Starting phenix.real_space_refine on Thu Mar 5 22:12:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g71_29793/03_2026/8g71_29793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g71_29793/03_2026/8g71_29793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g71_29793/03_2026/8g71_29793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g71_29793/03_2026/8g71_29793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g71_29793/03_2026/8g71_29793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g71_29793/03_2026/8g71_29793.map" } resolution = 2.1 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= 0.032 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 16386 2.51 5 N 4239 2.21 5 O 5022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25761 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8367 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "B" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "D" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.30, per 1000 atoms: 0.24 Number of scatterers: 25761 At special positions: 0 Unit cell: (151.84, 161.33, 195.64, 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 5022 8.00 N 4239 7.00 C 16386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 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 D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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 C 1 " - " NAG C 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 234 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B1074 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1074 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN D 717 " " NAG L 1 " - " ASN D 801 " " NAG M 1 " - " ASN D1098 " " NAG N 1 " - " ASN D1134 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 25.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.143A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.035A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.071A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.650A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.775A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.144A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.169A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 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: 3.809A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.115A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.649A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.616A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.625A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.581A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.638A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.818A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.994A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.727A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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: 3.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.893A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.045A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 370 removed outlier: 4.096A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 3.941A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 3.936A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 411 " --> pdb=" O ARG D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.605A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.782A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 919 removed outlier: 3.961A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.733A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.498A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 4.087A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.379A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.932A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 135 current: chain 'A' and resid 153 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.848A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 removed outlier: 7.190A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.741A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.214A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.691A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.830A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.108A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.271A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.224A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.865A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.989A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.639A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 