Starting phenix.real_space_refine on Fri Mar 6 01:06:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s6i_24876/03_2026/7s6i_24876.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s6i_24876/03_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_24876/03_2026/7s6i_24876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s6i_24876/03_2026/7s6i_24876.map" model { file = "/net/cci-nas-00/data/ceres_data/7s6i_24876/03_2026/7s6i_24876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s6i_24876/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.82, per 1000 atoms: 0.25 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: 2.50 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: 1.19 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: 6.88 Time building geometry restraints manager: 3.21 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: 16616 17.77 - 35.53: 394 35.53 - 53.30: 117 53.30 - 71.06: 42 71.06 - 88.83: 24 Dihedral angle restraints: 17193 sinusoidal: 7563 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 17190 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: 0.06 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.630 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 9.814 88.826 10863 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 covalent geometry : bond 0.02185 (27384) covalent geometry : angle 1.73437 (37281) SS BOND : bond 0.03911 ( 48) SS BOND : angle 2.24926 ( 96) hydrogen bonds : bond 0.16346 ( 1079) hydrogen bonds : angle 7.98530 ( 2967) link_BETA1-4 : bond 0.07288 ( 18) link_BETA1-4 : angle 4.97870 ( 54) link_NAG-ASN : bond 0.07918 ( 48) link_NAG-ASN : angle 2.60099 ( 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 : 1.050 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: 0.2175 time to fit residues: 121.8196 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 : 0.963 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 354 ASN 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 = 0.3626 r_free = 0.3626 target = 0.112198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.094303 restraints weight = 48230.545| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.45 r_work: 0.3206 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27498 Z= 0.173 Angle : 0.718 10.418 37575 Z= 0.370 Chirality : 0.047 0.273 4401 Planarity : 0.004 0.031 4749 Dihedral : 5.674 50.792 4944 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.73 % Allowed : 4.29 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3285 helix: 1.06 (0.19), residues: 780 sheet: 0.84 (0.19), residues: 696 loop : -0.16 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 905 TYR 0.021 0.002 TYR B1067 PHE 0.016 0.002 PHE A 55 TRP 0.021 0.002 TRP C 886 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00387 (27384) covalent geometry : angle 0.68004 (37281) SS BOND : bond 0.00462 ( 48) SS BOND : angle 1.95460 ( 96) hydrogen bonds : bond 0.06022 ( 1079) hydrogen bonds : angle 6.32872 ( 2967) link_BETA1-4 : bond 0.00595 ( 18) link_BETA1-4 : angle 3.28726 ( 54) link_NAG-ASN : bond 0.00561 ( 48) link_NAG-ASN : angle 2.83697 ( 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 217 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.020 Fit side-chains REVERT: A 111 ASP cc_start: 0.7539 (p0) cc_final: 0.7115 (t70) REVERT: A 241 LEU cc_start: 0.8298 (mt) cc_final: 0.7983 (mp) REVERT: B 241 LEU cc_start: 0.8195 (mt) cc_final: 0.7746 (mp) REVERT: B 281 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: B 405 ASP cc_start: 0.8948 (m-30) cc_final: 0.8726 (m-30) REVERT: B 994 ASP cc_start: 0.8660 (t0) cc_final: 0.8347 (t0) REVERT: C 111 ASP cc_start: 0.7467 (p0) cc_final: 0.7103 (t70) REVERT: C 434 ILE cc_start: 0.9050 (tt) cc_final: 0.8746 (mt) REVERT: C 979 ASP cc_start: 0.8591 (m-30) cc_final: 0.8368 (m-30) REVERT: C 988 GLU cc_start: 0.8513 (tp30) cc_final: 0.8122 (tp30) outliers start: 21 outliers final: 10 residues processed: 209 average time/residue: 0.1775 time to fit residues: 60.8546 Evaluate side-chains 150 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 675 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 954 GLN Chi-restraints excluded: chain C residue 607 GLN 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: 0.0970 chunk 157 optimal weight: 2.9990 chunk 312 optimal weight: 0.0980 chunk 313 