Starting phenix.real_space_refine on Mon Aug 25 07:38:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xym_38778/08_2025/8xym_38778.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xym_38778/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xym_38778/08_2025/8xym_38778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xym_38778/08_2025/8xym_38778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xym_38778/08_2025/8xym_38778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xym_38778/08_2025/8xym_38778.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.93, per 1000 atoms: 0.27 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.42 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: 8.78 Time building geometry restraints manager: 3.53 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 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: 13.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 31.300 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.630 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (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 ARG 0.003 0.000 ARG A1103 TYR 0.030 0.001 TYR C 266 PHE 0.022 0.001 PHE B 902 TRP 0.012 0.001 TRP B 882 HIS 0.004 0.001 HIS C1079 Details of bonding type rmsd covalent geometry : bond 0.00352 (26571) covalent geometry : angle 0.59182 (36167) SS BOND : bond 0.00202 ( 39) SS BOND : angle 1.32773 ( 78) hydrogen bonds : bond 0.15358 ( 1006) hydrogen bonds : angle 6.84683 ( 2850) link_BETA1-4 : bond 0.02031 ( 5) link_BETA1-4 : angle 6.45834 ( 15) link_NAG-ASN : bond 0.00546 ( 44) link_NAG-ASN : angle 2.28091 ( 132) *********************** 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 : 1.113 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: 0.7313 (t80) REVERT: A 1107 GLU cc_start: 0.8862 (tt0) cc_final: 0.8465 (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: 0.7206 time to fit residues: 104.6415 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 : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.2980 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.065750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.050719 restraints weight = 87259.444| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.57 r_work: 0.2840 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26659 Z= 0.206 Angle : 0.631 9.241 36392 Z= 0.330 Chirality : 0.047 0.307 4234 Planarity : 0.004 0.050 4625 Dihedral : 6.973 59.778 4507 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 0.60 % Allowed : 4.63 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.14), residues: 3206 helix: 1.17 (0.20), residues: 722 sheet: 0.23 (0.20), residues: 713 loop : -2.06 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.023 0.002 TYR C 266 PHE 0.024 0.001 PHE A 819 TRP 0.031 0.002 TRP B 882 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00485 (26571) covalent geometry : angle 0.61469 (36167) SS BOND : bond 0.00344 ( 39) SS BOND : angle 1.42261 ( 78) hydrogen bonds : bond 0.06700 ( 1006) hydrogen bonds : angle 5.50888 ( 2850) link_BETA1-4 : bond 0.00894 ( 5) link_BETA1-4 : angle 3.76851 ( 15) link_NAG-ASN : bond 0.00346 ( 44) link_NAG-ASN : angle 1.85019 ( 132) *********************** 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 89 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 776 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8390 (mt-10) REVERT: A 900 TYR cc_start: 0.7887 (t80) cc_final: 0.7448 (t80) REVERT: A 1107 GLU cc_start: 0.9092 (tt0) cc_final: 0.8573 (tm-30) REVERT: B 565 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7447 (p90) REVERT: B 900 TYR cc_start: 0.8143 (t80) cc_final: 0.7774 (t80) REVERT: B 984 GLU cc_start: 0.8539 (mp0) cc_final: 0.8305 (mp0) REVERT: B 998 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8342 (tm-30) REVERT: B 1121 ASN cc_start: 0.8578 (t0) cc_final: 0.7851 (t0) REVERT: C 986 GLU cc_start: 0.8304 (pm20) cc_final: 0.7892 (pm20) outliers start: 17 outliers final: 5 residues processed: 85 average time/residue: 0.6798 time to fit residues: 68.0434 Evaluate side-chains 70 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 116 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 294 optimal weight: 0.1980 chunk 131 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.066820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.051756 restraints weight = 86675.054| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.60 