Starting phenix.real_space_refine on Thu Mar 5 20:01:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m8k_23718/03_2026/7m8k_23718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m8k_23718/03_2026/7m8k_23718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m8k_23718/03_2026/7m8k_23718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m8k_23718/03_2026/7m8k_23718.map" model { file = "/net/cci-nas-00/data/ceres_data/7m8k_23718/03_2026/7m8k_23718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m8k_23718/03_2026/7m8k_23718.cif" } resolution = 3.8 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= 0.001 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 105 5.16 5 C 15836 2.51 5 N 4043 2.21 5 O 4842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 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: 24826 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8020 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1025, 8014 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 50, 'TRANS': 974} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1025, 8014 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 50, 'TRANS': 974} Chain breaks: 8 bond proxies already assigned to first conformer: 8190 Chain: "B" Number of atoms: 8072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8072 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 52, 'TRANS': 980} Chain breaks: 8 Chain: "C" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8020 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.28, per 1000 atoms: 0.29 Number of scatterers: 24826 At special positions: 0 Unit cell: (134.82, 143.38, 196.88, 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 105 16.00 O 4842 8.00 N 4043 7.00 C 15836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.00 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=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 603 " " NAG B1301 " - " ASN B 61 " " 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 B1074 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 282 " " NAG B1310 " - " ASN B 234 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN B1134 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN C 801 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.3 seconds 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5784 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 51 sheets defined 26.2% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.671A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.588A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.031A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.666A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.616A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.668A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 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 removed outlier: 3.535A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.636A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.647A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.530A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.484A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.905A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.726A pdb=" N ASP B 420 " --> pdb=" O THR B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.859A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.564A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.637A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.388A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.817A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.537A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.495A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.564A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.907A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.657A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 removed outlier: 3.635A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 removed outlier: 3.802A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 853 through 856' Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.504A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 907 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.173A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.520A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.524A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.136A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 4.015A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.956A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.592A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.190A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.559A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.823A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.034A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (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 361 through 362 removed outlier: 7.025A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 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: 3.740A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.653A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 