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 239 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN C1048 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.103907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086819 restraints weight = 47901.414| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.18 r_work: 0.3063 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27498 Z= 0.155 Angle : 0.614 9.451 37575 Z= 0.312 Chirality : 0.047 0.519 4401 Planarity : 0.004 0.033 4749 Dihedral : 5.139 50.423 4944 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.22 % Favored : 97.69 % Rotamer: Outliers : 0.80 % Allowed : 5.43 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3285 helix: 1.35 (0.20), residues: 759 sheet: 0.60 (0.19), residues: 696 loop : -0.43 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.019 0.001 TYR A 248 PHE 0.016 0.001 PHE B 55 TRP 0.019 0.001 TRP A 886 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00355 (27384) covalent geometry : angle 0.58417 (37281) SS BOND : bond 0.00400 ( 48) SS BOND : angle 1.48970 ( 96) hydrogen bonds : bond 0.04850 ( 1079) hydrogen bonds : angle 5.88282 ( 2967) link_BETA1-4 : bond 0.00641 ( 18) link_BETA1-4 : angle 2.47397 ( 54) link_NAG-ASN : bond 0.00528 ( 48) link_NAG-ASN : angle 2.51432 ( 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 185 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.049 Fit side-chains REVERT: A 111 ASP cc_start: 0.7549 (p0) cc_final: 0.7090 (t70) REVERT: A 241 LEU cc_start: 0.8426 (mt) cc_final: 0.8118 (mp) REVERT: A 1029 MET cc_start: 0.9174 (tpp) cc_final: 0.8875 (ttm) REVERT: B 487 ASN cc_start: 0.7109 (m-40) cc_final: 0.6880 (m110) REVERT: B 994 ASP cc_start: 0.8585 (t0) cc_final: 0.8287 (t0) REVERT: B 1119 ASN cc_start: 0.7977 (m-40) cc_final: 0.7762 (m-40) REVERT: C 40 ASP cc_start: 0.8096 (m-30) cc_final: 0.7890 (m-30) REVERT: C 111 ASP cc_start: 0.7497 (p0) cc_final: 0.7058 (t70) REVERT: C 434 ILE cc_start: 0.8999 (tt) cc_final: 0.8774 (mt) REVERT: C 487 ASN cc_start: 0.7343 (m-40) cc_final: 0.6997 (m-40) REVERT: C 556 ASN cc_start: 0.8418 (t0) cc_final: 0.8164 (t0) REVERT: C 988 GLU cc_start: 0.8364 (tp30) cc_final: 0.8042 (tp30) REVERT: C 994 ASP cc_start: 0.8431 (t70) cc_final: 0.8192 (t70) outliers start: 23 outliers final: 9 residues processed: 177 average time/residue: 0.1654 time to fit residues: 49.3133 Evaluate side-chains 148 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 383 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 74 optimal weight: 4.9990 chunk 186 optimal weight: 0.0030 chunk 108 optimal weight: 1.9990 chunk 297 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A1048 HIS B1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.091526 restraints weight = 50771.320| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.56 r_work: 0.3137 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27498 Z= 0.120 Angle : 0.578 14.507 37575 Z= 0.287 Chirality : 0.045 0.439 4401 Planarity : 0.004 0.041 4749 Dihedral : 4.965 51.145 4944 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.81 % Rotamer: Outliers : 1.14 % Allowed : 5.61 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3285 helix: 1.49 (0.20), residues: 759 sheet: 0.53 (0.19), residues: 696 loop : -0.54 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.018 0.001 TYR A 200 PHE 0.012 0.001 PHE B 55 TRP 0.034 0.001 TRP A 886 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00268 (27384) covalent geometry : angle 0.54185 (37281) SS BOND : bond 0.00368 ( 48) SS BOND : angle 1.32932 ( 96) hydrogen bonds : bond 0.04247 ( 1079) hydrogen bonds : angle 5.65602 ( 2967) link_BETA1-4 : bond 0.00577 ( 18) link_BETA1-4 : angle 2.17903 ( 54) link_NAG-ASN : bond 0.00538 ( 48) link_NAG-ASN : angle 2.84174 ( 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 181 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.111 Fit side-chains REVERT: A 111 ASP cc_start: 0.7523 (p0) cc_final: 0.7043 (t70) REVERT: A 779 GLN cc_start: 0.8846 (tp40) cc_final: 0.8640 (tp40) REVERT: A 1029 MET cc_start: 0.9235 (tpp) cc_final: 0.8809 (ttm) REVERT: B 1119 ASN cc_start: 0.8165 (m-40) cc_final: 0.7936 (m-40) REVERT: C 40 ASP cc_start: 0.8234 (m-30) cc_final: 0.8017 (m-30) REVERT: C 111 ASP cc_start: 0.7429 (p0) cc_final: 0.6961 (t70) REVERT: C 487 ASN cc_start: 0.7908 (m-40) cc_final: 0.7367 (m110) REVERT: