Starting phenix.real_space_refine on Sun Jul 5 08:48:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s6i_24876/07_2026/7s6i_24876.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s6i_24876/07_2026/7s6i_24876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s6i_24876/07_2026/7s6i_24876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s6i_24876/07_2026/7s6i_24876.map" model { file = "/net/cci-nas-00/data/ceres_data/7s6i_24876/07_2026/7s6i_24876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s6i_24876/07_2026/7s6i_24876.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s6i_24876/07_2026/7s6i_24876.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s6i_24876/07_2026/7s6i_24876.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 126 5.16 5 C 17013 2.51 5 N 4383 2.21 5 O 5250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26772 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8616 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 57, 'TRANS': 1045} Chain breaks: 3 Chain: "B" Number of atoms: 8616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8616 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 57, 'TRANS': 1045} Chain breaks: 3 Chain: "C" Number of atoms: 8616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8616 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 57, 'TRANS': 1045} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 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 chiralities: 10 Chain: "C" 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 chiralities: 10 Time building chain proxies: 6.14, per 1000 atoms: 0.23 Number of scatterers: 26772 At special positions: 0 Unit cell: (150.65, 146.05, 179.4, 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 126 16.00 O 5250 8.00 N 4383 7.00 C 17013 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.08 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.15 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.09 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.08 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.15 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.08 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.15 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 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=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.08 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.08 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.09 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=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.08 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 17 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 149 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 17 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 149 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 17 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 149 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN B 234 " " NAG L 1 " - " ASN B 616 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 616 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 51 sheets defined 25.3% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.919A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.878A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.245A 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 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.693A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 843 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.502A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.120A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.160A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.919A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.879A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.246A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.693A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.503A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.120A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.159A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.919A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.878A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.246A