126 through 135 current: chain 'B' and resid 154 through 157 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.227A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.678A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.481A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.032A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.080A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.920A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.259A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.331A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.278A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.970A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 68 through 70 removed outlier: 3.683A pdb=" N HIS D 69 " --> pdb=" O ARG D 78 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 85 current: chain 'D' and resid 116 through 121 removed outlier: 7.974A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N CYS D 136 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N SER D 162 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.312A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AE3, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.925A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.188A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'D' and resid 718 through 728 removed outlier: 7.095A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'D' and resid 1094 through 1097 990 hydrogen bonds defined for protein. 2724 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: 6.64 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8200 1.34 - 1.46: 6462 1.46 - 1.59: 11549 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 26355 Sorted by residual: bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL B 401 " pdb=" CA VAL B 401 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.95e+00 bond pdb=" N VAL D 227 " pdb=" CA VAL D 227 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.22e-02 6.72e+03 8.17e+00 bond pdb=" N PHE B 400 " pdb=" CA PHE B 400 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.20e-02 6.94e+03 7.97e+00 bond pdb=" N SER B 399 " pdb=" CA SER B 399 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.23e-02 6.61e+03 7.68e+00 ... (remaining 26350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 35028 1.87 - 3.74: 775 3.74 - 5.61: 61 5.61 - 7.48: 13 7.48 - 9.35: 8 Bond angle restraints: 35885 Sorted by residual: angle pdb=" C ASN D 61 " pdb=" CA ASN D 61 " pdb=" CB ASN D 61 " ideal model delta sigma weight residual 109.75 116.56 -6.81 1.65e+00 3.67e-01 1.70e+01 angle pdb=" CA LYS A 187 " pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " pdb=" CD LYS A 187 " ideal model delta sigma weight residual 111.30 119.75 -8.45 2.30e+00 1.89e-01 1.35e+01 angle pdb=" CA VAL D 382 " pdb=" C VAL D 382 " pdb=" O VAL D 382 " ideal model delta sigma weight residual 121.64 118.23 3.41 9.80e-01 1.04e+00 1.21e+01 angle pdb=" CA GLU D 132 " pdb=" C GLU D 132 " pdb=" O GLU D 132 " ideal model delta sigma weight residual 122.36 118.23 4.13 1.21e+00 6.83e-01 1.17e+01 ... (remaining 35880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 14406 18.04 - 36.07: 1413 36.07 - 54.11: 343 54.11 - 72.15: 89 72.15 - 90.18: 40 Dihedral angle restraints: 16291 sinusoidal: 6934 harmonic: 9357 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 164.39 -71.39 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS D 336 " pdb=" SG CYS D 336 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -37.24 -48.76 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -39.06 -46.94 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 16288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3925 0.098 - 0.196: 261 0.196 - 0.294: 2 0.294 - 0.391: 0 0.391 - 0.489: 1 Chirality restraints: 4189 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE D 128 " pdb=" N ILE D 128 " pdb=" C ILE D 128 " pdb=" CB ILE D 128 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 4186 not shown) Planarity restraints: 4637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 353 " -0.033 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP B 353 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 353 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 353 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 