Starting phenix.real_space_refine on Sun Jul 5 05:46:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ios_35622/07_2026/8ios_35622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ios_35622/07_2026/8ios_35622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ios_35622/07_2026/8ios_35622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ios_35622/07_2026/8ios_35622.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ios_35622/07_2026/8ios_35622.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ios_35622/07_2026/8ios_35622.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ios_35622/07_2026/8ios_35622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ios_35622/07_2026/8ios_35622.cif" } resolution = 2.5 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= 0.016 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 16371 2.51 5 N 4215 2.21 5 O 4995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25695 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8313 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 6 Chain: "B" Number of atoms: 8313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8313 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 6 Chain: "C" Number of atoms: 8313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8313 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.66, per 1000 atoms: 0.22 Number of scatterers: 25695 At special positions: 0 Unit cell: (137.685, 131.655, 165.825, 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 4995 8.00 N 4215 7.00 C 16371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.04 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 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.04 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 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5982 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 51 sheets defined 26.0% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.511A pdb=" N ARG A 158 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.933A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.625A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.548A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.708A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.729A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.508A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.659A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.138A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.590A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.643A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.163A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.510A pdb=" N ARG B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.934A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.625A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.549A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.707A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.729A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.509A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.659A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.137A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.589A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.643A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.164A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.511A pdb=" N ARG C 158 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.934A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.624A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.549A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.708A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.729A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.509A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.660A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.137A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.643A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.164A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 7.987A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.624A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.995A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.860A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117 removed outlier: 