r_work: 0.2856 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26659 Z= 0.132 Angle : 0.568 9.776 36392 Z= 0.296 Chirality : 0.045 0.283 4234 Planarity : 0.004 0.046 4625 Dihedral : 6.341 57.081 4507 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.20 % Rotamer: Outliers : 0.53 % Allowed : 7.24 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.15), residues: 3206 helix: 1.48 (0.20), residues: 713 sheet: 0.26 (0.20), residues: 731 loop : -2.02 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.024 0.001 TYR A1134 PHE 0.019 0.001 PHE A 819 TRP 0.022 0.001 TRP B 882 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00297 (26571) covalent geometry : angle 0.55235 (36167) SS BOND : bond 0.00264 ( 39) SS BOND : angle 1.20193 ( 78) hydrogen bonds : bond 0.05582 ( 1006) hydrogen bonds : angle 5.18215 ( 2850) link_BETA1-4 : bond 0.00944 ( 5) link_BETA1-4 : angle 3.84267 ( 15) link_NAG-ASN : bond 0.00312 ( 44) link_NAG-ASN : angle 1.70547 ( 132) *********************** 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 91 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8231 (mt-10) REVERT: A 900 TYR cc_start: 0.7865 (t80) cc_final: 0.7431 (t80) REVERT: A 1107 GLU cc_start: 0.9085 (tt0) cc_final: 0.8574 (tm-30) REVERT: B 565 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7314 (p90) REVERT: B 900 TYR cc_start: 0.8155 (t80) cc_final: 0.7856 (t80) REVERT: B 984 GLU cc_start: 0.8587 (mp0) cc_final: 0.8318 (mp0) REVERT: B 998 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 1121 ASN cc_start: 0.8588 (t0) cc_final: 0.7811 (t0) REVERT: C 782 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8670 (mmmm) outliers start: 15 outliers final: 5 residues processed: 86 average time/residue: 0.6956 time to fit residues: 70.4548 Evaluate side-chains 70 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 211 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 153 optimal weight: 0.0270 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 GLN C 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.065261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050246 restraints weight = 86286.457| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.56 r_work: 0.2813 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26659 Z= 0.212 Angle : 0.616 10.170 36392 Z= 0.321 Chirality : 0.046 0.275 4234 Planarity : 0.004 0.050 4625 Dihedral : 6.234 58.164 4507 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.95 % Favored : 92.01 % Rotamer: Outliers : 0.81 % Allowed : 8.30 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.15), residues: 3206 helix: 1.35 (0.20), residues: 722 sheet: 0.19 (0.19), residues: 755 loop : -2.08 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.017 0.001 TYR C 266 PHE 0.019 0.001 PHE B 902 TRP 0.021 0.002 TRP C 152 HIS 0.004 0.001 HIS B1079 Details of bonding type rmsd covalent geometry : bond 0.00505 (26571) covalent geometry : angle 0.59975 (36167) SS BOND : bond 0.00338 ( 39) SS BOND : angle 1.36056 ( 78) hydrogen bonds : bond 0.06313 ( 1006) hydrogen bonds : angle 5.22155 ( 2850) link_BETA1-4 : bond 0.00742 ( 5) link_BETA1-4 : angle 3.71437 ( 15) link_NAG-ASN : bond 0.00285 ( 44) link_NAG-ASN : angle 1.80461 ( 132) *********************** 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 87 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 776 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8328 (mt-10) REVERT: A 900 TYR cc_start: 0.7906 (t80) cc_final: 0.7464 (t80) REVERT: A 1107 GLU cc_start: 0.9127 (tt0) cc_final: 0.8620 (tm-30) REVERT: B 565 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7339 (p90) REVERT: B 900 TYR cc_start: 0.8193 (t80) cc_final: 0.7904 (t80) REVERT: B 984 GLU cc_start: 0.8601 (mp0) cc_final: 0.8316 (mp0) REVERT: B 998 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 1121 ASN cc_start: 0.8589 (t0) cc_final: 0.7751 (t0) REVERT: C 144 TYR cc_start: 0.2556 (t80) cc_final: 0.2228 (t80) REVERT: C 153 MET cc_start: 0.9066 (mmm) cc_final: 0.8835 (mmm) REVERT: C 319 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6664 (ptt90) REVERT: C 986 GLU cc_start: 0.8260 (pm20) cc_final: 0.7701 (pm20) outliers start: 23 outliers final: 10 residues processed: 83 average time/residue: 0.6069 time to fit residues: 60.8929 Evaluate side-chains 71 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 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 1129 