Starting phenix.real_space_refine on Fri Mar 6 02:06:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgv_32490/03_2026/7wgv_32490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgv_32490/03_2026/7wgv_32490.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 { model { file = "/net/cci-nas-00/data/ceres_data/7wgv_32490/03_2026/7wgv_32490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgv_32490/03_2026/7wgv_32490.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wgv_32490/03_2026/7wgv_32490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgv_32490/03_2026/7wgv_32490.map" } 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= 0.003 sd= 0.140 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 120 5.16 5 C 17145 2.51 5 N 4398 2.21 5 O 5268 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: 26931 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8620 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 51, 'TRANS': 1051} Chain breaks: 3 Chain: "B" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8620 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 51, 'TRANS': 1051} Chain breaks: 3 Chain: "C" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8620 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 51, 'TRANS': 1051} 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: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLR': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLR': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLR': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.37, per 1000 atoms: 0.24 Number of scatterers: 26931 At special positions: 0 Unit cell: (156.4, 144.16, 180.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5268 8.00 N 4398 7.00 C 17145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG 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-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A 165 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 343 " " NAG A1310 " - " ASN A 17 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 149 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B 165 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 343 " " NAG B1310 " - " ASN B 17 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 149 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C 165 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 343 " " NAG C1310 " - " ASN C 17 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 149 " " NAG D 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 234 " " NAG I 1 " - " ASN B 717 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 234 " " NAG N 1 " - " ASN C 717 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 234 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 933.0 milliseconds 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: 66 helices and 48 sheets defined 23.8% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.831A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.586A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.368A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.649A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 756 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.709A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.824A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.509A 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 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.723A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 removed outlier: 3.773A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.832A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 370' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.586A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.367A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.649A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 756 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.707A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.823A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 3.509A 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 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.722A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 removed outlier: 3.773A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.832A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 370' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.586A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.368A 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 438 through 443 removed outlier: 3.649A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 756 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.707A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.824A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.509A 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 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.723A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.773A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1033 Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.269A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.423A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.511A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS A 146 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.527A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.039A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.443A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.298A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.389A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.113A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.622A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.628A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.699A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.269A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.423A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.510A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS B 146 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.526A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.039A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.443A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.298A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.389A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.113A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.623A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.622A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.700A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.269A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.423A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.511A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 146 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.526A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.039A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.444A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.298A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.390A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.114A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.623A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.699A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 2883 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: 5.83 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.31: 4366 1.31 - 1.49: 11637 1.49 - 1.68: 11351 1.68 - 1.87: 168 1.87 - 2.06: 12 Bond restraints: 27534 Sorted by residual: bond pdb=" C1A BLR A1313 " pdb=" CHA BLR A1313 " ideal model delta sigma weight residual 1.498 2.057 -0.559 2.00e-02 2.50e+03 7.82e+02 bond pdb=" C1A BLR C1313 " pdb=" CHA BLR C1313 " ideal model delta sigma weight residual 1.498 2.057 -0.559 2.00e-02 2.50e+03 7.80e+02 bond pdb=" C1A BLR B1313 " pdb=" CHA BLR B1313 " ideal model delta sigma weight residual 1.498 2.057 -0.559 2.00e-02 2.50e+03 7.80e+02 bond pdb=" C2B BLR C1313 " pdb=" CMB BLR C1313 " ideal model delta sigma weight residual 1.489 1.953 -0.464 2.00e-02 2.50e+03 5.38e+02 bond pdb=" C2B BLR A1313 " pdb=" CMB BLR A1313 " ideal model delta sigma weight residual 1.489 1.953 -0.464 2.00e-02 2.50e+03 5.37e+02 ... (remaining 27529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.25: 37413 10.25 - 20.51: 21 20.51 - 30.76: 3 30.76 - 41.01: 9 41.01 - 51.27: 9 Bond angle restraints: 37455 Sorted by residual: angle pdb=" C2B BLR C1313 " pdb=" C1B BLR C1313 " pdb=" CHB BLR C1313 " ideal model delta sigma weight residual 123.24 174.51 -51.27 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C2B BLR A1313 " pdb=" C1B BLR A1313 " pdb=" CHB BLR A1313 " ideal model delta sigma weight residual 123.24 174.49 -51.25 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C2B BLR B1313 " pdb=" C1B BLR B1313 " pdb=" CHB BLR B1313 " ideal model delta sigma weight residual 123.24 174.46 -51.22 3.00e+00 1.11e-01 2.92e+02 angle pdb=" NB BLR A1313 " pdb=" C1B BLR A1313 " pdb=" CHB BLR A1313 " ideal model delta sigma weight residual 130.12 84.75 45.37 3.00e+00 1.11e-01 2.29e+02 angle pdb=" NB BLR C1313 " pdb=" C1B BLR C1313 " pdb=" CHB BLR C1313 " ideal model delta sigma weight residual 130.12 84.78 45.34 3.00e+00 1.11e-01 2.28e+02 ... (remaining 37450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15542 17.99 - 35.98: 1264 35.98 - 53.98: 234 53.98 - 71.97: 99 71.97 - 89.96: 42 Dihedral angle restraints: 17181 sinusoidal: 7551 harmonic: 9630 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -161.56 75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -161.53 75.53 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -161.53 75.53 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 17178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4134 0.103 - 0.207: 234 0.207 - 0.310: 6 0.310 - 0.413: 0 0.413 - 0.517: 6 Chirality restraints: 4380 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 4377 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.030 2.00e-02 2.50e+03 2.84e-02 1.01e+01 pdb=" CG ASN A 616 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.030 2.00e-02 2.50e+03 2.83e-02 