4.336A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.248A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.649A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.731A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.560A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.178A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.019A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.731A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.632A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 23 through 30 removed outlier: 7.987A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.995A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.860A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 117 removed outlier: 4.335A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.248A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.649A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.731A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.559A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.178A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 7.014A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.731A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.632A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 23 through 30 removed outlier: 7.987A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.994A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.860A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AE5, first strand: chain 'C' and resid 116 through 117 removed outlier: 4.335A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.248A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.731A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.559A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.177A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.732A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.632A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 1002 hydrogen bonds defined for protein. 2682 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: 6.19 Time building geometry restraints manager: 3.10 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: 8147 1.34 - 1.46: 6541 1.46 - 1.59: 11451 1.59 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 26280 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.63e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.38e+00 ... (remaining 26275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 34354 1.26 - 2.53: 1144 2.53 - 3.79: 235 3.79 - 5.05: 21 5.05 - 6.31: 12 Bond angle restraints: 35766 Sorted by residual: angle pdb=" N ASN A 343 " pdb=" CA ASN A 343 " pdb=" C ASN A 343 " ideal model delta sigma weight residual 111.30 117.61 -6.31 1.36e+00 5.41e-01 2.16e+01 angle pdb=" N ASN B 343 " pdb=" CA ASN B 343 " pdb=" C ASN B 343 " ideal model delta sigma weight residual 111.30 117.61 -6.31 1.36e+00 5.41e-01 2.15e+01 angle pdb=" N ASN C 343 " pdb=" CA ASN C 343 " pdb=" C ASN C 343 " ideal model delta sigma weight residual 111.30 117.58 -6.28 1.36e+00 5.41e-01 2.13e+01 angle pdb=" C ALA A 344 " pdb=" N THR A 345 " pdb=" CA THR A 345 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C ALA C 344 " pdb=" N THR C 345 " pdb=" CA THR C 345 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 ... (remaining 35761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 13985 17.77 - 35.54: 1039 35.54 - 53.31: 156 53.31 - 71.09: 33 71.09 - 88.86: 27 Dihedral angle restraints: 15240 sinusoidal: 5946 harmonic: 9294 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -141.64 55.64 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -141.62 55.62 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -141.61 55.61 1 1.00e+01 1.00e-02 4.18e+01 ... (remaining 15237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3728 0.075 - 0.151: 467 0.151 - 0.226: 11 0.226 - 0.301: 3 0.301 - 0.377: 3 Chirality restraints: 4212 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 4209 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.002 2.00e-02 2.50e+03 3.60e-02 1.62e+01 pdb=" CG ASN A 343 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG A1307 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.002 2.00e-02 2.50e+03 3.60e-02 1.62e+01 pdb=" CG ASN C 343 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.002 2.00e-02 2.50e+03 3.60e-02 1.62e+01 pdb=" CG ASN B 343 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " 0.038 2.00e-02 2.50e+03 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1545 2.74 - 3.28: 23821 3.28 - 3.82: 38865 3.82 - 4.36: 46837 4.36 - 4.90: 84509 Nonbonded interactions: 195577 Sorted by model distance: nonbonded pdb=" O PRO A 589 " pdb=" OH TYR B 837 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.198 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.198 3.040 nonbonded pdb=" OG SER B 735 " pdb=" OG1 THR B 859 " model vdw 2.198 3.040 nonbonded pdb=" O PRO B 589 " pdb=" OH TYR C 837 " model vdw 2.201 3.040 ... (remaining 195572 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.610 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 : 0.003 0.039 26376 Z= 0.157 Angle : 0.584 10.868 36012 Z= 0.287 Chirality : 0.047 0.377 4212 Planarity : 0.004 0.040 4551 Dihedral : 12.868 88.858 9132 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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 are not related in a simple way. whole: 0.45 (0.15), residues: 3147 helix: 2.44 (0.21), residues: 687 sheet: 1.27 (0.18), residues: 762 loop : -1.16 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.021 0.001 TYR C 904 PHE 0.028 0.001 PHE B 906 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (26280) covalent geometry : angle 0.53704 / 0.28 (35766) SS BOND : bond 0.00311 / 0.21 ( 42) SS BOND : angle 1.11450 / 0.78 ( 84) hydrogen bonds : bond 0.13422 / 8.86 ( 996) hydrogen bonds : angle 5.66490 / 3.91 ( 2682) link_BETA1-4 : bond 0.00316 / 0.17 ( 9) link_BETA1-4 : angle 0.88271 / 0.53 ( 27) link_NAG-ASN : bond 0.00543 / 0.34 ( 45) link_NAG-ASN : angle 3.69256 / 2.70 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.991 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 190 average time/residue: 0.6369 time to fit residues: 140.2290 Evaluate side-chains 115 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 745 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0010 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 965 GLN A1005 GLN B 519 HIS B 965 GLN C 52 GLN C 121 ASN C 519 HIS C 965 GLN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.106067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071714 restraints weight = 43810.167| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.02 r_work: 0.2840 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26376 Z= 0.190 Angle : 0.621 10.070 36012 Z= 0.321 Chirality : 0.049 0.363 4212 Planarity : 0.005 0.042 4551 Dihedral : 4.339 44.373 3422 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.76 % Allowed : 5.47 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3147 helix: 2.03 (0.20), residues: 714 sheet: 1.21 (0.18), residues: 765 loop : -1.32 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1107 TYR 0.031 0.002 TYR B 904 PHE 0.031 0.002 PHE B 906 TRP 0.007 0.001 TRP B 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (26280) covalent geometry : angle 0.59162 / 0.31 (35766) SS BOND : bond 0.00313 / 0.21 ( 42) SS BOND : angle 1.56649 / 1.06 ( 84) hydrogen bonds : bond 0.06931 / 4.64 ( 996) hydrogen bonds : angle 5.14459 / 3.54 ( 2682) link_BETA1-4 : bond 0.00215 / 0.11 ( 9) link_BETA1-4 : angle 1.10140 / 0.68 ( 27) link_NAG-ASN : bond 0.00485 / 0.27 ( 45) link_NAG-ASN : angle 2.92033 / 2.03 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.998 Fit side-chains REVERT: A 661 GLU cc_start: 0.8301 (mp0) cc_final: 0.8064 (pm20) REVERT: B 111 ASP cc_start: 0.7405 (t0) cc_final: 0.6602 (t0) REVERT: B 868 GLU cc_start: 0.8276 (mp0) cc_final: 0.8059 (mp0) REVERT: B 900 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8686 (mtm) REVERT: C 200 TYR cc_start: 0.8100 (m-80) cc_final: 0.7754 (m-80) REVERT: C 868 GLU cc_start: 0.8475 (mp0) cc_final: 0.8139 (mp0) REVERT: C 869 MET cc_start: 0.9010 (mtt) cc_final: 0.8665 (mtt) outliers start: 21 outliers final: 7 residues processed: 141 average time/residue: 0.7091 time to fit residues: 115.7482 Evaluate side-chains 124 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 153 optimal weight: 0.3980 chunk 268 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 280 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073931 restraints weight = 43608.615| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.01 r_work: 0.2890 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26376 Z= 0.115 Angle : 0.543 9.832 36012 Z= 0.278 Chirality : 0.046 0.333 4212 Planarity : 0.004 0.045 4551 Dihedral : 4.038 19.579 3420 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.79 % Allowed : 7.16 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3147 helix: 