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.693A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.503A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.120A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.160A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.733A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.665A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.355A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.162A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.448A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.504A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.427A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.534A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.471A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.997A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.596A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.509A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.734A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.355A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.162A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.449A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.505A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.427A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.534A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.470A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.997A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.596A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.508A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.734A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.355A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.162A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.449A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.427A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.535A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.997A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.596A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.510A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1097 hydrogen bonds defined for protein. 2967 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: 7.31 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5522 1.32 - 1.46: 9866 1.46 - 1.60: 11822 1.60 - 1.75: 33 1.75 - 1.89: 141 Bond restraints: 27384 Sorted by residual: bond pdb=" CB ILE C 312 " pdb=" CG1 ILE C 312 " ideal model delta sigma weight residual 1.530 1.421 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CB ILE A 312 " pdb=" CG1 ILE A 312 " ideal model delta sigma weight residual 1.530 1.421 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" CB ILE B 312 " pdb=" CG1 ILE B 312 " ideal model delta sigma weight residual 1.530 1.421 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" CB HIS B1058 " pdb=" CG HIS B1058 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" CB HIS A1058 " pdb=" CG HIS A1058 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.77e+01 ... (remaining 27379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 32050 2.42 - 4.83: 4555 4.83 - 7.25: 591 7.25 - 9.67: 73 9.67 - 12.08: 12 Bond angle restraints: 37281 Sorted by residual: angle pdb=" C LYS B 811 " pdb=" N PRO B 812 " pdb=" CA PRO B 812 " ideal model delta sigma weight residual 119.56 127.66 -8.10 1.02e+00 9.61e-01 6.30e+01 angle pdb=" C PRO C 862 " pdb=" N PRO C 863 " pdb=" CA PRO C 863 " ideal model delta sigma weight residual 120.03 127.87 -7.84 9.90e-01 1.02e+00 6.27e+01 angle pdb=" C LYS C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta sigma weight residual 119.56 127.63 -8.07 1.02e+00 9.61e-01 6.26e+01 angle pdb=" C PRO B 862 " pdb=" N PRO B 863 " pdb=" CA PRO B 863 " ideal model delta sigma weight residual 120.03 127.86 -7.83 9.90e-01 1.02e+00 6.26e+01 angle pdb=" C LYS A 811 " pdb=" N PRO A 812 " pdb=" CA PRO A 812 " ideal model delta sigma weight residual 119.56 127.61 -8.05 1.02e+00 9.61e-01 6.23e+01 ... (remaining 37276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 15269 17.77 - 35.53: 367 35.53 - 53.30: 105 53.30 - 71.06: 42 71.06 - 88.83: 24 Dihedral angle restraints: 15807 sinusoidal: 6177 harmonic: 9630 Sorted by residual: dihedral pdb=" N PHE