353 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 353 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 353 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 353 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 353 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 353 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 588 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 589 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 61 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ASN D 61 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN D 61 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL D 62 " -0.012 2.00e-02 2.50e+03 ... (remaining 4634 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 203 2.62 - 3.19: 22188 3.19 - 3.76: 39503 3.76 - 4.33: 56006 4.33 - 4.90: 90094 Nonbonded interactions: 207994 Sorted by model distance: nonbonded pdb=" OG1 THR A1076 " pdb=" OG SER A1097 " model vdw 2.055 3.040 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.073 3.040 nonbonded pdb=" OG SER D 735 " pdb=" OG1 THR D 859 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.183 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.186 3.040 ... (remaining 207989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1307)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1307)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 9.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.480 Find NCS groups from input model: 0.720 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:9.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 0.042 26439 Z= 0.186 Angle : 0.658 13.929 36098 Z= 0.348 Chirality : 0.047 0.489 4189 Planarity : 0.004 0.071 4603 Dihedral : 15.865 90.184 10160 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 2.27 % Allowed : 18.88 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3187 helix: 1.49 (0.20), residues: 676 sheet: -0.58 (0.17), residues: 785 loop : -1.21 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 21 TYR 0.021 0.001 TYR D 453 PHE 0.023 0.001 PHE D 192 TRP 0.045 0.002 TRP B 353 HIS 0.014 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00345 (26355) covalent geometry : angle 0.63871 (35885) SS BOND : bond 0.00342 ( 39) SS BOND : angle 1.15014 ( 78) hydrogen bonds : bond 0.11787 ( 990) hydrogen bonds : angle 7.16527 ( 2724) link_BETA1-4 : bond 0.00526 ( 11) link_BETA1-4 : angle 1.49618 ( 33) link_NAG-ASN : bond 0.00515 ( 34) link_NAG-ASN : angle 2.80948 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 150 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 SER cc_start: 0.0069 (OUTLIER) cc_final: -0.0931 (p) REVERT: A 438 SER cc_start: 0.5280 (OUTLIER) cc_final: 0.4775 (p) REVERT: A 573 THR cc_start: 0.7171 (OUTLIER) cc_final: 0.6962 (p) REVERT: A 902 MET cc_start: 0.9220 (tpp) cc_final: 0.8944 (tpp) outliers start: 64 outliers final: 45 residues processed: 212 average time/residue: 0.5448 time to fit residues: 137.7222 Evaluate side-chains 186 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 188 ASN A 394 ASN A 501 ASN A 603 ASN A 913 GLN A1002 GLN B 69 HIS B 207 HIS B 542 ASN B 957 GLN B1002 GLN D 121 ASN D 196 ASN D 218 GLN D 321 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.240482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.202130 restraints weight = 23201.991| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 1.68 r_work: 0.3871 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26439 Z= 0.139 Angle : 0.601 13.196 36098 Z= 0.311 Chirality : 0.046 0.458 4189 Planarity : 0.004 0.050 4603 Dihedral : 6.715 65.059 4461 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 2.98 % Allowed : 17.89 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.46 (0.14), residues: 3187 helix: 1.98 (0.20), residues: 677 sheet: -0.49 (0.18), residues: 766 loop : -1.16 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 21 TYR 0.022 0.001 TYR A1067 PHE 0.027 0.001 PHE B 400 TRP 0.014 0.001 TRP B 353 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00302 (26355) covalent geometry : angle 0.58111 (35885) SS BOND : bond 0.00307 ( 39) SS BOND : angle 1.15535 ( 78) hydrogen bonds : bond 0.05415 ( 990) hydrogen bonds : angle 5.93480 ( 2724) link_BETA1-4 : bond 0.00380 ( 11) link_BETA1-4 : angle 1.30973 ( 33) link_NAG-ASN : bond 0.00500 ( 34) link_NAG-ASN : angle 2.72090 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 144 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 552 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7766 (mt) REVERT: B 619 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: D 69 HIS cc_start: 0.2590 (OUTLIER) cc_final: 0.1673 (t-170) outliers start: 84 outliers final: 32 residues processed: 224 average time/residue: 0.5417 time to fit residues: 145.2238 Evaluate side-chains 167 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 311 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 212 optimal weight: 0.0980 chunk 240 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 265 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 603 ASN A1002 GLN B 218 GLN B 354 ASN B 542 ASN B 580 GLN B 957 GLN B1002 GLN D 121 ASN D 196 ASN D 540 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.240584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.200045 restraints weight = 23136.465| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.67 r_work: 0.3948 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26439 Z= 0.128 Angle : 0.576 13.028 36098 Z= 0.298 Chirality : 0.046 0.433 4189 Planarity : 0.004 0.050 4603 Dihedral : 5.949 59.028 4416 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 3.26 % Allowed : 17.85 % Favored : 78.89 % 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: -0.35 (0.14), residues: 3187 helix: 2.09 (0.20), residues: 677 sheet: -0.41 (0.18), residues: 757 loop : -1.11 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 457 TYR 0.020 0.001 TYR B1067 PHE 0.028 0.001 PHE B 400 TRP 0.009 0.001 TRP B 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00276 (26355) covalent geometry : angle 0.55657 (35885) SS BOND : bond 0.00602 ( 39) SS BOND : angle 1.14297 ( 78) hydrogen bonds : bond 0.05146 ( 990) hydrogen bonds : angle 5.74087 ( 2724) link_BETA1-4 : bond 0.00385 ( 11) link_BETA1-4 : angle 1.39614 ( 33) link_NAG-ASN : bond 0.00469 ( 34) link_NAG-ASN : angle 2.60364 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 146 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0882 (OUTLIER) cc_final: 0.0634 (m) REVERT: A 131 CYS cc_start: 0.1715 (OUTLIER) cc_final: 0.1476 (p) REVERT: B 153 MET cc_start: 0.0739 (OUTLIER) cc_final: -0.0393 (ttm) REVERT: B 177 MET cc_start: 0.3135 (OUTLIER) cc_final: 0.2463 (mpm) REVERT: B 318 PHE cc_start: 0.8083 (t80) cc_final: 0.7741 (p90) REVERT: B 442 ASP cc_start: 0.1107 (OUTLIER) cc_final: 0.0738 (p0) REVERT: B 619 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: D 69 HIS cc_start: 0.2576 (OUTLIER) cc_final: 0.1551 (t-170) REVERT: D 149 ASN cc_start: 0.2446 (OUTLIER) cc_final: 0.1995 (p0) REVERT: D 1081 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8561 (mt) outliers start: 92 outliers final: 37 residues processed: 227 average time/residue: 0.5607 time to fit residues: 153.1334 Evaluate side-chains 182 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 201 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 955 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 506 GLN B 542 ASN B 580 GLN B 764 ASN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.236110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.190449 restraints weight = 22705.422| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.74 r_work: 0.3836 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 26439 Z= 0.260 Angle : 0.762 13.714 36098 Z= 0.395 Chirality : 0.055 0.517 4189 Planarity : 0.006 0.074 4603 Dihedral : 6.494 56.015 4408 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 3.87 % Allowed : 17.57 % Favored : 78.57 % 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: -0.63 (0.14), residues: 3187 helix: 1.77 (0.20), residues: 658 sheet: -0.52 (0.18), residues: 719 loop : -1.23 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1014 TYR 0.023 0.003 TYR A1067 PHE 0.031 0.003 PHE A 898 TRP 0.013 0.002 TRP B 64 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00584 (26355) covalent geometry : angle 0.73881 (35885) SS BOND : bond 0.00495 ( 39) SS BOND : angle 1.54327 ( 78) hydrogen bonds : bond 0.06969 ( 990) hydrogen bonds : angle 6.19066 ( 2724) link_BETA1-4 : bond 0.00461 ( 11) link_BETA1-4 : angle 1.97219 ( 33) link_NAG-ASN : bond 0.00617 ( 34) link_NAG-ASN : angle 3.22046 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 139 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0941 (OUTLIER) cc_final: 0.0625 (m) REVERT: A 212 LEU cc_start: 0.3276 (OUTLIER) cc_final: 0.2824 (mm) REVERT: A 574 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6668 (p0) REVERT: B 153 MET cc_start: 0.0895 (OUTLIER) cc_final: -0.0218 (ttm) REVERT: B 177 MET cc_start: 0.3361 (OUTLIER) cc_final: 0.2645 (mpm) REVERT: B 340 GLU cc_start: 0.3594 (OUTLIER) cc_final: 0.3258 (tt0) REVERT: B 353 TRP cc_start: 0.1167 (OUTLIER) cc_final: -0.0199 (m-10) REVERT: B 442 ASP cc_start: 0.1449 (OUTLIER) cc_final: 0.0852 (p0) REVERT: B 619 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: B 916 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8475 (tp) REVERT: D 149 ASN cc_start: 0.2343 (OUTLIER) cc_final: 0.1920 (p0) REVERT: D 571 ASP cc_start: 0.5896 (OUTLIER) cc_final: 0.5104 (p0) REVERT: D 1081 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8549 (mt) outliers start: 109 outliers final: 55 residues processed: 237 average time/residue: 0.5411 time to fit residues: 153.9773 Evaluate side-chains 205 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 137 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 159 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 284 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 255 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 290 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 542 ASN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN D1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.237244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.195935 restraints weight = 22675.713| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 1.72 r_work: 0.3878 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 26439 Z= 0.238 Angle : 0.732 14.531 36098 Z= 0.380 Chirality : 0.053 0.465 4189 Planarity : 0.005 0.068 4603 Dihedral : 6.385 55.287 4408 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 4.01 % Allowed : 17.46 % Favored : 78.53 % 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: -0.68 (0.14), residues: 3187 helix: 1.73 (0.20), residues: 661 sheet: -0.51 (0.18), residues: 718 loop : -1.29 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 905 TYR 0.024 0.002 TYR A1067 PHE 0.031 0.002 PHE A 898 TRP 0.014 0.002 TRP B 64 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00537 (26355) covalent geometry : angle 0.70707 (35885) SS BOND : bond 0.00553 ( 39) SS BOND : angle 1.80473 ( 78) hydrogen bonds : bond 0.06598 ( 990) hydrogen bonds : angle 6.13729 ( 2724) link_BETA1-4 : bond 0.00359 ( 11) link_BETA1-4 : angle 1.90775 ( 33) link_NAG-ASN : bond 0.00574 ( 34) link_NAG-ASN : angle 3.15603 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 135 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0883 (OUTLIER) cc_final: 0.0586 (m) REVERT: A 131 CYS cc_start: 0.2200 (OUTLIER) cc_final: 0.1920 (p) REVERT: A 574 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6621 (p0) REVERT: B 153 MET cc_start: 0.0934 (OUTLIER) cc_final: -0.0163 (ttm) REVERT: B 177 MET cc_start: 0.3643 (OUTLIER) cc_final: 0.2927 (mpm) REVERT: B 340 GLU cc_start: 0.3632 (OUTLIER) cc_final: 0.3287 (tt0) REVERT: B 353 TRP cc_start: 0.1382 (OUTLIER) cc_final: -0.0044 (m-10) REVERT: B 442 ASP cc_start: 0.1595 (OUTLIER) cc_final: 0.1006 (p0) REVERT: B 619 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: B 916 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8514 (tp) REVERT: D 149 ASN cc_start: 0.2418 (OUTLIER) cc_final: 0.1962 (p0) REVERT: D 902 MET cc_start: 0.9108 (tpp) cc_final: 0.8744 (tpp) REVERT: D 1081 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8558 (mt) outliers start: 113 outliers final: 63 residues processed: 239 average time/residue: 0.5319 time to fit residues: 154.3234 Evaluate side-chains 204 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 129 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 300 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 287 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 0.0670 chunk 235 optimal weight: 0.0770 chunk 173 optimal weight: 7.9990 chunk 102 optimal weight: 0.2980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 603 ASN A1002 GLN B 542 ASN B 580 GLN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.240256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.199927 restraints weight = 23161.943| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.64 r_work: 0.3950 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 26439 Z= 0.112 Angle : 0.570 12.598 36098 Z= 0.292 Chirality : 0.045 0.422 4189 Planarity : 0.004 0.050 4603 Dihedral : 5.532 56.847 4406 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 2.34 % Allowed : 19.13 % Favored : 78.53 % 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 (0.14), residues: 