2.20 (0.21), residues: 714 sheet: 1.33 (0.18), residues: 765 loop : -1.25 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.017 0.001 TYR C1067 PHE 0.012 0.001 PHE A 906 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (26280) covalent geometry : angle 0.51297 / 0.27 (35766) SS BOND : bond 0.00235 / 0.15 ( 42) SS BOND : angle 1.15618 / 0.78 ( 84) hydrogen bonds : bond 0.05476 / 3.64 ( 996) hydrogen bonds : angle 4.87257 / 3.37 ( 2682) link_BETA1-4 : bond 0.00280 / 0.15 ( 9) link_BETA1-4 : angle 0.96370 / 0.61 ( 27) link_NAG-ASN : bond 0.00485 / 0.30 ( 45) link_NAG-ASN : angle 2.82642 / 1.95 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.024 Fit side-chains REVERT: A 661 GLU cc_start: 0.8240 (mp0) cc_final: 0.8025 (pm20) REVERT: B 111 ASP cc_start: 0.7361 (t0) cc_final: 0.6597 (t0) REVERT: B 900 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8631 (mtm) REVERT: C 990 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7879 (mp0) outliers start: 22 outliers final: 8 residues processed: 142 average time/residue: 0.7025 time to fit residues: 115.7159 Evaluate side-chains 126 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 10 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.105524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.071159 restraints weight = 43356.326| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.99 r_work: 0.2833 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26376 Z= 0.192 Angle : 0.612 9.979 36012 Z= 0.315 Chirality : 0.049 0.347 4212 Planarity : 0.004 0.049 4551 Dihedral : 4.306 21.245 3420 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.15 % Allowed : 7.77 % Favored : 91.08 % 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 are not related in a simple way. whole: 0.22 (0.15), residues: 3147 helix: 1.91 (0.20), residues: 729 sheet: 1.28 (0.18), residues: 765 loop : -1.30 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 319 TYR 0.020 0.002 TYR C1067 PHE 0.018 0.002 PHE A 906 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (26280) covalent geometry : angle 0.58153 / 0.31 (35766) SS BOND : bond 0.00322 / 0.21 ( 42) SS BOND : angle 1.59998 / 1.09 ( 84) hydrogen bonds : bond 0.07019 / 4.71 ( 996) hydrogen bonds : angle 5.05552 / 3.48 ( 2682) link_BETA1-4 : bond 0.00160 / 0.09 ( 9) link_BETA1-4 : angle 1.16142 / 0.73 ( 27) link_NAG-ASN : bond 0.00459 / 0.26 ( 45) link_NAG-ASN : angle 2.88266 / 1.98 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.037 Fit side-chains REVERT: A 111 ASP cc_start: 0.7413 (t0) cc_final: 0.6789 (t0) REVERT: A 661 GLU cc_start: 0.8350 (mp0) cc_final: 0.8110 (pm20) REVERT: B 111 ASP cc_start: 0.7404 (t0) cc_final: 0.6635 (t0) REVERT: B 900 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8807 (mtm) REVERT: C 111 ASP cc_start: 0.7375 (t0) cc_final: 0.6756 (t0) REVERT: C 634 ARG cc_start: 0.6589 (tpt170) cc_final: 0.5805 (tmt-80) REVERT: C 990 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7981 (mp0) outliers start: 32 outliers final: 14 residues processed: 149 average time/residue: 0.7062 time to fit residues: 121.6531 Evaluate side-chains 135 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 34 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.071399 restraints weight = 43437.215| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.01 r_work: 0.2839 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26376 Z= 0.167 Angle : 0.594 10.108 36012 Z= 0.306 Chirality : 0.048 0.344 4212 Planarity : 0.004 0.046 4551 Dihedral : 4.302 20.370 3420 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.19 % Allowed : 8.38 % Favored : 90.44 % 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 are not related in a simple way. whole: 0.22 (0.15), residues: 3147 helix: 1.89 (0.20), residues: 729 sheet: 1.33 (0.18), residues: 759 loop : -1.32 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 319 TYR 0.018 0.001 TYR C1067 PHE 0.012 0.001 PHE C 898 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (26280) covalent geometry : angle 0.56303 / 0.30 (35766) SS BOND : bond 0.00298 / 0.19 ( 42) SS BOND : angle 1.47081 / 0.99 ( 84) hydrogen bonds : bond 0.06578 / 4.41 ( 996) hydrogen bonds : angle 4.99829 / 3.45 ( 2682) link_BETA1-4 : bond 0.00211 / 0.11 ( 9) link_BETA1-4 : angle 1.10209 / 0.71 ( 27) link_NAG-ASN : bond 0.00449 / 0.26 ( 45) link_NAG-ASN : angle 2.91690 / 2.00 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.073 