A 898 " pdb=" C PHE A 898 " pdb=" CA PHE A 898 " pdb=" CB PHE A 898 " ideal model delta harmonic sigma weight residual 122.80 130.62 -7.82 0 2.50e+00 1.60e-01 9.77e+00 dihedral pdb=" N PHE B 898 " pdb=" C PHE B 898 " pdb=" CA PHE B 898 " pdb=" CB PHE B 898 " ideal model delta harmonic sigma weight residual 122.80 130.59 -7.79 0 2.50e+00 1.60e-01 9.72e+00 dihedral pdb=" N PHE C 898 " pdb=" C PHE C 898 " pdb=" CA PHE C 898 " pdb=" CB PHE C 898 " ideal model delta harmonic sigma weight residual 122.80 130.57 -7.77 0 2.50e+00 1.60e-01 9.65e+00 ... (remaining 15804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3068 0.104 - 0.208: 983 0.208 - 0.312: 205 0.312 - 0.417: 89 0.417 - 0.521: 56 Chirality restraints: 4401 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 ... (remaining 4398 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 17 " 0.066 2.00e-02 2.50e+03 7.01e-02 6.15e+01 pdb=" CG ASN B 17 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 17 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 17 " -0.110 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 17 " 0.066 2.00e-02 2.50e+03 7.01e-02 6.13e+01 pdb=" CG ASN C 17 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 17 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 17 " -0.110 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " -0.066 2.00e-02 2.50e+03 6.99e-02 6.11e+01 pdb=" CG ASN A 17 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " 0.110 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.085 2.00e-02 2.50e+03 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 10841 2.90 - 3.40: 24286 3.40 - 3.90: 45386 3.90 - 4.40: 53646 4.40 - 4.90: 86360 Nonbonded interactions: 220519 Sorted by model distance: nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.394 2.496 nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.395 2.496 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.395 2.496 nonbonded pdb=" OE1 GLU C 340 " pdb=" NZ LYS C 356 " model vdw 2.415 3.120 nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.415 3.120 ... (remaining 220514 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.670 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.022 0.146 27498 Z= 1.160 Angle : 1.749 12.084 37575 Z= 1.167 Chirality : 0.124 0.521 4401 Planarity : 0.008 0.049 4749 Dihedral : 10.136 88.826 9477 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.13), residues: 3285 helix: -0.36 (0.17), residues: 777 sheet: 1.39 (0.19), residues: 699 loop : 0.11 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1000 TYR 0.063 0.009 TYR B 837 PHE 0.038 0.005 PHE B 58 TRP 0.042 0.009 TRP A 886 HIS 0.009 0.002 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.02185 / 1.14 (27384) covalent geometry : angle 1.73437 / 1.17 (37281) SS BOND : bond 0.03911 / 2.68 ( 48) SS BOND : angle 2.24926 / 1.52 ( 96) hydrogen bonds : bond 0.16346 / 10.74 ( 1079) hydrogen bonds : angle 7.98530 / 5.51 ( 2967) link_BETA1-4 : bond 0.07288 / 4.99 ( 18) link_BETA1-4 : angle 4.97870 / 3.33 ( 54) link_NAG-ASN : bond 0.07918 / 5.23 ( 48) link_NAG-ASN : angle 2.60099 / 1.74 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 369 time to evaluate : 1.077 Fit side-chains REVERT: B 900 MET cc_start: 0.8617 (mtp) cc_final: 0.8377 (mtm) outliers start: 3 outliers final: 0 residues processed: 372 average time/residue: 0.2080 time to fit residues: 117.3852 Evaluate side-chains 132 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN C 354 ASN C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094959 restraints weight = 50217.852| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.49 r_work: 0.3197 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27498 Z= 0.174 Angle : 0.710 11.082 37575 Z= 0.365 Chirality : 0.048 0.248 4401 Planarity : 0.004 0.032 4749 Dihedral : 5.197 23.225 3558 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.83 % Allowed : 4.12 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3285 helix: 1.08 (0.19), residues: 777 sheet: 0.88 (0.19), residues: 690 loop : -0.19 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 905 TYR 0.021 0.002 TYR B1067 PHE 0.017 0.002 PHE A 55 TRP 0.022 0.002 TRP C 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (27384) covalent geometry : angle 