C 556 ASN cc_start: 0.8536 (t0) cc_final: 0.8261 (t0) REVERT: C 745 ASP cc_start: 0.7324 (m-30) cc_final: 0.7110 (m-30) REVERT: C 773 GLU cc_start: 0.8896 (tt0) cc_final: 0.8690 (tt0) REVERT: C 1029 MET cc_start: 0.9109 (tpp) cc_final: 0.8782 (ttm) outliers start: 33 outliers final: 21 residues processed: 173 average time/residue: 0.1574 time to fit residues: 47.2905 Evaluate side-chains 151 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 675 GLN Chi-restraints excluded: chain A residue 828 LEU 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 705 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 988 GLU 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 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: 2.9990 chunk 71 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 303 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN B 556 ASN C 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.087962 restraints weight = 48759.720| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.47 r_work: 0.3122 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 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 : 0.004 0.050 27498 Z= 0.172 Angle : 0.608 13.179 37575 Z= 0.301 Chirality : 0.046 0.343 4401 Planarity : 0.004 0.038 4749 Dihedral : 4.935 49.735 4944 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 1.38 % Allowed : 5.78 % Favored : 92.83 % 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: 0.10 (0.14), residues: 3285 helix: 1.48 (0.19), residues: 759 sheet: 0.43 (0.20), residues: 669 loop : -0.66 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.018 0.001 TYR A1067 PHE 0.014 0.002 PHE C 898 TRP 0.034 0.001 TRP A 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00410 (27384) covalent geometry : angle 0.57893 (37281) SS BOND : bond 0.00338 ( 48) SS BOND : angle 1.23621 ( 96) hydrogen bonds : bond 0.04506 ( 1079) hydrogen bonds : angle 5.61470 ( 2967) link_BETA1-4 : bond 0.00503 ( 18) link_BETA1-4 : angle 1.91451 ( 54) link_NAG-ASN : bond 0.00448 ( 48) link_NAG-ASN : angle 2.70946 ( 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 187 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 1.016 Fit side-chains REVERT: A 111 ASP cc_start: 0.7615 (p0) cc_final: 0.7090 (t70) REVERT: A 569 ILE cc_start: 0.9107 (mp) cc_final: 0.8900 (mp) REVERT: C 111 ASP cc_start: 0.7481 (p0) cc_final: 0.7009 (t70) REVERT: C 556 ASN cc_start: 0.8539 (t0) cc_final: 0.8315 (t0) REVERT: C 773 GLU cc_start: 0.8894 (tt0) cc_final: 0.8671 (tt0) outliers start: 40 outliers final: 32 residues processed: 176 average time/residue: 0.1508 time to fit residues: 46.6285 Evaluate side-chains 162 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 675 GLN 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 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 393 THR Chi-restraints excluded: chain B residue 705 VAL 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 988 GLU 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 607 GLN 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: 0.3980 chunk 51 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 chunk 290 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 324 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089083 restraints weight = 48977.750| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.41 r_work: 0.3105 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27498 Z= 0.195 Angle : 0.622 14.777 37575 Z= 0.305 Chirality : 0.047 0.546 4401 Planarity : 0.004 0.038 4749 Dihedral : 5.072 49.306 4944 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 1.38 % Allowed : 6.16 % Favored : 92.45 % 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: 0.00 (0.14), residues: 3285 helix: 1.46 (0.19), residues: 759 sheet: 0.44 (0.20), residues: 660 loop : -0.79 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.018 0.001 TYR A1067 PHE 0.014 0.002 PHE B 238 TRP 0.018 0.001 TRP B 886 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00467 (27384) covalent geometry : angle 0.59214 (37281) SS BOND : bond 0.00304 ( 48) SS BOND : angle 1.19240 ( 96) hydrogen bonds : bond 0.04519 ( 1079) hydrogen bonds : angle 5.59405 ( 2967) link_BETA1-4 : bond 0.00537 ( 18) link_BETA1-4 : angle 1.81894 ( 54) link_NAG-ASN : bond 0.00383 ( 48) link_NAG-ASN : angle 2.85337 ( 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: 