7.072A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.330A 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 728 removed outlier: 6.696A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.696A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.680A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.806A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.571A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.044A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.781A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.491A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.231A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 578 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.982A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 401 through 403 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.166A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.613A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.761A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.761A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.810A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.027A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.926A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.214A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.109A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.510A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.267A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 7.012A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 5.406A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 655 through 656 removed outlier: 4.230A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.523A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.129A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.358A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF6, first strand: chain 'C' and resid 1088 through 1090 997 hydrogen bonds defined for protein. 2732 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: 6.07 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3996 1.31 - 1.45: 7377 1.45 - 1.59: 13879 1.59 - 1.73: 0 1.73 - 1.87: 129 Bond restraints: 25381 Sorted by residual: bond pdb=" CA CYS A 662 " pdb=" C CYS A 662 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.34e-02 5.57e+03 2.77e+01 bond pdb=" N GLN A 321 " pdb=" CA GLN A 321 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.10e-03 1.98e+04 2.44e+01 bond pdb=" C TYR C 660 " pdb=" O TYR C 660 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.30e-02 5.92e+03 2.29e+01 bond pdb=" C CYS A 662 " pdb=" O CYS A 662 " ideal model delta sigma weight residual 1.235 1.176 0.059 1.26e-02 6.30e+03 2.19e+01 bond pdb=" N ILE C 664 " pdb=" CA ILE C 664 " ideal model delta sigma weight residual 1.457 1.499 -0.042 9.00e-03 1.23e+04 2.14e+01 ... (remaining 25376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 32418 2.64 - 5.29: 1873 5.29 - 7.93: 233 7.93 - 10.57: 17 10.57 - 13.22: 5 Bond angle restraints: 34546 Sorted by residual: angle pdb=" CA PHE A 329 " pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 117.68 123.93 -6.25 7.10e-01 1.98e+00 7.76e+01 angle pdb=" CA PHE B 133 " pdb=" C PHE B 133 " pdb=" O PHE B 133 " ideal model delta sigma weight residual 120.66 111.59 9.07 1.15e+00 7.56e-01 6.23e+01 angle pdb=" CA GLY A 107 " pdb=" C GLY A 107 " pdb=" O GLY A 107 " ideal model delta sigma weight residual 121.86 113.96 7.90 1.04e+00 9.25e-01 5.77e+01 angle pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" O GLY B 107 " ideal model delta sigma weight residual 121.35 113.38 7.97 1.05e+00 9.07e-01 5.76e+01 angle pdb=" CA PHE C 106 " pdb=" C PHE C 106 " pdb=" O PHE C 106 " ideal model delta sigma weight residual 121.33 113.27 8.06 1.08e+00 8.57e-01 5.57e+01 ... (remaining 34541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.31: 14624 19.31 - 38.61: 903 38.61 - 57.92: 164 57.92 - 77.22: 37 77.22 - 96.53: 25 Dihedral angle restraints: 15753 sinusoidal: 6763 harmonic: 8990 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -153.33 67.33 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 150.28 -57.28 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -123.11 37.11 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 15750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3897 0.144 - 0.289: 165 0.289 - 0.433: 8 0.433 - 0.578: 9 0.578 - 0.722: 5 Chirality restraints: 4084 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-02 2.50e+03 5.30e+02 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.39e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.75e+01 ... (remaining 4081 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.308 2.00e-02 2.50e+03 2.61e-01 8.51e+02 pdb=" C7 NAG N 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.452 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.300 2.00e-02 2.50e+03 2.55e-01 8.12e+02 pdb=" C7 NAG L 1 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.178 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.442 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " -0.284 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG A1310 