0.67671 / 0.36 (37281) SS BOND : bond 0.00674 / 0.47 ( 48) SS BOND : angle 1.67697 / 1.06 ( 96) hydrogen bonds : bond 0.05793 / 3.84 ( 1079) hydrogen bonds : angle 6.29033 / 4.34 ( 2967) link_BETA1-4 : bond 0.00756 / 0.48 ( 18) link_BETA1-4 : angle 3.06359 / 2.12 ( 54) link_NAG-ASN : bond 0.00492 / 0.37 ( 48) link_NAG-ASN : angle 2.73313 / 1.84 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.106 Fit side-chains REVERT: A 111 ASP cc_start: 0.7535 (p0) cc_final: 0.7105 (t70) REVERT: A 241 LEU cc_start: 0.8243 (mt) cc_final: 0.7916 (mp) REVERT: B 241 LEU cc_start: 0.8154 (mt) cc_final: 0.7732 (mp) REVERT: B 281 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: B 390 LEU cc_start: 0.8877 (mt) cc_final: 0.8664 (mt) REVERT: B 405 ASP cc_start: 0.8950 (m-30) cc_final: 0.8716 (m-30) REVERT: B 994 ASP cc_start: 0.8675 (t0) cc_final: 0.8357 (t0) REVERT: C 111 ASP cc_start: 0.7474 (p0) cc_final: 0.7081 (t70) REVERT: C 434 ILE cc_start: 0.9047 (tt) cc_final: 0.8747 (mt) REVERT: C 556 ASN cc_start: 0.8491 (t0) cc_final: 0.8259 (t0) REVERT: C 988 GLU cc_start: 0.8508 (tp30) cc_final: 0.8101 (tp30) REVERT: C 994 ASP cc_start: 0.8579 (t70) cc_final: 0.8291 (t70) outliers start: 24 outliers final: 10 residues processed: 212 average time/residue: 0.1595 time to fit residues: 55.9001 Evaluate side-chains 155 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 828 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 235 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 chunk 313 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN A1048 HIS C1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.084776 restraints weight = 47702.590| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.35 r_work: 0.3038 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27498 Z= 0.165 Angle : 0.626 9.959 37575 Z= 0.316 Chirality : 0.047 0.558 4401 Planarity : 0.004 0.033 4749 Dihedral : 4.863 20.895 3558 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.31 % Favored : 97.60 % Rotamer: Outliers : 0.97 % Allowed : 4.95 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3285 helix: 1.35 (0.20), residues: 759 sheet: 0.61 (0.19), residues: 696 loop : -0.43 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 905 TYR 0.019 0.001 TYR A 248 PHE 0.015 0.002 PHE B 55 TRP 0.017 0.001 TRP A 886 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (27384) covalent geometry : angle 0.59511 / 0.31 (37281) SS BOND : bond 0.00322 / 0.22 ( 48) SS BOND : angle 1.49194 / 0.93 ( 96) hydrogen bonds : bond 0.04921 / 3.25 ( 1079) hydrogen bonds : angle 5.89420 / 4.06 ( 2967) link_BETA1-4 : bond 0.00582 / 0.38 ( 18) link_BETA1-4 : angle 2.32743 / 1.59 ( 54) link_NAG-ASN : bond 0.00606 / 0.45 ( 48) link_NAG-ASN : angle 2.66511 / 1.81 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.028 Fit side-chains REVERT: A 111 ASP cc_start: 0.7569 (p0) cc_final: 0.7075 (t70) REVERT: A 241 LEU cc_start: 0.8499 (mt) cc_final: 0.8193 (mp) REVERT: A 773 GLU cc_start: 0.8844 (tt0) cc_final: 0.8617 (tt0) REVERT: A 1029 MET cc_start: 0.9266 (tpp) cc_final: 0.8947 (ttm) REVERT: B 988 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8193 (mp0) REVERT: B 994 ASP cc_start: 0.8627 (t0) cc_final: 0.8322 (t0) REVERT: C 40 ASP cc_start: 0.8199 (m-30) cc_final: 0.7986 (m-30) REVERT: C 111 ASP cc_start: 0.7498 (p0) cc_final: 0.7019 (t70) REVERT: C 212 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7746 (mt) REVERT: C 434 ILE cc_start: 0.9006 (tt) cc_final: 0.8753 (mt) REVERT: C 487 ASN cc_start: 0.7423 (m-40) cc_final: 0.7130 (m110) REVERT: C 988 GLU cc_start: 0.8427 (tp30) cc_final: 0.8076 (tp30) REVERT: C 994 ASP cc_start: 0.8491 (t70) cc_final: 0.8244 (t70) outliers start: 28 outliers final: 15 residues processed: 181 average time/residue: 0.1571 time to fit residues: 48.3716 Evaluate side-chains 159 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 74 optimal weight: 0.1980 chunk 186 optimal weight: 0.0570 chunk 108 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 159 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 289 optimal weight: 0.0030 chunk 125 optimal weight: 0.4980 overall best weight: 0.1646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN B 556 ASN B1048 HIS