.285 Chirality : 0.044 0.268 4234 Planarity : 0.004 0.046 4625 Dihedral : 5.593 57.085 4507 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 1.06 % Allowed : 9.54 % Favored : 89.40 % 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: -0.79 (0.15), residues: 3206 helix: 1.67 (0.20), residues: 707 sheet: 0.39 (0.20), residues: 698 loop : -1.93 (0.13), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 152 HIS 0.003 0.001 HIS B 66 PHE 0.013 0.001 PHE C 157 TYR 0.021 0.001 TYR A1134 ARG 0.006 0.000 ARG B1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 44) link_NAG-ASN : angle 1.67196 ( 132) link_BETA1-4 : bond 0.00876 ( 5) link_BETA1-4 : angle 3.58761 ( 15) hydrogen bonds : bond 0.05170 ( 1006) hydrogen bonds : angle 4.94400 ( 2850) SS BOND : bond 0.00263 ( 39) SS BOND : angle 1.17109 ( 78) covalent geometry : bond 0.00296 (26571) covalent geometry : angle 0.53514 (36167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 3.366 Fit side-chains revert: symmetry clash REVERT: A 900 TYR cc_start: 0.7899 (t80) cc_final: 0.7489 (t80) REVERT: A 1107 GLU cc_start: 0.9156 (tt0) cc_final: 0.8638 (tm-30) REVERT: B 565 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7214 (p90) REVERT: B 900 TYR cc_start: 0.8167 (t80) cc_final: 0.7907 (t80) REVERT: B 984 GLU cc_start: 0.8589 (mp0) cc_final: 0.8282 (mp0) REVERT: B 998 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 1121 ASN cc_start: 0.8561 (t0) cc_final: 0.7677 (t0) REVERT: C 96 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: C 319 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6560 (ptt90) REVERT: C 782 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8626 (mmmm) outliers start: 30 outliers final: 14 residues processed: 93 average time/residue: 1.2719 time to fit residues: 142.6261 Evaluate side-chains 78 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 310 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 228 optimal weight: 1.9990 chunk 294 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.066677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.051666 restraints weight = 85507.214| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.59 r_work: 0.2850 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26659 Z= 0.135 Angle : 0.552 9.929 36392 Z= 0.286 Chirality : 0.044 0.267 4234 Planarity : 0.004 0.091 4625 Dihedral : 5.493 56.995 4507 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.05 % Favored : 92.92 % Rotamer: Outliers : 1.20 % Allowed : 9.75 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 3206 helix: 1.68 (0.20), residues: 707 sheet: 0.43 (0.20), residues: 698 loop : -1.95 (0.13), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 152 HIS 0.003 0.001 HIS B 66 PHE 0.013 0.001 PHE C 157 TYR 0.014 0.001 TYR C 265 ARG 0.017 0.000 ARG A 843 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 44) link_NAG-ASN : angle 1.65606 ( 132) link_BETA1-4 : bond 0.00858 ( 5) link_BETA1-4 : angle 3.55800 ( 15) hydrogen bonds : bond 0.05180 ( 1006) hydrogen bonds : angle 4.92920 ( 2850) SS BOND : bond 0.00248 ( 39) SS BOND : angle 1.13476 ( 78) covalent geometry : bond 0.00309 (26571) covalent geometry : angle 0.53677 (36167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 3.007 Fit side-chains REVERT: A 776 GLU cc_start: 0.8918 (tp30) cc_final: 0.8696 (mt-10) REVERT: A 900 TYR cc_start: 0.7913 (t80) cc_final: 0.7484 (t80) REVERT: A 1107 GLU cc_start: 0.9151 (tt0) cc_final: 0.8635 (tm-30) REVERT: B 565 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7243 (p90) REVERT: B 900 TYR cc_start: 0.8182 (t80) cc_final: 0.7917 (t80) REVERT: B 984 GLU cc_start: 0.8610 (mp0) cc_final: 0.8290 (mp0) REVERT: B 998 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 1121 ASN cc_start: 0.8605 (t0) cc_final: 0.7719 (t0) REVERT: C 96 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: C 259 THR cc_start: 0.7276 (OUTLIER) cc_final: 0.7066 (p) REVERT: C 319 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6552 (ptt90) REVERT: C 782 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8614 (mmmm) REVERT: C 986 GLU cc_start: 0.8199 (pm20) cc_final: 0.7614 (pm20) outliers start: 34 outliers final: 17 residues processed: 93 average time/residue: 1.1858 time to fit residues: 134.3615 Evaluate side-chains 85 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 