40 poor density : 142 time to evaluate : 1.009 Fit side-chains REVERT: A 111 ASP cc_start: 0.7678 (p0) cc_final: 0.7133 (t70) REVERT: A 556 ASN cc_start: 0.8581 (t160) cc_final: 0.8361 (t0) REVERT: A 569 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8934 (mp) REVERT: A 1029 MET cc_start: 0.9321 (tpp) cc_final: 0.8700 (ttm) REVERT: B 556 ASN cc_start: 0.8363 (t160) cc_final: 0.8156 (t0) REVERT: B 786 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7867 (mmmm) REVERT: C 111 ASP cc_start: 0.7550 (p0) cc_final: 0.7083 (t70) REVERT: C 487 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7462 (m110) REVERT: C 556 ASN cc_start: 0.8532 (t0) cc_final: 0.8327 (t0) REVERT: C 773 GLU cc_start: 0.8882 (tt0) cc_final: 0.8654 (tt0) REVERT: C 902 MET cc_start: 0.8871 (tpp) cc_final: 0.8631 (tpp) outliers start: 40 outliers final: 35 residues processed: 170 average time/residue: 0.1647 time to fit residues: 47.5630 Evaluate side-chains 168 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 675 GLN 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 988 GLU 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 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 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 988 GLU 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 487 ASN Chi-restraints excluded: chain C residue 607 GLN 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 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 262 optimal weight: 0.0030 chunk 13 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A1142 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN C 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089377 restraints weight = 50794.941| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.52 r_work: 0.3099 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27498 Z= 0.119 Angle : 0.560 13.106 37575 Z= 0.276 Chirality : 0.044 0.380 4401 Planarity : 0.004 0.037 4749 Dihedral : 4.846 50.529 4944 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 1.28 % Allowed : 6.51 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3285 helix: 1.63 (0.20), residues: 759 sheet: 0.41 (0.20), residues: 666 loop : -0.76 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.016 0.001 TYR A1067 PHE 0.012 0.001 PHE A1121 TRP 0.023 0.001 TRP C 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00269 (27384) covalent geometry : angle 0.53218 (37281) SS BOND : bond 0.00229 ( 48) SS BOND : angle 1.02573 ( 96) hydrogen bonds : bond 0.04026 ( 1079) hydrogen bonds : angle 5.43908 ( 2967) link_BETA1-4 : bond 0.00522 ( 18) link_BETA1-4 : angle 1.70684 ( 54) link_NAG-ASN : bond 0.00410 ( 48) link_NAG-ASN : angle 2.61462 ( 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 183 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.099 Fit side-chains REVERT: A 111 ASP cc_start: 0.7595 (p0) cc_final: 0.7081 (t70) REVERT: A 556 ASN cc_start: 0.8611 (t0) cc_final: 0.8376 (t0) REVERT: A 569 ILE cc_start: 0.9104 (mp) cc_final: 0.8887 (mp) REVERT: A 1029 MET cc_start: 0.9300 (tpp) cc_final: 0.8679 (ttm) REVERT: C 111 ASP cc_start: 0.7608 (p0) cc_final: 0.7138 (t70) REVERT: C 556 ASN cc_start: 0.8504 (t0) cc_final: 0.8250 (t0) REVERT: C 773 GLU cc_start: 0.8867 (tt0) cc_final: 0.8649 (tt0) outliers start: 37 outliers final: 30 residues processed: 177 average time/residue: 0.1528 time to fit residues: 46.7702 Evaluate side-chains 161 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 705 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1001 LEU 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 383 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 882 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: 0.4980 chunk 50 optimal weight: 0.0020 chunk 226 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.086498 restraints weight = 50234.592| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.56 r_work: 0.3106 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27498 Z= 0.110 Angle : 0.545 11.574 37575 Z= 0.269 Chirality : 0.044 0.308 4401 Planarity : 0.004 0.036 4749 Dihedral : 4.708 51.120 4944 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.62 % Favored : 97.29 % Rotamer: Outliers : 1.42 % Allowed : 6.44 % 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: 0.12 (0.14), residues: 3285 helix: 1.77 (0.20), residues: 