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 398 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 292 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 291 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.064926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.049923 restraints weight = 85923.963| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.55 r_work: 0.2805 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26659 Z= 0.219 Angle : 0.623 10.846 36392 Z= 0.326 Chirality : 0.046 0.276 4234 Planarity : 0.004 0.049 4625 Dihedral : 6.175 57.559 4507 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.80 % Favored : 92.17 % Rotamer: Outliers : 1.13 % Allowed : 9.40 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.15), residues: 3206 helix: 1.28 (0.20), residues: 723 sheet: 0.13 (0.20), residues: 752 loop : -2.07 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.021 0.002 TYR A1134 PHE 0.020 0.001 PHE B 902 TRP 0.024 0.002 TRP C 152 HIS 0.004 0.001 HIS B1079 Details of bonding type rmsd covalent geometry : bond 0.00523 (26571) covalent geometry : angle 0.60637 (36167) SS BOND : bond 0.00350 ( 39) SS BOND : angle 1.48153 ( 78) hydrogen bonds : bond 0.06403 ( 1006) hydrogen bonds : angle 5.24958 ( 2850) link_BETA1-4 : bond 0.00822 ( 5) link_BETA1-4 : angle 3.71731 ( 15) link_NAG-ASN : bond 0.00285 ( 44) link_NAG-ASN : angle 1.85755 ( 132) *********************** 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 94 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 776 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8375 (mt-10) REVERT: A 900 TYR cc_start: 0.7894 (t80) cc_final: 0.7483 (t80) REVERT: A 1107 GLU cc_start: 0.9109 (tt0) cc_final: 0.8633 (tm-30) REVERT: B 565 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7324 (p90) REVERT: B 646 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8719 (ttp80) REVERT: B 900 TYR cc_start: 0.8176 (t80) cc_final: 0.7885 (t80) REVERT: B 984 GLU cc_start: 0.8630 (mp0) cc_final: 0.8339 (mp0) REVERT: B 998 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8376 (tm-30) REVERT: B 1121 ASN cc_start: 0.8643 (t0) cc_final: 0.7790 (t0) REVERT: C 144 TYR cc_start: 0.2735 (t80) cc_final: 0.2516 (t80) REVERT: C 319 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6589 (ptt90) REVERT: C 986 GLU cc_start: 0.8319 (pm20) cc_final: 0.7839 (pm20) REVERT: C 1015 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8192 (tpm170) outliers start: 32 outliers final: 15 residues processed: 89 average time/residue: 0.6286 time to fit residues: 66.9511 Evaluate side-chains 78 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 483 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 1096 THR Chi-restraints excluded: chain B residue 1124 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 Chi-restraints excluded: chain C residue 1015 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 169 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 226 optimal weight: 0.9980 chunk 271 optimal weight: 0.0980 chunk 85 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 249 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B1131 ASN C 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.067483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.052423 restraints weight = 85518.364| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.63 r_work: 0.2879 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26659 Z= 0.105 Angle : 0.539 10.394 36392 Z= 0.278 Chirality : 0.044 0.278 4234 Planarity : 0.004 0.044 4625 Dihedral : 5.565 56.643 4507 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.71 % Favored : 93.26 % Rotamer: Outliers : 0.99 % Allowed : 10.07 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.15), residues: 3206 helix: 1.61 (0.20), residues: 716 sheet: 0.40 (0.20), residues: 689 loop : -1.97 (0.13), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.015 0.001 TYR A 265 PHE 0.014 0.001 PHE C 157 TRP 0.028 0.001 TRP C 152 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00220 (26571) covalent geometry : angle 0.52413 (36167) SS BOND : bond 0.00230 ( 39) SS BOND : angle 1.03881 ( 78) hydrogen bonds : bond 0.04759 ( 1006) hydrogen bonds : angle 4.94173 ( 2850) link_BETA1-4 : bond 0.00985 ( 5) link_BETA1-4 : angle 3.63532 ( 15) link_NAG-ASN : bond 0.00334 ( 44) link_NAG-ASN : angle 1.62882 ( 132) *********************** 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 99 