1.00e+01 pdb=" CG ASN B 616 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " 0.030 2.00e-02 2.50e+03 2.81e-02 9.89e+00 pdb=" CG ASN C 616 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.032 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 633 2.70 - 3.25: 24401 3.25 - 3.80: 38961 3.80 - 4.35: 51767 4.35 - 4.90: 89805 Nonbonded interactions: 205567 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.151 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 274 " model vdw 2.152 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.273 3.040 ... (remaining 205562 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.400 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.017 0.559 27636 Z= 0.864 Angle : 1.319 51.266 37716 Z= 0.495 Chirality : 0.051 0.517 4380 Planarity : 0.003 0.031 4764 Dihedral : 14.424 89.961 10860 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.59 (0.14), residues: 3285 helix: 1.89 (0.21), residues: 726 sheet: 0.40 (0.18), residues: 768 loop : -1.83 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.014 0.001 TYR C1067 PHE 0.014 0.001 PHE A 486 TRP 0.008 0.001 TRP B 152 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.01732 (27534) covalent geometry : angle 1.28662 (37455) SS BOND : bond 0.00732 ( 45) SS BOND : angle 2.52331 ( 90) hydrogen bonds : bond 0.12189 ( 1045) hydrogen bonds : angle 6.30149 ( 2883) link_BETA1-4 : bond 0.00293 ( 15) link_BETA1-4 : angle 0.88873 ( 45) link_NAG-ASN : bond 0.00831 ( 42) link_NAG-ASN : angle 4.87237 ( 126) *********************** 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 218 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: B 111 ASP cc_start: 0.7011 (t0) cc_final: 0.6631 (t0) REVERT: B 817 PHE cc_start: 0.6591 (t80) cc_final: 0.6370 (t80) REVERT: C 111 ASP cc_start: 0.6694 (t0) cc_final: 0.6403 (t0) REVERT: C 177 MET cc_start: 0.8042 (ttp) cc_final: 0.7830 (ttm) REVERT: C 443 SER cc_start: 0.8097 (t) cc_final: 0.7729 (p) REVERT: C 781 VAL cc_start: 0.7561 (t) cc_final: 0.7234 (t) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1896 time to fit residues: 63.6676 Evaluate side-chains 134 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 801 ASN A 895 GLN A 935 GLN A 957 GLN B 493 GLN B 774 GLN B 801 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 493 GLN C 774 GLN C 801 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1011 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094936 restraints weight = 40161.208| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.04 r_work: 0.3005 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27636 Z= 0.145 Angle : 0.656 20.375 37716 Z= 0.311 Chirality : 0.047 0.444 4380 Planarity : 0.004 0.034 4764 Dihedral : 8.822 89.609 4965 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.49 % Allowed : 4.86 % Favored : 94.65 % 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: -0.60 (0.14), residues: 3285 helix: 1.82 (0.20), residues: 735 sheet: 0.30 (0.18), residues: 789 loop : -1.80 (0.13), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.020 0.001 TYR C1138 PHE 0.011 0.001 PHE B 194 TRP 0.008 0.001 TRP A 152 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00336 (27534) covalent geometry : angle 0.57935 (37455) SS BOND : bond 0.00618 ( 45) SS BOND : angle 1.83906 ( 90) hydrogen bonds : bond 0.04952 ( 1045) hydrogen bonds : angle 5.43153 ( 2883) link_BETA1-4 : bond 0.00299 ( 15) link_BETA1-4 : angle 1.27174 ( 45) link_NAG-ASN : bond 0.00745 ( 42) link_NAG-ASN : angle 5.10360 ( 126) *********************** 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 165 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 606 ASN cc_start: 0.8032 (m110) cc_final: 0.7529 (p0) REVERT: B 111 ASP cc_start: 0.8098 (t0) cc_final: 0.7590 (t0) REVERT: B 606 ASN cc_start: 0.8132 (m-40) cc_final: 0.7332 (p0) REVERT: B 817 PHE cc_start: 0.6804 (t80) cc_final: 0.6517 (t80) REVERT: C 111 ASP cc_start: 0.7783 (t0) cc_final: 0.7337 (t0) REVERT: C 177 MET cc_start: 0.8209 (ttp) cc_final: 0.7819 (ttm) REVERT: C 443 SER cc_start: 0.9105 (t) cc_final: 0.8788 (p) REVERT: C 731 MET cc_start: 0.8928 (ptm) cc_final: 0.8695 (ptp) REVERT: C 781 VAL cc_start: 0.7344 (t) cc_final: 0.7018 (t) outliers start: 14 outliers final: 5 residues processed: 161 average time/residue: 0.1856 time to fit residues: 46.8874 Evaluate side-chains 135 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 224 optimal weight: 0.9980 chunk 313 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN C 148 ASN C 895 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085874 restraints weight = 40008.741| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.23 r_work: 0.2914 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27636 Z= 0.214 Angle : 0.679 20.883 37716 Z= 0.332 Chirality : 0.048 0.415 4380 Planarity : 0.004 0.033 4764 Dihedral : 8.005 89.958 4965 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.66 % Allowed : 7.33 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3285 helix: 1.53 (0.20), residues: 741 sheet: 0.26 (0.18), residues: 