756 sheet: 0.43 (0.20), residues: 666 loop : -0.78 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.017 0.001 TYR A1067 PHE 0.032 0.001 PHE C 486 TRP 0.026 0.001 TRP C 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00246 (27384) covalent geometry : angle 0.51871 (37281) SS BOND : bond 0.00204 ( 48) SS BOND : angle 0.97236 ( 96) hydrogen bonds : bond 0.03816 ( 1079) hydrogen bonds : angle 5.34320 ( 2967) link_BETA1-4 : bond 0.00538 ( 18) link_BETA1-4 : angle 1.61893 ( 54) link_NAG-ASN : bond 0.00385 ( 48) link_NAG-ASN : angle 2.49089 ( 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 177 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 1.046 Fit side-chains REVERT: A 111 ASP cc_start: 0.7484 (p0) cc_final: 0.7008 (t70) REVERT: A 556 ASN cc_start: 0.8548 (t0) cc_final: 0.8320 (t0) REVERT: A 994 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8109 (t0) REVERT: A 1029 MET cc_start: 0.9280 (tpp) cc_final: 0.8666 (ttm) REVERT: B 887 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (p) REVERT: B 1119 ASN cc_start: 0.8222 (m-40) cc_final: 0.7988 (m-40) REVERT: C 111 ASP cc_start: 0.7569 (p0) cc_final: 0.7102 (t70) REVERT: C 212 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7968 (tp) REVERT: C 773 GLU cc_start: 0.8852 (tt0) cc_final: 0.8649 (tt0) REVERT: C 988 GLU cc_start: 0.7915 (mp0) cc_final: 0.7669 (mp0) outliers start: 41 outliers final: 25 residues processed: 171 average time/residue: 0.1536 time to fit residues: 45.8212 Evaluate side-chains 158 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 A residue 705 VAL Chi-restraints excluded: chain A residue 931 ILE 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 A residue 1142 GLN 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 763 LEU Chi-restraints excluded: chain B residue 828 LEU 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 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 828 LEU Chi-restraints excluded: chain C residue 882 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: 0.8980 chunk 177 optimal weight: 0.5980 chunk 317 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 133 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 249 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 306 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN B 487 ASN C 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.104460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.086372 restraints weight = 48316.647| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.45 r_work: 0.3076 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27498 Z= 0.117 Angle : 0.546 11.653 37575 Z= 0.271 Chirality : 0.044 0.306 4401 Planarity : 0.004 0.038 4749 Dihedral : 4.657 51.034 4944 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 1.18 % Allowed : 6.82 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3285 helix: 1.73 (0.20), residues: 762 sheet: 0.50 (0.21), residues: 642 loop : -0.76 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.017 0.001 TYR A1067 PHE 0.012 0.001 PHE A1121 TRP 0.025 0.001 TRP C 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00269 (27384) covalent geometry : angle 0.52115 (37281) SS BOND : bond 0.00269 ( 48) SS BOND : angle 0.98189 ( 96) hydrogen bonds : bond 0.03813 ( 1079) hydrogen bonds : angle 5.31000 ( 2967) link_BETA1-4 : bond 0.00519 ( 18) link_BETA1-4 : angle 1.57967 ( 54) link_NAG-ASN : bond 0.00371 ( 48) link_NAG-ASN : angle 2.45582 ( 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 168 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.970 Fit side-chains REVERT: A 111 ASP cc_start: 0.7458 (p0) cc_final: 0.6989 (t70) REVERT: A 556 ASN cc_start: 0.8515 (t0) cc_final: 0.8295 (t0) REVERT: A 994 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8051 (t0) REVERT: A 1029 MET cc_start: 0.9264 (tpp) cc_final: 0.8629 (ttm) REVERT: B 887 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8439 (p) REVERT: B 1119 ASN cc_start: 0.8174 (m-40) cc_final: 0.7939 (m-40) REVERT: C 111 ASP cc_start: 0.7545 (p0) cc_final: 0.7073 (t70) REVERT: C 212 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7963 (tp) outliers start: 34 outliers final: 27 residues processed: 162 average time/residue: 0.1490 time to fit residues: 42.2467 Evaluate side-chains 160 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 931 ILE 