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 1.124 Fit side-chains REVERT: A 776 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8055 (mt-10) REVERT: A 900 TYR cc_start: 0.7910 (t80) cc_final: 0.7452 (t80) REVERT: A 1107 GLU cc_start: 0.9177 (tt0) cc_final: 0.8648 (tm-30) REVERT: B 565 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7190 (p90) REVERT: B 900 TYR cc_start: 0.8181 (t80) cc_final: 0.7878 (t80) REVERT: B 984 GLU cc_start: 0.8605 (mp0) cc_final: 0.8289 (mp0) REVERT: B 998 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 1102 GLN cc_start: 0.8392 (mt0) cc_final: 0.8190 (mt0) REVERT: B 1121 ASN cc_start: 0.8605 (t0) cc_final: 0.7751 (t0) REVERT: C 96 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8020 (tt0) outliers start: 28 outliers final: 10 residues processed: 96 average time/residue: 0.6648 time to fit residues: 75.5095 Evaluate side-chains 71 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 907 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 565 PHE 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 586 ASP 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 79 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.065084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050045 restraints weight = 86312.155| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.56 r_work: 0.2809 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26659 Z= 0.227 Angle : 0.615 10.573 36392 Z= 0.321 Chirality : 0.046 0.269 4234 Planarity : 0.004 0.067 4625 Dihedral : 5.773 58.298 4507 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.77 % Favored : 92.20 % Rotamer: Outliers : 1.17 % Allowed : 10.49 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 3206 helix: 1.39 (0.20), residues: 723 sheet: 0.26 (0.20), residues: 736 loop : -2.05 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 843 TYR 0.021 0.002 TYR A1134 PHE 0.018 0.001 PHE B 902 TRP 0.047 0.002 TRP C 152 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00542 (26571) covalent geometry : angle 0.59940 (36167) SS BOND : bond 0.00334 ( 39) SS BOND : angle 1.41599 ( 78) hydrogen bonds : bond 0.06160 ( 1006) hydrogen bonds : angle 5.10298 ( 2850) link_BETA1-4 : bond 0.00768 ( 5) link_BETA1-4 : angle 3.59329 ( 15) link_NAG-ASN : bond 0.00279 ( 44) link_NAG-ASN : angle 1.79355 ( 132) *********************** 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 90 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 1.102 Fit side-chains REVERT: A 776 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8325 (mt-10) REVERT: A 900 TYR cc_start: 0.7919 (t80) cc_final: 0.7482 (t80) REVERT: A 1107 GLU cc_start: 0.9119 (tt0) cc_final: 0.8648 (tm-30) REVERT: B 565 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7296 (p90) REVERT: B 900 TYR cc_start: 0.8191 (t80) cc_final: 0.7895 (t80) REVERT: B 984 GLU cc_start: 0.8655 (mp0) cc_final: 0.8343 (mp0) REVERT: B 998 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8369 (tm-30) REVERT: B 1121 ASN cc_start: 0.8614 (t0) cc_final: 0.7748 (t0) REVERT: C 96 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: C 986 GLU cc_start: 0.8296 (pm20) cc_final: 0.7740 (pm20) outliers start: 33 outliers final: 15 residues processed: 85 average time/residue: 0.6272 time to fit residues: 64.0353 Evaluate side-chains 71 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 2.948 ------------------------------------------------------------------------------- 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 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 907 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 874 LEU 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 586 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 878 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 223 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.065357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050324 restraints weight = 86124.748| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.56 r_work: 0.2814 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1438 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 : 0.599 11.120 36392 Z= 0.313 Chirality : 0.046 0.270 4234 Planarity : 0.004 0.064 4625 Dihedral : 5.776 57.155 4507 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer: Outliers : 1.31 % Allowed : 10.