Fit side-chains REVERT: A 111 ASP cc_start: 0.7404 (t0) cc_final: 0.6792 (t0) REVERT: A 661 GLU cc_start: 0.8331 (mp0) cc_final: 0.8088 (pm20) REVERT: B 111 ASP cc_start: 0.7411 (t0) cc_final: 0.6936 (t0) REVERT: B 586 ASP cc_start: 0.8868 (m-30) cc_final: 0.8601 (m-30) REVERT: B 675 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: B 900 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8834 (mtm) REVERT: C 21 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.7017 (pp) REVERT: C 111 ASP cc_start: 0.7375 (t0) cc_final: 0.6796 (t0) REVERT: C 990 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7926 (mp0) outliers start: 33 outliers final: 12 residues processed: 149 average time/residue: 0.6195 time to fit residues: 107.7443 Evaluate side-chains 136 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 115 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.106096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071784 restraints weight = 43632.508| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.99 r_work: 0.2850 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26376 Z= 0.149 Angle : 0.582 10.016 36012 Z= 0.298 Chirality : 0.048 0.341 4212 Planarity : 0.004 0.046 4551 Dihedral : 4.247 20.040 3420 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.40 % Allowed : 8.81 % Favored : 89.79 % 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 are not related in a simple way. whole: 0.26 (0.15), residues: 3147 helix: 1.94 (0.20), residues: 729 sheet: 1.31 (0.18), residues: 765 loop : -1.29 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 319 TYR 0.018 0.001 TYR C1067 PHE 0.011 0.001 PHE C 898 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (26280) covalent geometry : angle 0.55056 / 0.29 (35766) SS BOND : bond 0.00282 / 0.18 ( 42) SS BOND : angle 1.43103 / 0.97 ( 84) hydrogen bonds : bond 0.06304 / 4.22 ( 996) hydrogen bonds : angle 4.94391 / 3.41 ( 2682) link_BETA1-4 : bond 0.00233 / 0.12 ( 9) link_BETA1-4 : angle 1.07206 / 0.68 ( 27) link_NAG-ASN : bond 0.00453 / 0.27 ( 45) link_NAG-ASN : angle 2.90004 / 1.99 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.972 Fit side-chains REVERT: A 111 ASP cc_start: 0.7385 (t0) cc_final: 0.6809 (t0) REVERT: A 661 GLU cc_start: 0.8339 (mp0) cc_final: 0.8101 (pm20) REVERT: A 1092 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: B 111 ASP cc_start: 0.7400 (t0) cc_final: 0.6909 (t0) REVERT: B 586 ASP cc_start: 0.8869 (m-30) cc_final: 0.8613 (m-30) REVERT: B 900 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8806 (mtm) REVERT: C 21 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6965 (pp) REVERT: C 111 ASP cc_start: 0.7337 (t0) cc_final: 0.6755 (t0) REVERT: C 990 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7854 (mp0) outliers start: 39 outliers final: 16 residues processed: 154 average time/residue: 0.6455 time to fit residues: 115.9720 Evaluate side-chains 140 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 301 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 313 optimal weight: 0.2980 chunk 144 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 189 optimal weight: 0.5980 chunk 292 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 316 optimal weight: 1.9990 chunk 142 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS A1005 GLN B 69 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074021 restraints weight = 43354.661| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.99 r_work: 0.2891 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26376 Z= 0.106 Angle : 0.544 9.865 36012 Z= 0.277 Chirality : 0.046 0.330 4212 Planarity : 0.004 0.048 4551 Dihedral : 4.036 17.952 3420 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.08 % Allowed : 9.64 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3147 helix: 2.24 (0.21), residues: 714 sheet: 1.43 (0.18), residues: 765 loop : -1.21 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 319 TYR 0.016 0.001 TYR C1067 PHE 0.008 0.001 PHE C1121 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (26280) covalent geometry : angle 0.51349 / 0.27 (35766) SS BOND : bond 0.00262 / 0.17 ( 42) SS BOND : angle 1.13418 / 0.78 ( 84) hydrogen bonds : bond 0.05100 / 3.40 ( 996) hydrogen bonds : angle 4.73972 / 3.28 ( 2682) link_BETA1-4 : bond 0.00296 / 0.16 ( 9) link_BETA1-4 : angle 0.93529 / 0.59 ( 27) link_NAG-ASN : bond 0.00490 / 0.30 ( 45) link_NAG-ASN : angle 2.83364 / 