18 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 271 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 273 optimal weight: 0.3980 chunk 269 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1079 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.067206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052153 restraints weight = 85556.353| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.61 r_work: 0.2863 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26659 Z= 0.118 Angle : 0.537 9.747 36392 Z= 0.278 Chirality : 0.044 0.264 4234 Planarity : 0.004 0.046 4625 Dihedral : 5.290 56.924 4507 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.20 % Rotamer: Outliers : 1.13 % Allowed : 10.07 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.15), residues: 3206 helix: 1.76 (0.20), residues: 707 sheet: 0.46 (0.20), residues: 696 loop : -1.93 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 152 HIS 0.003 0.001 HIS B 66 PHE 0.013 0.001 PHE C 157 TYR 0.023 0.001 TYR A1134 ARG 0.007 0.000 ARG A 843 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 44) link_NAG-ASN : angle 1.60460 ( 132) link_BETA1-4 : bond 0.00894 ( 5) link_BETA1-4 : angle 3.50350 ( 15) hydrogen bonds : bond 0.04865 ( 1006) hydrogen bonds : angle 4.85119 ( 2850) SS BOND : bond 0.00220 ( 39) SS BOND : angle 1.06636 ( 78) covalent geometry : bond 0.00264 (26571) covalent geometry : angle 0.52299 (36167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 3.116 Fit side-chains REVERT: A 900 TYR cc_start: 0.7893 (t80) cc_final: 0.7478 (t80) REVERT: A 1107 GLU cc_start: 0.9143 (tt0) cc_final: 0.8660 (tm-30) REVERT: B 565 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7190 (p90) REVERT: B 900 TYR cc_start: 0.8184 (t80) cc_final: 0.7917 (t80) REVERT: B 984 GLU cc_start: 0.8619 (mp0) cc_final: 0.8232 (mp0) REVERT: B 998 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 1121 ASN cc_start: 0.8592 (t0) cc_final: 0.7707 (t0) REVERT: C 96 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: C 319 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6589 (ptt90) REVERT: C 782 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8589 (mmmm) REVERT: C 986 GLU cc_start: 0.8177 (pm20) cc_final: 0.7598 (pm20) outliers start: 32 outliers final: 19 residues processed: 95 average time/residue: 1.1651 time to fit residues: 135.8994 Evaluate side-chains 83 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 153 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.066631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.051646 restraints weight = 85860.681| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.57 r_work: 0.2852 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26659 Z= 0.145 Angle : 0.559 10.628 36392 Z= 0.290 Chirality : 0.044 0.263 4234 Planarity : 0.004 0.048 4625 Dihedral : 5.322 57.127 4507 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.17 % Favored : 92.79 % Rotamer: Outliers : 1.17 % Allowed : 10.56 % Favored : 88.27 % 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: -0.76 (0.15), residues: 3206 helix: 1.71 (0.20), residues: 707 sheet: 0.44 (0.20), residues: 697 loop : -1.93 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 152 HIS 0.002 0.001 HIS B1079 PHE 0.013 0.001 PHE C 157 TYR 0.014 0.001 TYR C1063 ARG 0.004 0.000 ARG A 843 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 44) link_NAG-ASN : angle 1.64301 ( 132) link_BETA1-4 : bond 0.00843 ( 5) link_BETA1-4 : angle 3.47644 ( 15) hydrogen bonds : bond 0.05229 ( 1006) hydrogen bonds : angle 4.88493 ( 2850) SS BOND : bond 0.00254 ( 39) SS BOND : angle 1.18414 ( 78) covalent geometry : bond 0.00337 (26571) covalent geometry : angle 0.54466 (36167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 3.165 Fit side-chains REVERT: A 900 TYR cc_start: 0.7896 (t80) cc_final: 0.7490 (t80) REVERT: A 1107 GLU cc_start: 0.9117 (tt0) cc_final: 0.8669 (tm-30) REVERT: B 565 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7281 (p90) REVERT: B 900 TYR cc_start: 0.8140 (t80) cc_final: 0.7900 (t80) REVERT: B 984 GLU cc_start: 0.8637 (mp0) cc_final: 0.8248 (mp0) REVERT: B 998 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 1121 ASN cc_start: 0.8609 (t0) cc_final: 0.7720 (t0) REVERT: C 96 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: C 259 THR cc_start: 0.7236 (OUTLIER) cc_final: 0.7029 (p) REVERT: C 319 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6552 (ptt90) REVERT: C 986 GLU cc_start: 0.8209 (pm20) cc_final: 0.7611 (pm20) outliers start: 33 outliers final: 21 residues processed: 90 average time/residue: 1.1568 time to fit residues: 127.5599 Evaluate side-chains 85 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 878 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 147 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 219 optimal weight: 8.9990 chunk 131 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1131 ASN C1079 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.067069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051976 restraints weight = 85615.051| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.62 r_work: 0.2858 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26659 Z= 0.123 Angle : 0.548 10.445 36392 Z= 0.283 Chirality : 0.044 0.264 4234 Planarity : 0.004 0.047 4625 Dihedral : 5.263 56.934 4507 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.99 % Favored : 92.98 % Rotamer: Outliers : 1.02 % Allowed : 10.67 % Favored : 88.31 % 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: -0.72 (0.15), residues: 3206 helix: 1.74 (0.20), residues: 707 sheet: 0.48 (0.20), residues: 689 loop : -1.91 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 152 HIS 0.002 0.001 HIS B1079 PHE 0.013 0.001 PHE C 157 TYR 0.025 0.001 TYR A1134 ARG 0.005 0.000 ARG A 843 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 44) link_NAG-ASN : angle 1.61001 ( 132) link_BETA1-4 : bond 0.00898 ( 5) link_BETA1-4 : angle 3.45522 ( 15) hydrogen bonds : bond 0.04957 ( 1006) hydrogen bonds : angle 4.84417 ( 2850) SS BOND : bond 0.00234 ( 39) SS BOND : angle 1.34768 ( 78) covalent geometry : bond 0.00281 (26571) covalent geometry : angle 0.53314 (36167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 3.544 Fit side-chains REVERT: A 900 TYR cc_start: 0.7909 (t80) cc_final: 0.7493 (t80) REVERT: A 1107 GLU cc_start: 0.9154 (tt0) cc_final: 0.8672 (tm-30) REVERT: B 565 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7232 (p90) REVERT: B 900 TYR cc_start: 0.8153 (t80) cc_final: 0.7882 (t80) REVERT: B 984 GLU cc_start: 0.8643 (mp0) cc_final: 0.8208 (mp0) REVERT: B 998 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8343 (tm-30) REVERT: B 1121 ASN cc_start: 0.8612 (t0) cc_final: 0.7731 (t0) REVERT: C 96 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: C 319 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6531 (ptt90) REVERT: C 782 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8598 (mmmm) outliers start: 29 outliers final: 21 residues processed: 88 average time/residue: 1.2270 time to fit residues: 134.2034 Evaluate side-chains 85 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 290 optimal weight: 0.0980 chunk 296 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 ASN C1079 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.066370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051375 restraints weight = 86117.697| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.57 r_work: 0.2841 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26659 Z= 0.156 Angle : 0.571 10.479 36392 Z= 0.296 Chirality : 0.045 0.263 4234 Planarity : 0.004 0.048 4625 Dihedral : 5.347 57.312 4507 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.64 % Rotamer: Outliers : 1.02 % Allowed : 10.95 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 3206 helix: 1.67 (0.20), residues: 707 sheet: 0.42 (0.20), residues: 686 loop : -1.92 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 152 HIS 0.003 0.001 HIS B1079 PHE 0.013 0.001 PHE C 157 TYR 0.017 0.001 TYR B 266 ARG 0.004 0.000 ARG A 843 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 44) link_NAG-ASN : angle 1.66441 ( 132) link_BETA1-4 : bond 0.00819 ( 5) link_BETA1-4 : angle 3.43786 ( 15) hydrogen bonds : bond 0.05386 ( 1006) hydrogen bonds : angle 4.90689 ( 2850) SS BOND : bond 0.00271 ( 39) SS BOND : angle 1.48928 ( 78) covalent geometry : bond 0.00366 (26571) covalent geometry : angle 0.55492 (36167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12985.62 seconds wall clock time: 226 minutes 25.70 seconds (13585.70 seconds total)