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " 0.407 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " -0.208 2.00e-02 2.50e+03 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 948 2.70 - 3.25: 25222 3.25 - 3.80: 39156 3.80 - 4.35: 49759 4.35 - 4.90: 82978 Nonbonded interactions: 198063 Sorted by model distance: nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR A 581 " pdb=" OE1 GLU A 583 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR C 618 " pdb=" OE1 GLU C 619 " model vdw 2.217 3.040 nonbonded pdb=" NH2 ARG B 34 " pdb=" O GLY B 219 " model vdw 2.225 3.120 nonbonded pdb=" NH1 ARG B1091 " pdb=" O ASP B1118 " model vdw 2.229 3.120 ... (remaining 198058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 612 or resid 614 through 622 or resid 633 through 827 or resid 853 through 13 \ 09)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 612 or resid 614 throu \ gh 622 or resid 633 through 827 or resid 836 through 1309)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 612 or resid 614 throu \ gh 622 or resid 633 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.500 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.710 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.010 0.202 25470 Z= 0.563 Angle : 1.368 13.475 34775 Z= 0.849 Chirality : 0.076 0.722 4084 Planarity : 0.013 0.261 4388 Dihedral : 13.063 96.530 9855 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.15 % Allowed : 1.78 % Favored : 98.07 % 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: -1.10 (0.14), residues: 3031 helix: 0.77 (0.20), residues: 684 sheet: -0.47 (0.19), residues: 603 loop : -1.48 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1039 TYR 0.049 0.003 TYR B 904 PHE 0.047 0.003 PHE C1103 TRP 0.058 0.003 TRP B 104 HIS 0.009 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00878 (25381) covalent geometry : angle 1.32278 (34546) SS BOND : bond 0.00829 ( 38) SS BOND : angle 2.45242 ( 76) hydrogen bonds : bond 0.20828 ( 970) hydrogen bonds : angle 9.00870 ( 2732) link_BETA1-4 : bond 0.01146 ( 11) link_BETA1-4 : angle 5.68304 ( 33) link_NAG-ASN : bond 0.12611 ( 40) link_NAG-ASN : angle 5.12365 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8818 (mppt) cc_final: 0.8595 (mmtm) REVERT: B 572 THR cc_start: 0.8799 (m) cc_final: 0.8409 (p) outliers start: 4 outliers final: 1 residues processed: 77 average time/residue: 0.1733 time to fit residues: 21.7606 Evaluate side-chains 39 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN ** A 613 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1058 HIS A1071 GLN B 121 ASN B 122 ASN B 580 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 955 ASN C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.055123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.038164 restraints weight = 222414.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040033 restraints weight = 97744.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.040840 restraints weight = 50520.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.041168 restraints weight = 35205.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041269 restraints weight = 34147.335| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25470 Z= 0.179 Angle : 0.672 10.415 34775 Z= 0.336 Chirality : 0.046 0.252 4084 Planarity : 0.004 0.055 4388 Dihedral : 6.718 89.456 4377 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 0.30 % Allowed : 4.67 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3031 helix: 1.28 (0.20), residues: 691 sheet: -0.13 (0.19), residues: 654 loop : -1.13 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 509 TYR 0.034 0.002 TYR C 904 PHE 0.019 0.001 PHE A 133 TRP 0.010 0.001 TRP A 104 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00390 (25381) covalent geometry : angle 0.63842 (34546) SS BOND : bond 0.00286 ( 38) SS BOND : angle 0.98913 ( 76) hydrogen bonds : bond 0.04923 ( 970) hydrogen bonds : angle 6.40819 ( 2732) link_BETA1-4 : bond 0.01440 ( 11) link_BETA1-4 : angle 5.26886 ( 33) link_NAG-ASN : bond 0.00326 ( 40) link_NAG-ASN : angle 2.27475 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.9067 (ttm) cc_final: 0.8424 (ttm) REVERT: A 904 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: A 1019 ARG cc_start: 0.9305 (ttt90) cc_final: 0.8917 (ttp-110) REVERT: B 697 MET cc_start: 0.8581 (ptm) cc_final: 0.8204 (ptm) REVERT: C 740 MET cc_start: 0.9140 (tpp) cc_final: 0.8770 (tpp) REVERT: C 776 LYS cc_start: 0.9616 (tppt) cc_final: 0.9305 (tppt) REVERT: C 1050 MET cc_start: 0.8092 (ptp) cc_final: 0.7880 (ptp) REVERT: C 1092 GLU cc_start: 0.7454 (pm20) cc_final: 0.7193 (pm20) outliers start: 8 outliers final: 2 residues processed: 45 average time/residue: 0.1494 time to fit residues: 12.2614 Evaluate side-chains 37 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 175 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN B 207 HIS B 955 ASN B 965 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C1125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.051939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.035453 restraints weight = 179305.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.036729 restraints weight = 85644.