792 loop : -1.81 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 214 TYR 0.021 0.002 TYR B1138 PHE 0.022 0.002 PHE B 906 TRP 0.009 0.001 TRP A 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00525 (27534) covalent geometry : angle 0.60237 (37455) SS BOND : bond 0.00687 ( 45) SS BOND : angle 2.43924 ( 90) hydrogen bonds : bond 0.05955 ( 1045) hydrogen bonds : angle 5.43812 ( 2883) link_BETA1-4 : bond 0.00318 ( 15) link_BETA1-4 : angle 1.33247 ( 45) link_NAG-ASN : bond 0.00705 ( 42) link_NAG-ASN : angle 5.02934 ( 126) *********************** 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 168 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 606 ASN cc_start: 0.8006 (m110) cc_final: 0.7473 (p0) REVERT: A 979 ASP cc_start: 0.7808 (t0) cc_final: 0.7408 (t0) REVERT: A 1017 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7727 (tt0) REVERT: A 1050 MET cc_start: 0.8342 (ptp) cc_final: 0.8113 (ptm) REVERT: B 111 ASP cc_start: 0.8045 (t0) cc_final: 0.7519 (t0) REVERT: B 606 ASN cc_start: 0.8131 (m-40) cc_final: 0.7859 (m-40) REVERT: B 817 PHE cc_start: 0.7274 (t80) cc_final: 0.7074 (t80) REVERT: B 935 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 1050 MET cc_start: 0.8269 (ptp) cc_final: 0.7983 (ptp) REVERT: C 177 MET cc_start: 0.8459 (ttp) cc_final: 0.8258 (ttm) REVERT: C 443 SER cc_start: 0.9090 (t) cc_final: 0.8845 (p) outliers start: 19 outliers final: 9 residues processed: 163 average time/residue: 0.1869 time to fit residues: 47.3529 Evaluate side-chains 144 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 870 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 327 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 241 optimal weight: 0.6980 chunk 326 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087556 restraints weight = 39589.458| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.22 r_work: 0.2939 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27636 Z= 0.137 Angle : 0.614 20.741 37716 Z= 0.299 Chirality : 0.046 0.364 4380 Planarity : 0.003 0.033 4764 Dihedral : 7.440 87.447 4965 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.01 % Allowed : 8.44 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3285 helix: 1.56 (0.20), residues: 744 sheet: 0.22 (0.18), residues: 798 loop : -1.69 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.020 0.001 TYR B1138 PHE 0.015 0.001 PHE B 194 TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00319 (27534) covalent geometry : angle 0.53689 (37455) SS BOND : bond 0.00655 ( 45) SS BOND : angle 2.07807 ( 90) hydrogen bonds : bond 0.05133 ( 1045) hydrogen bonds : angle 5.26923 ( 2883) link_BETA1-4 : bond 0.00382 ( 15) link_BETA1-4 : angle 1.25514 ( 45) link_NAG-ASN : bond 0.00720 ( 42) link_NAG-ASN : angle 4.85064 ( 126) *********************** 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 173 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.8791 (t70) cc_final: 0.8276 (t70) REVERT: A 786 LYS cc_start: 0.8167 (pttm) cc_final: 0.7403 (tppt) REVERT: A 1019 ARG cc_start: 0.7908 (tmm160) cc_final: 0.7567 (ttp-110) REVERT: A 1050 MET cc_start: 0.8204 (ptp) cc_final: 0.7961 (ptm) REVERT: B 111 ASP cc_start: 0.8046 (t0) cc_final: 0.7557 (t0) REVERT: B 935 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7668 (tm-30) REVERT: C 346 ARG cc_start: 0.8391 (tpt90) cc_final: 0.8132 (mmm160) REVERT: C 443 SER cc_start: 0.9095 (t) cc_final: 0.8797 (p) outliers start: 29 outliers final: 16 residues processed: 168 average time/residue: 0.1775 time to fit residues: 47.1434 Evaluate side-chains 149 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 187 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 323 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 327 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 297 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 493 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.084053 restraints weight = 39903.660| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.21 r_work: 0.2869 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 27636 Z= 0.249 Angle : 0.704 21.143 37716 Z= 0.347 Chirality : 0.049 0.349 4380 Planarity : 0.004 0.036 4764 Dihedral : 7.418 87.195 4965 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.28 % Allowed : 9.48 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.83 (0.14), residues: 3285 helix: 1.31 (0.20), residues: 747 sheet: 0.21 (0.18), residues: 831 loop : -1.89 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 214 TYR 0.022 0.002 TYR A 365 PHE 0.022 0.002 PHE B 133 TRP 0.008 0.001 TRP A 353 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00615 (27534) covalent geometry : angle 0.62821 (37455) SS BOND : bond 0.00758 ( 45) SS BOND : angle 2.80606 ( 90) hydrogen bonds : bond 0.06328 ( 1045) hydrogen bonds : angle 5.45835 ( 2883) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 1.29340 ( 45) link_NAG-ASN : bond 0.00681 ( 42) link_NAG-ASN : angle 5.00012 ( 126) *********************** 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 183 