C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.110641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.092103 restraints weight = 50144.421| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.51 r_work: 0.3177 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27498 Z= 0.101 Angle : 0.562 9.716 37575 Z= 0.280 Chirality : 0.046 0.571 4401 Planarity : 0.004 0.044 4749 Dihedral : 4.562 23.132 3558 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.78 % Rotamer: Outliers : 0.93 % Allowed : 5.78 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3285 helix: 1.58 (0.20), residues: 759 sheet: 0.59 (0.19), residues: 705 loop : -0.50 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 905 TYR 0.017 0.001 TYR A 200 PHE 0.012 0.001 PHE B 55 TRP 0.029 0.001 TRP A 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (27384) covalent geometry : angle 0.53227 / 0.27 (37281) SS BOND : bond 0.00226 / 0.15 ( 48) SS BOND : angle 1.21295 / 0.88 ( 96) hydrogen bonds : bond 0.03982 / 2.64 ( 1079) hydrogen bonds : angle 5.60324 / 3.86 ( 2967) link_BETA1-4 : bond 0.00537 / 0.36 ( 18) link_BETA1-4 : angle 2.04220 / 1.39 ( 54) link_NAG-ASN : bond 0.00526 / 0.38 ( 48) link_NAG-ASN : angle 2.54496 / 1.82 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.011 Fit side-chains REVERT: A 111 ASP cc_start: 0.7383 (p0) cc_final: 0.6935 (t70) REVERT: A 994 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8087 (t0) REVERT: A 1029 MET cc_start: 0.9203 (tpp) cc_final: 0.8871 (ttm) REVERT: B 1119 ASN cc_start: 0.8105 (m-40) cc_final: 0.7869 (m-40) REVERT: C 40 ASP cc_start: 0.8204 (m-30) cc_final: 0.7993 (m-30) REVERT: C 111 ASP cc_start: 0.7376 (p0) cc_final: 0.6898 (t70) REVERT: C 212 LEU cc_start: 0.8072 (mp) cc_final: 0.7860 (tp) REVERT: C 487 ASN cc_start: 0.7814 (m-40) cc_final: 0.7315 (m110) REVERT: C 556 ASN cc_start: 0.8428 (t0) cc_final: 0.8215 (t0) REVERT: C 745 ASP cc_start: 0.7197 (m-30) cc_final: 0.6981 (m-30) REVERT: C 773 GLU cc_start: 0.8827 (tt0) cc_final: 0.8546 (tt0) outliers start: 27 outliers final: 13 residues processed: 183 average time/residue: 0.1586 time to fit residues: 48.8767 Evaluate side-chains 146 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 205 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 0.1980 chunk 293 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN B 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.086994 restraints weight = 48786.954| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.47 r_work: 0.3111 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27498 Z= 0.195 Angle : 0.625 13.130 37575 Z= 0.309 Chirality : 0.047 0.294 4401 Planarity : 0.004 0.037 4749 Dihedral : 4.669 19.146 3558 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.05 % Rotamer: Outliers : 1.38 % Allowed : 5.50 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3285 helix: 1.47 (0.19), residues: 762 sheet: 0.42 (0.19), residues: 675 loop : -0.62 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 905 TYR 0.019 0.002 TYR A1067 PHE 0.017 0.002 PHE B 898 TRP 0.015 0.001 TRP B 886 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (27384) covalent geometry : angle 0.59985 / 0.30 (37281) SS BOND : bond 0.00337 / 0.23 ( 48) SS BOND : angle 1.27415 / 0.83 ( 96) hydrogen bonds : bond 0.04631 / 3.06 ( 1079) hydrogen bonds : angle 5.64504 / 3.89 ( 2967) link_BETA1-4 : bond 0.00450 / 0.29 ( 18) link_BETA1-4 : angle 1.85960 / 1.25 ( 54) link_NAG-ASN : bond 0.00467 / 0.34 ( 48) link_NAG-ASN : angle 2.50183 / 1.66 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.965 Fit side-chains REVERT: A 78 ARG cc_start: 0.7636 (ttt180) cc_final: 0.7297 (ttt90) REVERT: A 111 ASP cc_start: 0.7607 (p0) cc_final: 0.7076 (t70) REVERT: A 556 ASN cc_start: 0.8581 (t0) cc_final: 0.8357 (t0) REVERT: C 111 ASP cc_start: 0.7493 (p0) cc_final: 0.7009 (t70) REVERT: C 212 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8042 (tp) REVERT: C 556 ASN cc_start: 0.8544 (t0) cc_final: 0.8320 (t0) REVERT: C 773 GLU cc_start: 0.8880 (tt0) cc_final: 0.8559 (tt0) REVERT: C 988 GLU cc_start: 0.7836 (mp0) cc_final: 0.7472 (mp0) outliers start: 40 outliers final: 30 residues processed: 172 average time/residue: 0.1365 time to fit residues: 41.2341 Evaluate side-chains 160 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 