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.037546 restraints weight = 54043.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.038100 restraints weight = 40172.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.038439 restraints weight = 33043.371| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25470 Z= 0.177 Angle : 0.614 10.281 34775 Z= 0.305 Chirality : 0.044 0.242 4084 Planarity : 0.004 0.050 4388 Dihedral : 6.572 91.928 4376 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.33 % Allowed : 6.23 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3031 helix: 1.56 (0.20), residues: 677 sheet: 0.01 (0.19), residues: 639 loop : -0.98 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.032 0.001 TYR C 904 PHE 0.017 0.001 PHE A 133 TRP 0.009 0.001 TRP A 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00383 (25381) covalent geometry : angle 0.58540 (34546) SS BOND : bond 0.00236 ( 38) SS BOND : angle 0.78504 ( 76) hydrogen bonds : bond 0.04326 ( 970) hydrogen bonds : angle 5.82697 ( 2732) link_BETA1-4 : bond 0.01559 ( 11) link_BETA1-4 : angle 4.94175 ( 33) link_NAG-ASN : bond 0.00293 ( 40) link_NAG-ASN : angle 1.89296 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.8993 (ttm) cc_final: 0.8394 (ttm) REVERT: A 904 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: A 1019 ARG cc_start: 0.9289 (ttt90) cc_final: 0.8942 (ttp-110) REVERT: B 62 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9017 (p) REVERT: B 697 MET cc_start: 0.8514 (ptm) cc_final: 0.8223 (ptm) REVERT: C 196 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8123 (m-40) REVERT: C 571 ASP cc_start: 0.8585 (m-30) cc_final: 0.8206 (t0) REVERT: C 740 MET cc_start: 0.9095 (tpp) cc_final: 0.8766 (tpp) outliers start: 9 outliers final: 4 residues processed: 44 average time/residue: 0.1557 time to fit residues: 12.4430 Evaluate side-chains 39 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 261 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 284 optimal weight: 0.1980 chunk 155 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 235 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 207 HIS C 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.052091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.035684 restraints weight = 166724.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.036924 restraints weight = 82689.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.037715 restraints weight = 53311.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.038252 restraints weight = 40130.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.038574 restraints weight = 33166.048| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25470 Z= 0.133 Angle : 0.569 10.944 34775 Z= 0.279 Chirality : 0.044 0.242 4084 Planarity : 0.004 0.050 4388 Dihedral : 6.369 89.128 4376 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.37 % Allowed : 7.04 % Favored : 92.59 % 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: -0.09 (0.15), residues: 3031 helix: 1.67 (0.20), residues: 683 sheet: 0.05 (0.19), residues: 654 loop : -0.83 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.029 0.001 TYR C 904 PHE 0.015 0.001 PHE A 133 TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00286 (25381) covalent geometry : angle 0.53881 (34546) SS BOND : bond 0.00194 ( 38) SS BOND : angle 0.65334 ( 76) hydrogen bonds : bond 0.03936 ( 970) hydrogen bonds : angle 5.55963 ( 2732) link_BETA1-4 : bond 0.01527 ( 11) link_BETA1-4 : angle 4.96225 ( 33) link_NAG-ASN : bond 0.00225 ( 40) link_NAG-ASN : angle 1.80461 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.710 Fit side-chains REVERT: A 740 MET cc_start: 0.9072 (ttm) cc_final: 0.8808 (ttm) REVERT: A 904 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: A 1019 ARG cc_start: 0.9314 (ttt90) cc_final: 0.8936 (ttp-110) REVERT: B 62 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9152 (p) REVERT: B 697 MET cc_start: 0.8451 (ptm) cc_final: 0.8126 (ptm) REVERT: C 740 MET cc_start: 0.9177 (tpp) cc_final: 0.8763 (tpp) outliers start: 10 outliers final: 3 residues processed: 41 average time/residue: 0.1485 time to fit residues: 11.2400 Evaluate side-chains 33 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 85 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 235 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 207 HIS B1142 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.051097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.034388 restraints weight = 184876.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.035584 restraints weight = 90917.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036361 restraints weight = 58654.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.036880 restraints weight = 44229.