3187 helix: 2.13 (0.20), residues: 674 sheet: -0.35 (0.18), residues: 710 loop : -1.17 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 454 TYR 0.016 0.001 TYR A1067 PHE 0.020 0.001 PHE D 192 TRP 0.012 0.001 TRP D 64 HIS 0.010 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00237 (26355) covalent geometry : angle 0.54632 (35885) SS BOND : bond 0.00446 ( 39) SS BOND : angle 1.42369 ( 78) hydrogen bonds : bond 0.04630 ( 990) hydrogen bonds : angle 5.61963 ( 2724) link_BETA1-4 : bond 0.00378 ( 11) link_BETA1-4 : angle 1.53786 ( 33) link_NAG-ASN : bond 0.00466 ( 34) link_NAG-ASN : angle 2.75703 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 144 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6565 (p0) REVERT: B 153 MET cc_start: 0.0736 (OUTLIER) cc_final: -0.0288 (ttm) REVERT: B 177 MET cc_start: 0.3631 (OUTLIER) cc_final: 0.2933 (mpm) REVERT: B 318 PHE cc_start: 0.8108 (t80) cc_final: 0.7867 (p90) REVERT: B 442 ASP cc_start: 0.1087 (OUTLIER) cc_final: 0.0689 (p0) REVERT: B 1029 MET cc_start: 0.8899 (tpp) cc_final: 0.8674 (tpp) REVERT: D 149 ASN cc_start: 0.2314 (OUTLIER) cc_final: 0.1881 (p0) REVERT: D 646 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7465 (mtp-110) REVERT: D 902 MET cc_start: 0.9049 (tpp) cc_final: 0.8707 (tpp) outliers start: 66 outliers final: 29 residues processed: 205 average time/residue: 0.4905 time to fit residues: 121.2161 Evaluate side-chains 168 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.0170 chunk 145 optimal weight: 30.0000 chunk 39 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 603 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN D1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.238341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.196718 restraints weight = 22719.268| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 1.67 r_work: 0.3904 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 26439 Z= 0.178 Angle : 0.656 13.401 36098 Z= 0.336 Chirality : 0.048 0.454 4189 Planarity : 0.004 0.049 4603 Dihedral : 5.683 54.647 4403 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 2.95 % Allowed : 18.45 % Favored : 78.60 % 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: -0.44 (0.14), residues: 3187 helix: 2.02 (0.20), residues: 665 sheet: -0.36 (0.18), residues: 709 loop : -1.18 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 454 TYR 0.023 0.002 TYR A1067 PHE 0.026 0.002 PHE A 898 TRP 0.010 0.001 TRP B 64 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00399 (26355) covalent geometry : angle 0.62676 (35885) SS BOND : bond 0.00408 ( 39) SS BOND : angle 1.80887 ( 78) hydrogen bonds : bond 0.05943 ( 990) hydrogen bonds : angle 5.85026 ( 2724) link_BETA1-4 : bond 0.00359 ( 11) link_BETA1-4 : angle 1.70520 ( 33) link_NAG-ASN : bond 0.00496 ( 34) link_NAG-ASN : angle 3.25488 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 142 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.2163 (OUTLIER) cc_final: 0.1954 (p) REVERT: A 153 MET cc_start: -0.0321 (mmm) cc_final: -0.0526 (tpt) REVERT: A 212 LEU cc_start: 0.3055 (OUTLIER) cc_final: 0.2613 (tp) REVERT: A 574 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6600 (p0) REVERT: B 153 MET cc_start: 0.0811 (OUTLIER) cc_final: -0.0249 (ttm) REVERT: B 177 MET cc_start: 0.3732 (OUTLIER) cc_final: 0.3002 (mmp) REVERT: B 353 TRP cc_start: 0.1214 (OUTLIER) cc_final: -0.0070 (m-10) REVERT: B 442 ASP cc_start: 0.1352 (OUTLIER) cc_final: 0.0911 (p0) REVERT: D 149 ASN cc_start: 0.2306 (OUTLIER) cc_final: 0.1819 (p0) REVERT: D 646 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7430 (mtp-110) REVERT: D 902 MET cc_start: 0.9053 (tpp) cc_final: 0.8677 (tpp) outliers start: 83 outliers final: 48 residues processed: 215 average time/residue: 0.5160 time to fit residues: 133.6199 Evaluate side-chains 195 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 213 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 603 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN D1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.237888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.194685 restraints weight = 22752.955| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.73 r_work: 0.3877 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 26439 Z= 0.188 Angle : 0.669 12.934 36098 Z= 0.345 Chirality : 0.049 0.452 4189 Planarity : 0.005 0.052 4603 Dihedral : 5.801 54.850 4403 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 2.95 % Allowed : 18.56 % Favored : 78.50 % 