303 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 160 optimal weight: 0.3980 chunk 324 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 556 ASN C 487 ASN C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.087031 restraints weight = 49070.442| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.43 r_work: 0.3079 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 27498 Z= 0.241 Angle : 0.673 15.739 37575 Z= 0.327 Chirality : 0.049 0.569 4401 Planarity : 0.004 0.041 4749 Dihedral : 4.889 28.201 3558 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 1.35 % Allowed : 6.02 % Favored : 92.63 % 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: -0.14 (0.14), residues: 3285 helix: 1.35 (0.19), residues: 759 sheet: 0.24 (0.19), residues: 690 loop : -0.85 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 357 TYR 0.019 0.002 TYR A1067 PHE 0.016 0.002 PHE B 238 TRP 0.019 0.001 TRP B 886 HIS 0.006 0.002 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 (27384) covalent geometry : angle 0.64280 / 0.32 (37281) SS BOND : bond 0.00349 / 0.24 ( 48) SS BOND : angle 1.28119 / 0.82 ( 96) hydrogen bonds : bond 0.04840 / 3.19 ( 1079) hydrogen bonds : angle 5.70501 / 3.93 ( 2967) link_BETA1-4 : bond 0.00398 / 0.25 ( 18) link_BETA1-4 : angle 1.78565 / 1.20 ( 54) link_NAG-ASN : bond 0.00542 / 0.40 ( 48) link_NAG-ASN : angle 2.96282 / 2.14 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.918 Fit side-chains REVERT: A 111 ASP cc_start: 0.7715 (p0) cc_final: 0.7194 (t70) REVERT: A 556 ASN cc_start: 0.8574 (t0) cc_final: 0.8349 (t0) REVERT: A 1029 MET cc_start: 0.9333 (tpp) cc_final: 0.8723 (ttm) REVERT: B 556 ASN cc_start: 0.8629 (t0) cc_final: 0.8400 (t0) REVERT: B 823 PHE cc_start: 0.8525 (t80) cc_final: 0.8291 (t80) REVERT: C 111 ASP cc_start: 0.7617 (p0) cc_final: 0.7169 (t70) REVERT: C 212 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8157 (tp) REVERT: C 487 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7306 (m-40) REVERT: C 556 ASN cc_start: 0.8566 (t0) cc_final: 0.8357 (t0) REVERT: C 773 GLU cc_start: 0.8961 (tt0) cc_final: 0.8662 (tt0) REVERT: C 994 ASP cc_start: 0.8597 (t70) cc_final: 0.8389 (t70) outliers start: 39 outliers final: 29 residues processed: 172 average time/residue: 0.1500 time to fit residues: 43.6926 Evaluate side-chains 167 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 262 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 264 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.090076 restraints weight = 48669.330| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.44 r_work: 0.3103 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27498 Z= 0.157 Angle : 0.598 14.591 37575 Z= 0.293 Chirality : 0.046 0.414 4401 Planarity : 0.004 0.038 4749 Dihedral : 4.631 19.914 3558 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 1.32 % Allowed : 6.54 % Favored : 92.14 % 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: -0.04 (0.14), residues: 3285 helix: 1.50 (0.20), residues: 759 sheet: 0.25 (0.19), residues: 711 loop : -0.81 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.018 0.001 TYR A1067 PHE 0.012 0.001 PHE A1121 TRP 0.023 0.001 TRP C 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (27384) covalent geometry : angle 0.57207 / 0.29 (37281) SS BOND : bond 0.00262 / 0.18 ( 48) SS BOND : angle 1.11967 / 0.71 ( 96) hydrogen bonds : bond 0.04343 / 2.87 ( 1079) hydrogen bonds : angle 5.55367 / 3.83 ( 2967) link_BETA1-4 : bond 0.00492 / 0.33 ( 18) link_BETA1-4 : angle 1.66487 / 1.11 ( 54) link_NAG-ASN : bond 0.00396 / 0.29 ( 48) link_NAG-ASN : angle 2.59755 / 1.76 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.989 Fit side-chains REVERT: A 111 ASP cc_start: 0.7675 (p0) cc_final: 0.7131 (t70) REVERT: A 556 ASN cc_start: 0.8541 (t0) cc_final: 0.8327 (t0) REVERT: A 1029 MET cc_start: 0.9320 (tpp) cc_final: 0.8678 (ttm) REVERT: B 556 ASN cc_start: 0.8574 (t0) cc_final: 0.8347 (t0) REVERT: B 823 PHE cc_start: 0.8527 (t80) cc_final: 0.8277 (t80) REVERT: C 111 ASP cc_start: 0.7622 (p0) cc_final: 0.7172 (t70) REVERT: C 212 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8175 (tp) REVERT: C 378 LYS cc_start: 0.8862 (mttt) cc_final: 0.8613 (mtpp) REVERT: C 556 ASN cc_start: 0.8522 (t0) cc_final: 0.8261 (t0) REVERT: C 773 GLU cc_start: 0.8868 (tt0) cc_final: 0.8562 (tt0) outliers start: 38 outliers final: 30 residues processed: 171 average time/residue: 0.1555 time to fit residues: 45.4597 Evaluate side-chains 166 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 302 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 226 optimal weight: 0.0270 chunk 228 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS B 901 GLN C 69 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085867 restraints weight = 50271.698| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.57 r_work: 0.3063 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27498 Z= 0.117 Angle : 0.554 12.206 37575 Z= 0.274 Chirality : 0.044 0.300 4401 Planarity : 0.004 0.038 4749 Dihedral : 4.381 19.575 3558 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 1.18 % Allowed : 6.72 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3285 helix: 1.66 (0.20), residues: 762 sheet: 0.33 (0.19), residues: 702 loop : -0.80 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.018 0.001 TYR A1067 PHE 0.013 0.001 PHE C 486 TRP 0.027 0.001 TRP C 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (27384) covalent geometry : angle 0.53137 / 0.27 (37281) SS BOND : bond 0.00225 / 0.15 ( 48) SS BOND : angle 0.98996 / 0.62 ( 96) hydrogen bonds : bond 0.03885 / 2.56 ( 1079) hydrogen bonds : angle 5.38355 / 3.71 ( 2967) link_BETA1-4 : bond 0.00464 / 0.30 ( 18) link_BETA1-4 : angle 1.55972 / 1.04 ( 54) link_NAG-ASN : bond 0.00334 / 0.24 ( 48) link_NAG-ASN : angle 2.34244 / 1.58 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.882 Fit side-chains REVERT: A 111 ASP cc_start: 0.7570 (p0) cc_final: 0.7051 (t70) REVERT: A 1029 MET cc_start: 0.9270 (tpp) cc_final: 0.8674 (ttm) REVERT: B 823 PHE cc_start: 0.8484 (t80) cc_final: 0.8250 (t80) REVERT: B 887 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8464 (p) REVERT: C 111 ASP cc_start: 0.7590 (p0) cc_final: 0.7113 (t70) REVERT: C 212 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8210 (tp) REVERT: C 556 ASN cc_start: 0.8447 (t0) cc_final: 0.8236 (t0) outliers start: 34 outliers final: 23 residues processed: 176 average time/residue: 0.1416 time to fit residues: 43.4759 Evaluate side-chains 158 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 176 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 133 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 306 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN A 779 GLN B 69 HIS B 556 ASN B 955 ASN C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091606 restraints weight = 51005.726| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.42 r_work: 0.3084 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27498 Z= 0.130 Angle : 0.563 12.327 37575 Z= 0.279 Chirality : 0.044 0.279 4401 Planarity : 0.004 0.040 4749 Dihedral : 4.350 17.916 3558 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 1.21 % Allowed : 7.10 % Favored : 91.69 % 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: 0.06 (0.14), residues: 3285 helix: 1.67 (0.20), residues: 762 sheet: 0.33 (0.19), residues: 693 loop : -0.78 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.018 0.001 TYR A1067 PHE 0.012 0.001 PHE C1121 TRP 0.025 0.001 TRP C 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (27384) covalent geometry : angle 0.54125 / 0.27 (37281) SS BOND : bond 0.00244 / 0.16 ( 48) SS BOND : angle 1.01079 / 0.63 ( 96) hydrogen bonds : bond 0.03952 / 2.60 ( 1079) hydrogen bonds : angle 5.34031 / 3.68 ( 2967) link_BETA1-4 : bond 0.00432 / 0.29 ( 18) link_BETA1-4 : angle 1.51148 / 1.01 ( 54) link_NAG-ASN : bond 0.00298 / 0.21 ( 48) link_NAG-ASN : angle 2.29051 / 1.53 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.107 Fit side-chains REVERT: A 111 ASP cc_start: 0.7558 (p0) cc_final: 0.7046 (t70) REVERT: A 994 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8068 (t0) REVERT: A 1029 MET cc_start: 0.9300 (tpp) cc_final: 0.8664 (ttm) REVERT: B 823 PHE cc_start: 0.8507 (t80) cc_final: 0.8261 (t80) REVERT: B 887 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8407 (p) REVERT: C 111 ASP cc_start: 0.7558 (p0) cc_final: 0.7121 (t70) REVERT: C 212 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8242 (tp) outliers start: 35 outliers final: 25 residues processed: 160 average time/residue: 0.1641 time to fit residues: 45.1096 Evaluate side-chains 163 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 32 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 153 optimal weight: 0.0670 chunk 48 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 chunk 291 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 298 optimal weight: 0.7980 chunk 268 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 556 ASN C 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.102831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.084425 restraints weight = 48500.731| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.50 r_work: 0.3072 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27498 Z= 0.101 Angle : 0.537 11.108 37575 Z= 0.268 Chirality : 0.044 0.257 4401 Planarity : 0.004 0.040 4749 Dihedral : 4.198 17.996 3558 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.71 % Favored : 97.20 % Rotamer: Outliers : 0.93 % Allowed : 7.37 % Favored : 91.69 % 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: 0.11 (0.14), residues: 3285 helix: 1.78 (0.20), residues: 762 sheet: 0.31 (0.19), residues: 717 loop : -0.77 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.017 0.001 TYR A1067 PHE 0.012 0.001 PHE A1121 TRP 0.030 0.001 TRP A 886 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (27384) covalent geometry : angle 0.51703 / 0.26 (37281) SS BOND : bond 0.00202 / 0.14 ( 48) SS BOND : angle 0.89496 / 0.55 ( 96) hydrogen bonds : bond 0.03623 / 2.39 ( 1079) hydrogen bonds : angle 5.21982 / 3.59 ( 2967) link_BETA1-4 : bond 0.00435 / 0.29 ( 18) link_BETA1-4 : angle 1.47544 / 0.98 ( 54) link_NAG-ASN : bond 0.00322 / 0.22 ( 48) link_NAG-ASN : angle 2.18715 / 1.47 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.061 Fit side-chains REVERT: A 111 ASP cc_start: 0.7416 (p0) cc_final: 0.6932 (t70) REVERT: A 994 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8003 (t0) REVERT: A 1029 MET cc_start: 0.9244 (tpp) cc_final: 0.8955 (ttm) REVERT: B 823 PHE cc_start: 0.8502 (t80) cc_final: 0.8275 (t80) REVERT: B 887 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8413 (p) REVERT: B 1119 ASN cc_start: 0.8243 (m-40) cc_final: 0.8008 (m-40) REVERT: C 111 ASP cc_start: 0.7477 (p0) cc_final: 0.7016 (t70) REVERT: C 212 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8154 (tp) outliers start: 27 outliers final: 19 residues processed: 159 average time/residue: 0.1595 time to fit residues: 43.7579 Evaluate side-chains 155 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 220 optimal weight: 7.9990 chunk 133 optimal weight: 0.0000 chunk 1 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 chunk 61 optimal weight: 0.5980 chunk 257 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 329 optimal weight: 8.9990 overall best weight: 0.7306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN A 955 ASN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088554 restraints weight = 49092.920| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.43 r_work: 0.3062 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27498 Z= 0.118 Angle : 0.544 10.894 37575 Z= 0.272 Chirality : 0.044 0.245 4401 Planarity : 0.004 0.038 4749 Dihedral : 4.187 17.636 3558 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 0.93 % Allowed : 7.41 % Favored : 91.66 % 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: 0.12 (0.14), residues: 3285 helix: 1.80 (0.20), residues: 762 sheet: 0.30 (0.20), residues: 708 loop : -0.76 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.017 0.001 TYR A1067 PHE 0.012 0.001 PHE B 486 TRP 0.026 0.001 TRP A 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (27384) covalent geometry : angle 0.52420 / 0.27 (37281) SS BOND : bond 0.00223 / 0.15 ( 48) SS BOND : angle 0.93264 / 0.58 ( 96) hydrogen bonds : bond 0.03699 / 2.44 ( 1079) hydrogen bonds : angle 5.20629 / 3.59 ( 2967) link_BETA1-4 : bond 0.00423 / 0.28 ( 18) link_BETA1-4 : angle 1.44791 / 0.96 ( 54) link_NAG-ASN : bond 0.00286 / 0.20 ( 48) link_NAG-ASN : angle 2.16791 / 1.44 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6079.05 seconds wall clock time: 118 minutes 29.14 seconds (7109.14 seconds total)