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.037201 restraints weight = 36670.598| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 25470 Z= 0.281 Angle : 0.696 10.138 34775 Z= 0.340 Chirality : 0.045 0.236 4084 Planarity : 0.004 0.048 4388 Dihedral : 6.631 87.347 4376 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.78 % Allowed : 8.34 % Favored : 90.88 % 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: -0.23 (0.15), residues: 3031 helix: 1.37 (0.20), residues: 680 sheet: 0.11 (0.19), residues: 625 loop : -0.89 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1107 TYR 0.031 0.002 TYR C 904 PHE 0.015 0.002 PHE A 329 TRP 0.013 0.002 TRP B 886 HIS 0.005 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00608 (25381) covalent geometry : angle 0.66852 (34546) SS BOND : bond 0.00327 ( 38) SS BOND : angle 0.96704 ( 76) hydrogen bonds : bond 0.04313 ( 970) hydrogen bonds : angle 5.68687 ( 2732) link_BETA1-4 : bond 0.01301 ( 11) link_BETA1-4 : angle 5.08526 ( 33) link_NAG-ASN : bond 0.00453 ( 40) link_NAG-ASN : angle 1.99425 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 28 time to evaluate : 0.994 Fit side-chains REVERT: A 904 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: A 1019 ARG cc_start: 0.9276 (ttt90) cc_final: 0.8992 (ttp-110) REVERT: B 425 LEU cc_start: 0.5732 (OUTLIER) cc_final: 0.5359 (pp) REVERT: B 697 MET cc_start: 0.8380 (ptm) cc_final: 0.8009 (ptm) REVERT: C 581 THR cc_start: 0.9562 (OUTLIER) cc_final: 0.9346 (p) REVERT: C 740 MET cc_start: 0.9171 (tpp) cc_final: 0.8803 (tpp) outliers start: 21 outliers final: 10 residues processed: 47 average time/residue: 0.1554 time to fit residues: 13.0591 Evaluate side-chains 41 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 246 optimal weight: 0.7980 chunk 252 optimal weight: 9.9990 chunk 108 optimal weight: 0.1980 chunk 249 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 279 optimal weight: 0.8980 chunk 280 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.054416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.037018 restraints weight = 251256.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.038542 restraints weight = 102666.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.039520 restraints weight = 60659.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.040163 restraints weight = 43249.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.040562 restraints weight = 34699.223| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25470 Z= 0.103 Angle : 0.556 11.679 34775 Z= 0.270 Chirality : 0.044 0.248 4084 Planarity : 0.004 0.049 4388 Dihedral : 6.353 86.892 4376 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.52 % Allowed : 8.71 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3031 helix: 1.76 (0.21), residues: 675 sheet: 0.26 (0.20), residues: 627 loop : -0.73 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 509 TYR 0.026 0.001 TYR C 904 PHE 0.022 0.001 PHE C 374 TRP 0.016 0.001 TRP B 886 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00216 (25381) covalent geometry : angle 0.52578 (34546) SS BOND : bond 0.00175 ( 38) SS BOND : angle 0.64484 ( 76) hydrogen bonds : bond 0.03732 ( 970) hydrogen bonds : angle 5.28862 ( 2732) link_BETA1-4 : bond 0.01636 ( 11) link_BETA1-4 : angle 4.97073 ( 33) link_NAG-ASN : bond 0.00236 ( 40) link_NAG-ASN : angle 1.69140 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.954 Fit side-chains REVERT: A 900 MET cc_start: 0.8506 (mtt) cc_final: 0.8277 (mtt) REVERT: A 904 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: A 1019 ARG cc_start: 0.9269 (ttt90) cc_final: 0.9054 (ttp-110) REVERT: B 62 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9138 (p) REVERT: B 425 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5383 (pp) REVERT: B 697 MET cc_start: 0.8371 (ptm) cc_final: 0.8112 (ptm) REVERT: B 985 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.9047 (t70) REVERT: C 740 MET cc_start: 0.9159 (tpp) cc_final: 0.8719 (tpp) outliers start: 14 outliers final: 7 residues processed: 45 average time/residue: 0.1598 time to fit residues: 12.8402 Evaluate side-chains 40 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 257 optimal weight: 0.0770 chunk 77 optimal weight: 0.0870 chunk 220 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 270 optimal weight: 0.1980 chunk 259 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.052602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.035803 restraints weight = 220425.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.037250 restraints weight = 95486.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038174 restraints weight = 57488.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038797 restraints weight = 41370.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039184 restraints weight = 33173.567| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25470 Z= 0.094 Angle : 0.538 11.658 34775 Z= 0.259 Chirality : 0.043 0.240 4084 Planarity : 0.004 0.049 4388 Dihedral : 6.114 85.590 4376 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.52 % Allowed : 8.93 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.16), residues: 3031 helix: 1.87 (0.21), residues: 676 sheet: 0.49 (0.20), residues: 615 loop : -0.62 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1107 TYR 0.025 0.001 TYR C 904 PHE 0.013 0.001 PHE A 392 TRP 0.015 0.001 TRP B 886 HIS 0.003 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00201 (25381) covalent geometry : angle 0.50840 (34546) SS BOND : bond 0.00202 ( 38) SS BOND : angle 0.68004 ( 76) hydrogen