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: -0.49 (0.14), residues: 3187 helix: 1.98 (0.20), residues: 661 sheet: -0.41 (0.18), residues: 713 loop : -1.21 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1014 TYR 0.024 0.002 TYR A1067 PHE 0.027 0.002 PHE A 898 TRP 0.012 0.002 TRP B 64 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00424 (26355) covalent geometry : angle 0.64205 (35885) SS BOND : bond 0.00400 ( 39) SS BOND : angle 1.83963 ( 78) hydrogen bonds : bond 0.06045 ( 990) hydrogen bonds : angle 5.91758 ( 2724) link_BETA1-4 : bond 0.00331 ( 11) link_BETA1-4 : angle 1.74585 ( 33) link_NAG-ASN : bond 0.00497 ( 34) link_NAG-ASN : angle 3.11242 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 144 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0916 (OUTLIER) cc_final: 0.0612 (m) REVERT: A 131 CYS cc_start: 0.2263 (OUTLIER) cc_final: 0.2018 (p) REVERT: A 153 MET cc_start: -0.0322 (mmm) cc_final: -0.0565 (tpt) REVERT: A 212 LEU cc_start: 0.3021 (OUTLIER) cc_final: 0.2533 (tp) REVERT: A 314 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7304 (tp40) REVERT: A 396 TYR cc_start: 0.7175 (m-10) cc_final: 0.6956 (m-10) REVERT: A 574 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6596 (p0) REVERT: B 153 MET cc_start: 0.0851 (OUTLIER) cc_final: -0.0234 (ttm) REVERT: B 177 MET cc_start: 0.3864 (OUTLIER) cc_final: 0.3118 (mmp) REVERT: B 353 TRP cc_start: 0.1396 (OUTLIER) cc_final: 0.0045 (m-10) REVERT: B 442 ASP cc_start: 0.1336 (OUTLIER) cc_final: 0.0902 (p0) REVERT: B 619 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: D 149 ASN cc_start: 0.2287 (OUTLIER) cc_final: 0.1802 (p0) REVERT: D 902 MET cc_start: 0.9028 (tpp) cc_final: 0.8669 (tpp) outliers start: 83 outliers final: 52 residues processed: 216 average time/residue: 0.5306 time to fit residues: 137.1437 Evaluate side-chains 200 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 137 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 259 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 655 HIS A1002 GLN A1010 GLN A1011 GLN B 542 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN D 121 ASN D 196 ASN D 501 ASN D 540 ASN D1101 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.237848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.194889 restraints weight = 22917.987| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.71 r_work: 0.3882 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 26439 Z= 0.184 Angle : 0.673 15.912 36098 Z= 0.344 Chirality : 0.049 0.451 4189 Planarity : 0.005 0.056 4603 Dihedral : 5.800 54.954 4403 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 3.12 % Allowed : 18.45 % Favored : 78.42 % 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: -0.50 (0.14), residues: 3187 helix: 1.94 (0.20), residues: 669 sheet: -0.39 (0.18), residues: 712 loop : -1.22 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 454 TYR 0.023 0.002 TYR A1067 PHE 0.027 0.002 PHE A 898 TRP 0.011 0.002 TRP B 64 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00416 (26355) covalent geometry : angle 0.63793 (35885) SS BOND : bond 0.00400 ( 39) SS BOND : angle 1.89094 ( 78) hydrogen bonds : bond 0.05999 ( 990) hydrogen bonds : angle 5.91407 ( 2724) link_BETA1-4 : bond 0.00328 ( 11) link_BETA1-4 : angle 1.74520 ( 33) link_NAG-ASN : bond 0.00518 ( 34) link_NAG-ASN : angle 3.63455 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 137 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0931 (OUTLIER) cc_final: 0.0610 (m) REVERT: A 131 CYS cc_start: 0.2206 (OUTLIER) cc_final: 0.1949 (p) REVERT: A 153 MET cc_start: -0.0483 (mmm) cc_final: -0.0701 (tpt) REVERT: A 212 LEU cc_start: 0.3037 (OUTLIER) cc_final: 0.2532 (tp) REVERT: A 314 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7287 (tp40) REVERT: A 396 TYR cc_start: 0.7156 (m-10) cc_final: 0.6926 (m-10) REVERT: A 452 LEU cc_start: 0.4673 (OUTLIER) cc_final: 0.4063 (mt) REVERT: A 574 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6612 (p0) REVERT: B 153 MET cc_start: 0.0812 (OUTLIER) cc_final: -0.0271 (ttm) REVERT: B 177 MET cc_start: 0.4000 (OUTLIER) cc_final: 0.3247 (mmp) REVERT: B 353 TRP cc_start: 0.1500 (OUTLIER) cc_final: 0.0202 (m-10) REVERT: B 442 ASP cc_start: 0.1534 (OUTLIER) cc_final: 0.1004 (p0) REVERT: B 619 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: D 149 ASN cc_start: 0.2248 (OUTLIER) cc_final: 0.1859 (p0) REVERT: D 902 MET cc_start: 0.9036 (tpp) cc_final: 0.8705 (tpp) outliers start: 88 outliers final: 57 residues