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 3206 helix: 1.39 (0.20), residues: 718 sheet: 0.17 (0.19), residues: 751 loop : -2.01 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 843 TYR 0.019 0.001 TYR B 266 PHE 0.013 0.001 PHE B 902 TRP 0.054 0.002 TRP C 152 HIS 0.004 0.001 HIS B1079 Details of bonding type rmsd covalent geometry : bond 0.00454 (26571) covalent geometry : angle 0.58287 (36167) SS BOND : bond 0.00311 ( 39) SS BOND : angle 1.42558 ( 78) hydrogen bonds : bond 0.05994 ( 1006) hydrogen bonds : angle 5.10473 ( 2850) link_BETA1-4 : bond 0.00826 ( 5) link_BETA1-4 : angle 3.59482 ( 15) link_NAG-ASN : bond 0.00270 ( 44) link_NAG-ASN : angle 1.77732 ( 132) *********************** 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 91 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 54 time to evaluate : 1.085 Fit side-chains REVERT: A 776 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8337 (mt-10) REVERT: A 900 TYR cc_start: 0.7906 (t80) cc_final: 0.7488 (t80) REVERT: A 1107 GLU cc_start: 0.9128 (tt0) cc_final: 0.8664 (tm-30) REVERT: B 565 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7301 (p90) REVERT: B 900 TYR cc_start: 0.8148 (t80) cc_final: 0.7874 (t80) REVERT: B 984 GLU cc_start: 0.8656 (mp0) cc_final: 0.8336 (mp0) REVERT: B 998 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8353 (tm-30) REVERT: B 1102 GLN cc_start: 0.8562 (mt0) cc_final: 0.8334 (mt0) REVERT: B 1121 ASN cc_start: 0.8641 (t0) cc_final: 0.7791 (t0) REVERT: C 96 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: C 259 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7131 (p) REVERT: C 986 GLU cc_start: 0.8315 (pm20) cc_final: 0.7746 (pm20) outliers start: 37 outliers final: 22 residues processed: 86 average time/residue: 0.5670 time to fit residues: 59.3850 Evaluate side-chains 79 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 518 LEU 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 907 VAL 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 382 VAL 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 599 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 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 239 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 104 optimal weight: 0.0170 chunk 115 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 overall best weight: 2.2222 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.065515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.050470 restraints weight = 86174.889| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.58 r_work: 0.2818 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26659 Z= 0.175 Angle : 0.594 11.020 36392 Z= 0.309 Chirality : 0.045 0.269 4234 Planarity : 0.004 0.048 4625 Dihedral : 5.726 57.216 4507 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.77 % Favored : 92.17 % Rotamer: Outliers : 1.24 % Allowed : 10.91 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.15), residues: 3206 helix: 1.42 (0.20), residues: 718 sheet: 0.21 (0.20), residues: 737 loop : -1.99 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 843 TYR 0.022 0.001 TYR A1134 PHE 0.013 0.001 PHE C 157 TRP 0.036 0.002 TRP C 152 HIS 0.004 0.001 HIS B1079 Details of bonding type rmsd covalent geometry : bond 0.00413 (26571) covalent geometry : angle 0.57662 (36167) SS BOND : bond 0.00298 ( 39) SS BOND : angle 1.58183 ( 78) hydrogen bonds : bond 0.05832 ( 1006) hydrogen bonds : angle 5.06904 ( 2850) link_BETA1-4 : bond 0.00831 ( 5) link_BETA1-4 : angle 3.56934 ( 15) link_NAG-ASN : bond 0.00264 ( 44) link_NAG-ASN : angle 1.77186 ( 132) *********************** 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 91 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 1.090 Fit side-chains REVERT: A 776 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8321 (mt-10) REVERT: A 900 TYR cc_start: 0.7909 (t80) cc_final: 0.7498 (t80) REVERT: A 1107 GLU cc_start: 0.9134 (tt0) cc_final: 0.8671 (tm-30) REVERT: B 565 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7280 (p90) REVERT: B 900 TYR cc_start: 0.8160 (t80) cc_final: 0.7876 (t80) REVERT: B 984 GLU cc_start: 0.8658 (mp0) cc_final: 0.8335 (mp0) REVERT: B 998 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8337 (tm-30) REVERT: B 1102 GLN cc_start: 0.8548 (mt0) cc_final: 0.8338 (mt0) REVERT: B 1121 ASN cc_start: 0.8638 (t0) cc_final: 0.7791 (t0) REVERT: C 96 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: C 986 GLU cc_start: 0.8308 (pm20) cc_final: 0.7772 (pm20) outliers start: 35 outliers