bonds : bond 0.03449 ( 970) hydrogen bonds : angle 5.08417 ( 2732) link_BETA1-4 : bond 0.01613 ( 11) link_BETA1-4 : angle 4.85083 ( 33) link_NAG-ASN : bond 0.00202 ( 40) link_NAG-ASN : angle 1.61741 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.929 Fit side-chains REVERT: A 904 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: A 1019 ARG cc_start: 0.9321 (ttt90) cc_final: 0.9044 (ttp-110) REVERT: B 62 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9162 (p) REVERT: B 425 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5357 (pp) REVERT: B 697 MET cc_start: 0.8401 (ptm) cc_final: 0.8173 (ptm) REVERT: B 754 LEU cc_start: 0.9636 (mt) cc_final: 0.9427 (mt) REVERT: B 985 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.9005 (t70) REVERT: C 740 MET cc_start: 0.9212 (tpp) cc_final: 0.8704 (tpp) outliers start: 14 outliers final: 9 residues processed: 48 average time/residue: 0.1697 time to fit residues: 14.0442 Evaluate side-chains 41 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 203 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.051412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.034676 restraints weight = 181622.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.035921 restraints weight = 87560.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.036724 restraints weight = 55986.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.037239 restraints weight = 41916.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.037589 restraints weight = 34818.412| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25470 Z= 0.200 Angle : 0.599 10.780 34775 Z= 0.291 Chirality : 0.043 0.237 4084 Planarity : 0.004 0.046 4388 Dihedral : 6.227 84.804 4376 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.78 % Allowed : 8.82 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.16), residues: 3031 helix: 1.76 (0.21), residues: 681 sheet: 0.44 (0.20), residues: 618 loop : -0.65 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1107 TYR 0.025 0.001 TYR C 904 PHE 0.013 0.001 PHE A 133 TRP 0.025 0.001 TRP B 886 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00433 (25381) covalent geometry : angle 0.57118 (34546) SS BOND : bond 0.00314 ( 38) SS BOND : angle 0.83794 ( 76) hydrogen bonds : bond 0.03736 ( 970) hydrogen bonds : angle 5.19731 ( 2732) link_BETA1-4 : bond 0.01397 ( 11) link_BETA1-4 : angle 4.91039 ( 33) link_NAG-ASN : bond 0.00277 ( 40) link_NAG-ASN : angle 1.72568 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.954 Fit side-chains REVERT: A 904 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: A 1019 ARG cc_start: 0.9284 (ttt90) cc_final: 0.9064 (ttp-110) REVERT: B 62 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9089 (p) REVERT: B 425 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5400 (pp) REVERT: B 697 MET cc_start: 0.8472 (ptm) cc_final: 0.8120 (ptm) REVERT: B 985 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.9038 (t70) REVERT: C 571 ASP cc_start: 0.8281 (m-30) cc_final: 0.7974 (t0) REVERT: C 641 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8518 (p0) REVERT: C 740 MET cc_start: 0.9139 (tpp) cc_final: 0.8756 (tpp) REVERT: C 957 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8677 (tm-30) outliers start: 21 outliers final: 12 residues processed: 52 average time/residue: 0.1536 time to fit residues: 14.3696 Evaluate side-chains 48 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 36 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 957 GLN C 196 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.051366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.034343 restraints weight = 216033.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.035689 restraints weight = 98569.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036547 restraints weight = 61135.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.037115 restraints weight = 45008.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.037475 restraints weight = 36783.439| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25470 Z= 0.183 Angle : 0.589 11.020 34775 Z= 0.285 Chirality : 0.043 0.234 4084 Planarity : 0.004 0.046 4388 Dihedral : 6.336 84.440 4376 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.89 % Allowed : 8.86 % Favored : 90.25 % 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: 0.17 (0.16), residues: 3031 helix: 1.76 (0.21), residues: 670 sheet: 0.41 (0.20), residues: 618 loop : -0.66 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.024 0.001 TYR C 904 PHE 0.012 0.001 PHE A 329 TRP 0.026 0.001 TRP B 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00397 (25381) covalent geometry : angle 0.56073 (34546) SS BOND : bond 0.00213 ( 38) SS BOND : angle 0.70817 ( 76) hydrogen bonds : bond 0.03749 ( 970) hydrogen bonds : angle 5.20119 ( 2732) link_BETA1-4 : bond 0.01454 ( 11) link_BETA1-4 : angle 4.97863 ( 33) link_NAG-ASN : bond 0.00260 ( 40) link_NAG-ASN : angle 1.70607 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.767 Fit side-chains REVERT: A 904 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: A 1019 ARG cc_start: 0.9311 (ttt90) cc_final: 0.9051 (ttp-110) REVERT: B 62 