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 A residue 1142 GLN 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 763 LEU Chi-restraints excluded: chain B residue 828 LEU 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 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 383 CYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 882 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: 4.9990 chunk 153 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 40 optimal weight: 0.0570 chunk 298 optimal weight: 0.8980 chunk 268 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 311 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A1142 GLN C 69 HIS C 556 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092270 restraints weight = 50529.272| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.43 r_work: 0.3120 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3794 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= 0.113 Angle : 0.545 11.619 37575 Z= 0.270 Chirality : 0.044 0.306 4401 Planarity : 0.004 0.039 4749 Dihedral : 4.616 51.037 4944 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.53 % Favored : 97.38 % Rotamer: Outliers : 1.00 % Allowed : 6.96 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3285 helix: 1.77 (0.20), residues: 762 sheet: 0.52 (0.21), residues: 642 loop : -0.75 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.017 0.001 TYR A1067 PHE 0.012 0.001 PHE A 927 TRP 0.027 0.001 TRP C 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00258 (27384) covalent geometry : angle 0.52027 (37281) SS BOND : bond 0.00208 ( 48) SS BOND : angle 0.96530 ( 96) hydrogen bonds : bond 0.03753 ( 1079) hydrogen bonds : angle 5.26495 ( 2967) link_BETA1-4 : bond 0.00517 ( 18) link_BETA1-4 : angle 1.55285 ( 54) link_NAG-ASN : bond 0.00372 ( 48) link_NAG-ASN : angle 2.42396 ( 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 158 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.128 Fit side-chains REVERT: A 111 ASP cc_start: 0.7465 (p0) cc_final: 0.7005 (t70) REVERT: A 556 ASN cc_start: 0.8495 (t0) cc_final: 0.8289 (t0) REVERT: A 994 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8040 (t0) REVERT: A 1029 MET cc_start: 0.9255 (tpp) cc_final: 0.8892 (ttm) REVERT: B 1119 ASN cc_start: 0.8168 (m-40) cc_final: 0.7958 (m-40) REVERT: C 111 ASP cc_start: 0.7515 (p0) cc_final: 0.7064 (t70) REVERT: C 212 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7994 (tp) outliers start: 29 outliers final: 23 residues processed: 154 average time/residue: 0.1487 time to fit residues: 40.1017 Evaluate side-chains 153 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 931 ILE 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 393 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU 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 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 828 LEU Chi-restraints excluded: chain C residue 882 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: 0.9980 chunk 1 optimal weight: 6.9990 chunk 259 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 329 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.083004 restraints weight = 49886.465| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.62 r_work: 0.3048 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3835 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= 0.143 Angle : 0.562 12.496 37575 Z= 0.278 Chirality : 0.045 0.303 4401 Planarity : 0.004 0.039 4749 Dihedral : 4.678 50.121 4944 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 1.00 % Allowed : 7.10 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3285 helix: 1.73 (0.20), residues: 756 sheet: 0.36 (0.20), residues: 672 loop : -0.80 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.018 0.001 TYR A1067 PHE 0.014 0.001 PHE A 898 TRP 0.025 0.001 TRP C 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00340 (27384) covalent geometry : angle 0.53769 (37281) SS BOND : bond 0.00246 ( 48) SS BOND : angle 1.03321 ( 96) hydrogen bonds : bond 0.03976 ( 1079) hydrogen bonds : angle 5.30327 ( 2967) link_BETA1-4 : bond 0.00483 ( 18) link_BETA1-4 : angle 1.51547 ( 54) link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 2.44889 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6168.10 seconds wall clock time: 106 minutes 29.45 seconds (6389.45 seconds total)