1.95 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.094 Fit side-chains REVERT: A 111 ASP cc_start: 0.7096 (t0) cc_final: 0.6510 (t0) REVERT: A 215 ASP cc_start: 0.7304 (t0) cc_final: 0.6552 (p0) REVERT: A 661 GLU cc_start: 0.8294 (mp0) cc_final: 0.8053 (pm20) REVERT: A 1092 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: B 111 ASP cc_start: 0.7358 (t0) cc_final: 0.6758 (t0) REVERT: B 586 ASP cc_start: 0.8808 (m-30) cc_final: 0.8598 (m-30) REVERT: B 790 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8642 (mtmm) REVERT: C 21 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6885 (pp) REVERT: C 111 ASP cc_start: 0.7312 (t0) cc_final: 0.6741 (t0) REVERT: C 200 TYR cc_start: 0.7987 (m-80) cc_final: 0.7705 (m-80) REVERT: C 990 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7700 (mp0) outliers start: 30 outliers final: 12 residues processed: 155 average time/residue: 0.6269 time to fit residues: 113.5415 Evaluate side-chains 140 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 50 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 209 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 273 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN C1108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069916 restraints weight = 43734.615| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.01 r_work: 0.2813 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 26376 Z= 0.237 Angle : 0.648 10.464 36012 Z= 0.336 Chirality : 0.051 0.350 4212 Planarity : 0.005 0.050 4551 Dihedral : 4.448 21.930 3420 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.04 % Allowed : 9.96 % Favored : 89.00 % 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 are not related in a simple way. whole: 0.16 (0.15), residues: 3147 helix: 1.82 (0.20), residues: 729 sheet: 1.27 (0.18), residues: 768 loop : -1.36 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 319 TYR 0.021 0.002 TYR C1067 PHE 0.018 0.002 PHE C 898 TRP 0.010 0.001 TRP C 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.24 (26280) covalent geometry : angle 0.61754 / 0.33 (35766) SS BOND : bond 0.00365 / 0.25 ( 42) SS BOND : angle 1.78038 / 1.21 ( 84) hydrogen bonds : bond 0.07531 / 5.06 ( 996) hydrogen bonds : angle 5.10082 / 3.51 ( 2682) link_BETA1-4 : bond 0.00204 / 0.11 ( 9) link_BETA1-4 : angle 1.28815 / 0.83 ( 27) link_NAG-ASN : bond 0.00457 / 0.25 ( 45) link_NAG-ASN : angle 2.94768 / 2.02 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.032 Fit side-chains REVERT: A 111 ASP cc_start: 0.7408 (t0) cc_final: 0.6865 (t0) REVERT: A 215 ASP cc_start: 0.7435 (t0) cc_final: 0.6715 (p0) REVERT: A 661 GLU cc_start: 0.8357 (mp0) cc_final: 0.8147 (pm20) REVERT: A 1092 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: B 111 ASP cc_start: 0.7432 (t0) cc_final: 0.6786 (t0) REVERT: B 586 ASP cc_start: 0.8881 (m-30) cc_final: 0.8601 (m-30) REVERT: C 21 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7010 (pp) REVERT: C 111 ASP cc_start: 0.7425 (t0) cc_final: 0.6851 (t0) outliers start: 29 outliers final: 17 residues processed: 146 average time/residue: 0.6746 time to fit residues: 114.1991 Evaluate side-chains 143 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 780 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 49 optimal weight: 0.7980 chunk 281 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073117 restraints weight = 43505.607| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.02 r_work: 0.2873 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26376 Z= 0.118 Angle : 0.567 9.973 36012 Z= 0.290 Chirality : 0.047 0.338 4212 Planarity : 0.004 0.060 4551 Dihedral : 4.183 20.522 3420 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.86 % Allowed : 10.39 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3147 helix: 2.03 (0.20), residues: 729 sheet: 1.41 (0.18), residues: 768 loop : -1.23 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 319 TYR 0.015 0.001 TYR B1067 PHE 0.008 0.001 PHE B 133 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (26280) covalent geometry : angle 0.53636 / 0.28 (35766) SS BOND : bond 0.00276 / 0.18 ( 42) SS BOND : angle 1.18815 / 0.81 ( 84) hydrogen bonds : bond 0.05504 / 3.67 ( 996) hydrogen bonds : angle 4.81829 / 3.33 ( 2682) link_BETA1-4 : bond 0.00310 / 0.16 ( 9) link_BETA1-4 : angle 0.95350 / 0.62 ( 27) link_NAG-ASN : bond 0.00494 / 0.31 ( 45) link_NAG-ASN : angle 2.89395 / 1.99 