processed: 216 average time/residue: 0.5679 time to fit residues: 146.0878 Evaluate side-chains 209 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 140 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 5 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 307 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A1002 GLN A1010 GLN B 542 ASN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN D1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.238112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.194706 restraints weight = 22863.543| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.67 r_work: 0.3853 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 26439 Z= 0.169 Angle : 0.653 15.989 36098 Z= 0.335 Chirality : 0.048 0.448 4189 Planarity : 0.005 0.058 4603 Dihedral : 5.690 55.323 4403 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 2.84 % Allowed : 18.95 % Favored : 78.21 % 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: -0.48 (0.14), residues: 3187 helix: 1.97 (0.20), residues: 665 sheet: -0.38 (0.18), residues: 711 loop : -1.21 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 454 TYR 0.023 0.002 TYR A1067 PHE 0.025 0.002 PHE A 898 TRP 0.011 0.001 TRP B 64 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00382 (26355) covalent geometry : angle 0.61951 (35885) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.93337 ( 78) hydrogen bonds : bond 0.05800 ( 990) hydrogen bonds : angle 5.86815 ( 2724) link_BETA1-4 : bond 0.00313 ( 11) link_BETA1-4 : angle 1.70339 ( 33) link_NAG-ASN : bond 0.00478 ( 34) link_NAG-ASN : angle 3.46878 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 139 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0800 (OUTLIER) cc_final: 0.0450 (m) REVERT: A 131 CYS cc_start: 0.2291 (OUTLIER) cc_final: 0.2023 (p) REVERT: A 153 MET cc_start: -0.0415 (mmm) cc_final: -0.0648 (tpt) REVERT: A 197 ILE cc_start: 0.3474 (OUTLIER) cc_final: 0.3266 (mp) REVERT: A 212 LEU cc_start: 0.3021 (OUTLIER) cc_final: 0.2520 (tp) REVERT: A 314 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7327 (tp40) REVERT: A 396 TYR cc_start: 0.7196 (m-10) cc_final: 0.6943 (m-10) REVERT: A 452 LEU cc_start: 0.4729 (OUTLIER) cc_final: 0.3930 (tp) REVERT: A 574 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6657 (p0) REVERT: B 177 MET cc_start: 0.3982 (OUTLIER) cc_final: 0.3228 (mmp) REVERT: B 353 TRP cc_start: 0.1405 (OUTLIER) cc_final: 0.0151 (m-10) REVERT: B 442 ASP cc_start: 0.1506 (OUTLIER) cc_final: 0.1038 (p0) REVERT: B 619 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: D 149 ASN cc_start: 0.2147 (OUTLIER) cc_final: 0.1913 (p0) REVERT: D 619 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: D 902 MET cc_start: 0.9027 (tpp) cc_final: 0.8671 (tpp) outliers start: 80 outliers final: 59 residues processed: 211 average time/residue: 0.5466 time to fit residues: 138.1063 Evaluate side-chains 208 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 136 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 195 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 238 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 655 HIS A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN D1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.237534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.194601 restraints weight = 22802.945| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.71 r_work: 0.3875 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 26439 Z= 0.197 Angle : 0.691 14.896 36098 Z= 0.355 Chirality : 0.050 0.457 4189 Planarity : 0.005 0.059 4603 Dihedral : 5.853 54.750 4403 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 2.87 % Allowed : 19.02 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.54 (0.14), residues: 3187 helix: 1.89 (0.20), residues: 667 sheet: -0.36 (0.18), residues: 713 loop : -1.26 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 454 TYR 0.024 0.002 TYR A1067 PHE 0.028 0.002 PHE A 898 TRP 0.012 0.002 TRP B 64 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00447 (26355) covalent geometry : angle 0.65758 (35885) SS BOND : bond 0.00400 ( 39) SS BOND : angle 2.08720 ( 78) hydrogen bonds : bond 0.06184 ( 990) hydrogen bonds : angle 5.96551 ( 2724) link_BETA1-4 : bond 0.00328 ( 11) link_BETA1-4 : angle 1.78533 ( 33) link_NAG-ASN : bond 0.00500 ( 34) link_NAG-ASN : angle 3.51277 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14377.06 seconds wall clock time: 244 minutes 18.01 seconds (14658.01 seconds total)