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9124 (p) REVERT: B 425 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5437 (pp) REVERT: B 697 MET cc_start: 0.8394 (ptm) cc_final: 0.7971 (ptm) REVERT: B 869 MET cc_start: 0.9230 (pmm) cc_final: 0.9000 (pmm) REVERT: B 957 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9161 (tp40) REVERT: B 985 ASP cc_start: 0.9273 (OUTLIER) cc_final: 0.9063 (t70) REVERT: C 571 ASP cc_start: 0.8372 (m-30) cc_final: 0.8075 (t0) REVERT: C 641 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8517 (p0) REVERT: C 740 MET cc_start: 0.9206 (tpp) cc_final: 0.8780 (tpp) REVERT: C 957 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8732 (tm-30) outliers start: 24 outliers final: 12 residues processed: 54 average time/residue: 0.1393 time to fit residues: 13.5000 Evaluate side-chains 49 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 275 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 302 optimal weight: 0.8980 chunk 262 optimal weight: 0.3980 chunk 251 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.054628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.037346 restraints weight = 190814.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.038723 restraints weight = 88420.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.039604 restraints weight = 55225.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.040187 restraints weight = 40784.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.040555 restraints weight = 33458.494| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25470 Z= 0.099 Angle : 0.541 11.546 34775 Z= 0.262 Chirality : 0.043 0.238 4084 Planarity : 0.004 0.048 4388 Dihedral : 6.199 84.045 4376 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.56 % Allowed : 9.30 % Favored : 90.14 % 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: 0.30 (0.16), residues: 3031 helix: 1.90 (0.21), residues: 670 sheet: 0.46 (0.20), residues: 624 loop : -0.57 (0.16), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.025 0.001 TYR C 904 PHE 0.041 0.001 PHE B 220 TRP 0.028 0.001 TRP B 886 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00210 (25381) covalent geometry : angle 0.51156 (34546) SS BOND : bond 0.00149 ( 38) SS BOND : angle 0.63744 ( 76) hydrogen bonds : bond 0.03548 ( 970) hydrogen bonds : angle 5.04973 ( 2732) link_BETA1-4 : bond 0.01620 ( 11) link_BETA1-4 : angle 4.91398 ( 33) link_NAG-ASN : bond 0.00204 ( 40) link_NAG-ASN : angle 1.59841 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.964 Fit side-chains REVERT: A 869 MET cc_start: 0.9135 (mtm) cc_final: 0.8885 (ptt) REVERT: A 904 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: B 62 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.9135 (p) REVERT: B 425 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5359 (pp) REVERT: B 697 MET cc_start: 0.8369 (ptm) cc_final: 0.8117 (ptm) REVERT: B 869 MET cc_start: 0.9234 (pmm) cc_final: 0.8992 (pmm) REVERT: B 985 ASP cc_start: 0.9235 (OUTLIER) cc_final: 0.9017 (t70) REVERT: C 571 ASP cc_start: 0.8323 (m-30) cc_final: 0.8039 (t0) REVERT: C 740 MET cc_start: 0.9115 (tpp) cc_final: 0.8678 (tpp) REVERT: C 957 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8610 (tm-30) outliers start: 15 outliers final: 10 residues processed: 46 average time/residue: 0.1473 time to fit residues: 12.1070 Evaluate side-chains 44 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 168 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 251 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 235 optimal weight: 0.3980 chunk 212 optimal weight: 0.0980 chunk 230 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.052857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.035979 restraints weight = 223899.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037412 restraints weight = 97642.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.038331 restraints weight = 59059.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.038933 restraints weight = 42636.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.039327 restraints weight = 34439.788| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25470 Z= 0.094 Angle : 0.529 11.716 34775 Z= 0.254 Chirality : 0.043 0.236 4084 Planarity : 0.004 0.048 4388 Dihedral : 6.028 82.877 4376 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.63 % Allowed : 9.27 % Favored : 90.10 % 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 (0.16), residues: 3031 helix: 2.08 (0.21), residues: 670 sheet: 0.57 (0.20), residues: 625 loop : -0.49 (0.16), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.025 0.001 TYR C 904 PHE 0.031 0.001 PHE B 220 TRP 0.022 0.001 TRP B 886 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00199 (25381) covalent geometry : angle 0.49980 (34546) SS BOND : bond 0.00148 ( 38) SS BOND : angle 0.60996 ( 76) hydrogen bonds : bond 0.03355 ( 970) hydrogen bonds : angle 4.91805 ( 2732) link_BETA1-4 : bond 0.01608 ( 11) link_BETA1-4 : angle 4.81834 ( 33) link_NAG-ASN : bond 0.00184 ( 40) link_NAG-ASN : angle 1.55343 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4705.52 seconds wall clock time: 81 minutes 45.73 seconds (4905.73 seconds total)