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.066 Fit side-chains REVERT: A 111 ASP cc_start: 0.7097 (t0) cc_final: 0.6508 (t0) REVERT: A 215 ASP cc_start: 0.7537 (t0) cc_final: 0.6770 (p0) REVERT: A 661 GLU cc_start: 0.8279 (mp0) cc_final: 0.8050 (pm20) REVERT: A 1092 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: B 111 ASP cc_start: 0.7353 (t0) cc_final: 0.6755 (t0) REVERT: B 586 ASP cc_start: 0.8825 (m-30) cc_final: 0.8603 (m-30) REVERT: C 21 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6970 (pp) REVERT: C 111 ASP cc_start: 0.7294 (t0) cc_final: 0.6731 (t0) REVERT: C 200 TYR cc_start: 0.7987 (m-80) cc_final: 0.7736 (m-80) outliers start: 24 outliers final: 14 residues processed: 147 average time/residue: 0.6556 time to fit residues: 112.7496 Evaluate side-chains 143 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 177 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN B 196 ASN B 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073347 restraints weight = 43425.119| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.00 r_work: 0.2879 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26376 Z= 0.117 Angle : 0.560 9.859 36012 Z= 0.286 Chirality : 0.046 0.332 4212 Planarity : 0.004 0.052 4551 Dihedral : 4.130 29.529 3420 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.72 % Allowed : 10.57 % Favored : 88.71 % 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 are not related in a simple way. whole: 0.43 (0.15), residues: 3147 helix: 2.12 (0.20), residues: 729 sheet: 1.47 (0.18), residues: 765 loop : -1.23 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 319 TYR 0.017 0.001 TYR C1067 PHE 0.009 0.001 PHE C 643 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (26280) covalent geometry : angle 0.52936 / 0.28 (35766) SS BOND : bond 0.00271 / 0.18 ( 42) SS BOND : angle 1.40816 / 0.96 ( 84) hydrogen bonds : bond 0.05427 / 3.62 ( 996) hydrogen bonds : angle 4.76435 / 3.29 ( 2682) link_BETA1-4 : bond 0.00281 / 0.15 ( 9) link_BETA1-4 : angle 0.97751 / 0.61 ( 27) link_NAG-ASN : bond 0.00473 / 0.29 ( 45) link_NAG-ASN : angle 2.83709 / 1.95 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.078 Fit side-chains REVERT: A 111 ASP cc_start: 0.7092 (t0) cc_final: 0.6510 (t0) REVERT: A 200 TYR cc_start: 0.7840 (m-80) cc_final: 0.7496 (m-80) REVERT: A 215 ASP cc_start: 0.7518 (t0) cc_final: 0.6743 (p0) REVERT: A 661 GLU cc_start: 0.8293 (mp0) cc_final: 0.8067 (pm20) REVERT: B 111 ASP cc_start: 0.7351 (t0) cc_final: 0.6755 (t0) REVERT: B 586 ASP cc_start: 0.8802 (m-30) cc_final: 0.8586 (m-30) REVERT: B 619 GLU cc_start: 0.8119 (mp0) cc_final: 0.7917 (mp0) REVERT: B 780 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: C 21 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6971 (pp) REVERT: C 111 ASP cc_start: 0.7297 (t0) cc_final: 0.6732 (t0) REVERT: C 200 TYR cc_start: 0.8038 (m-80) cc_final: 0.7775 (m-80) outliers start: 20 outliers final: 13 residues processed: 139 average time/residue: 0.6855 time to fit residues: 110.9307 Evaluate side-chains 138 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 780 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.105272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.070850 restraints weight = 43262.270| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.99 r_work: 0.2817 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26376 Z= 0.199 Angle : 0.632 10.170 36012 Z= 0.327 Chirality : 0.049 0.349 4212 Planarity : 0.005 0.048 4551 Dihedral : 4.413 32.030 3420 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.90 % Allowed : 10.61 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.22 (0.15), residues: 3147 helix: 1.91 (0.20), residues: 729 sheet: 1.30 (0.18), residues: 771 loop : -1.34 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 319 TYR 0.021 0.002 TYR C1067 PHE 0.016 0.001 PHE C 898 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 (26280) covalent geometry : angle 0.60181 / 0.32 (35766) SS BOND : bond 0.00345 / 0.22 ( 42) SS BOND : angle 1.80502 / 1.23 ( 84) hydrogen bonds : bond 0.07076 / 4.75 ( 996) hydrogen bonds : angle 5.02029 / 3.46 ( 2682) link_BETA1-4 : bond 0.00212 / 0.11 ( 9) link_BETA1-4 : angle 1.20938 / 0.77 ( 27) link_NAG-ASN : bond 0.00463 / 0.27 ( 45) link_NAG-ASN : angle 2.89360 / 1.98 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9528.28 seconds wall clock time: 163 minutes 2.32 seconds (9782.32 seconds total)