final: 22 residues processed: 88 average time/residue: 0.6288 time to fit residues: 66.3146 Evaluate side-chains 79 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 874 LEU Chi-restraints excluded: chain A residue 907 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 382 VAL 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 599 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 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 126 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 281 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.067443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.052397 restraints weight = 85758.538| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.59 r_work: 0.2868 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26659 Z= 0.108 Angle : 0.546 10.423 36392 Z= 0.282 Chirality : 0.044 0.269 4234 Planarity : 0.004 0.048 4625 Dihedral : 5.345 56.789 4507 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.46 % Favored : 93.51 % Rotamer: Outliers : 0.92 % Allowed : 11.44 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 3206 helix: 1.71 (0.20), residues: 708 sheet: 0.46 (0.21), residues: 675 loop : -1.92 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 843 TYR 0.020 0.001 TYR B 266 PHE 0.012 0.001 PHE C 157 TRP 0.025 0.001 TRP C 152 HIS 0.003 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00233 (26571) covalent geometry : angle 0.53124 (36167) SS BOND : bond 0.00227 ( 39) SS BOND : angle 1.18702 ( 78) hydrogen bonds : bond 0.04709 ( 1006) hydrogen bonds : angle 4.87014 ( 2850) link_BETA1-4 : bond 0.00971 ( 5) link_BETA1-4 : angle 3.51868 ( 15) link_NAG-ASN : bond 0.00314 ( 44) link_NAG-ASN : angle 1.61381 ( 132) ********************** 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 90 residues out of total 2831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 1.134 Fit side-chains REVERT: A 900 TYR cc_start: 0.7894 (t80) cc_final: 0.7467 (t80) REVERT: A 1107 GLU cc_start: 0.9117 (tt0) cc_final: 0.8703 (tm-30) REVERT: B 565 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7205 (p90) REVERT: B 900 TYR cc_start: 0.8140 (t80) cc_final: 0.7837 (t80) REVERT: B 984 GLU cc_start: 0.8626 (mp0) cc_final: 0.8249 (mp0) REVERT: B 998 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 1102 GLN cc_start: 0.8507 (mt0) cc_final: 0.8306 (mt0) REVERT: B 1121 ASN cc_start: 0.8611 (t0) cc_final: 0.7763 (t0) REVERT: C 96 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: C 471 GLU cc_start: 0.8063 (pp20) cc_final: 0.7722 (pp20) outliers start: 26 outliers final: 15 residues processed: 88 average time/residue: 0.5957 time to fit residues: 63.4476 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 : 1.088 ------------------------------------------------------------------------------- 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 1125 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 874 LEU 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 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 314 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 217 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.066714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051648 restraints weight = 85593.632| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.58 r_work: 0.2849 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1498 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= 0.140 Angle : 0.566 11.062 36392 Z= 0.293 Chirality : 0.044 0.266 4234 Planarity : 0.004 0.048 4625 Dihedral : 5.338 57.071 4507 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 0.74 % Allowed : 11.94 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.15), residues: 3206 helix: 1.69 (0.20), residues: 708 sheet: 0.49 (0.20), residues: 677 loop : -1.94 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 843 TYR 0.022 0.001 TYR A1134 PHE 0.012 0.001 PHE C 157 TRP 0.026 0.001 TRP C 152 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00326 (26571) covalent geometry : angle 0.55082 (36167) SS BOND : bond 0.00248 ( 39) SS BOND : angle 1.30908 ( 78) hydrogen bonds : bond 0.05097 ( 1006) hydrogen bonds : angle 4.87527 ( 2850) link_BETA1-4 : bond 0.00865 ( 5) link_BETA1-4 : angle 3.46463 ( 15) link_NAG-ASN : bond 0.00262 ( 44) link_NAG-ASN : angle 1.64456 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6987.56 seconds wall clock time: 121 minutes 1.64 seconds (7261.64 seconds total)