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8000 (pp) REVERT: A 574 ASP cc_start: 0.8767 (t70) cc_final: 0.8358 (t70) REVERT: A 786 LYS cc_start: 0.8158 (pttm) cc_final: 0.7303 (tppt) REVERT: A 1017 GLU cc_start: 0.8170 (tp30) cc_final: 0.7757 (tt0) REVERT: B 179 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7938 (pp) REVERT: B 606 ASN cc_start: 0.8235 (m-40) cc_final: 0.7876 (m-40) REVERT: B 935 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 986 LYS cc_start: 0.8760 (ptmm) cc_final: 0.8523 (ptmm) REVERT: B 1002 GLN cc_start: 0.7515 (tp40) cc_final: 0.7286 (tp40) REVERT: C 346 ARG cc_start: 0.8249 (tpt90) cc_final: 0.8000 (mmm160) REVERT: C 443 SER cc_start: 0.9103 (t) cc_final: 0.8863 (p) REVERT: C 1002 GLN cc_start: 0.7434 (tp40) cc_final: 0.7067 (tp40) REVERT: C 1019 ARG cc_start: 0.8008 (tmm160) cc_final: 0.7615 (ttp-170) REVERT: C 1076 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8306 (p) outliers start: 37 outliers final: 24 residues processed: 180 average time/residue: 0.1862 time to fit residues: 52.7691 Evaluate side-chains 161 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 235 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.084560 restraints weight = 39901.175| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.23 r_work: 0.2877 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27636 Z= 0.205 Angle : 0.668 21.142 37716 Z= 0.327 Chirality : 0.048 0.473 4380 Planarity : 0.004 0.037 4764 Dihedral : 7.231 84.039 4965 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.70 % Allowed : 9.79 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.83 (0.14), residues: 3285 helix: 1.33 (0.20), residues: 744 sheet: 0.15 (0.18), residues: 837 loop : -1.86 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 765 TYR 0.021 0.002 TYR B 365 PHE 0.017 0.002 PHE B 194 TRP 0.008 0.001 TRP C 353 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00503 (27534) covalent geometry : angle 0.59090 (37455) SS BOND : bond 0.00693 ( 45) SS BOND : angle 2.33485 ( 90) hydrogen bonds : bond 0.05940 ( 1045) hydrogen bonds : angle 5.39502 ( 2883) link_BETA1-4 : bond 0.00355 ( 15) link_BETA1-4 : angle 1.26794 ( 45) link_NAG-ASN : bond 0.00688 ( 42) link_NAG-ASN : angle 5.03154 ( 126) *********************** 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 194 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8079 (pp) REVERT: A 574 ASP cc_start: 0.8771 (t70) cc_final: 0.8386 (t70) REVERT: A 786 LYS cc_start: 0.8191 (pttm) cc_final: 0.7355 (tppt) REVERT: A 882 ILE cc_start: 0.8808 (mt) cc_final: 0.8546 (mt) REVERT: A 1017 GLU cc_start: 0.8161 (tp30) cc_final: 0.7738 (tt0) REVERT: B 179 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7938 (pp) REVERT: B 986 LYS cc_start: 0.8629 (ptmm) cc_final: 0.8377 (ptmm) REVERT: B 1002 GLN cc_start: 0.7507 (tp40) cc_final: 0.7305 (tp40) REVERT: C 244 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8066 (pp) REVERT: C 443 SER cc_start: 0.9098 (t) cc_final: 0.8829 (p) REVERT: C 1002 GLN cc_start: 0.7402 (tp40) cc_final: 0.7018 (tp40) REVERT: C 1019 ARG cc_start: 0.7941 (tmm160) cc_final: 0.7560 (ttp-170) REVERT: C 1076 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8281 (p) outliers start: 49 outliers final: 32 residues processed: 187 average time/residue: 0.1908 time to fit residues: 56.6165 Evaluate side-chains 175 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 40 optimal weight: 0.0010 chunk 118 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 108 optimal weight: 0.0170 chunk 48 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 overall best weight: 0.5626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.089130 restraints weight = 39255.842| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.21 r_work: 0.2960 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 27636 Z= 0.107 Angle : 0.586 20.745 37716 Z= 0.286 Chirality : 0.045 0.372 4380 Planarity : 0.003 0.036 4764 Dihedral : 6.620 73.596 4965 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.18 % Allowed : 10.38 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3285 helix: 1.65 (0.20), residues: 741 sheet: 0.36 (0.18), residues: 834 loop : -1.71 (0.13), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 214 TYR 0.019 0.001 TYR B 365 PHE 0.010 0.001 PHE B 194 TRP 0.009 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00230 (27534) covalent geometry : angle 0.51436 (37455) SS BOND : bond 0.00621 ( 45) SS BOND : angle 1.75948 ( 90) hydrogen bonds : bond 0.04530 ( 1045) hydrogen bonds : angle 5.11892 ( 2883) link_BETA1-4 : bond 0.00464 ( 15) link_BETA1-4 : angle 1.22028 ( 45) link_NAG-ASN : bond 0.00758 ( 42) link_NAG-ASN : angle 4.62644 ( 126) *********************** 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 196 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7904 (pp) REVERT: A 574 ASP cc_start: 0.8783 (t70) cc_final: 0.8430 (t70) REVERT: A 786 LYS cc_start: 0.8224 (pttm) cc_final: 0.7362 (tppt) REVERT: A 1017 GLU cc_start: 0.8089 (tp30) cc_final: 0.7680 (tt0) REVERT: B 111 ASP cc_start: 0.8018 (t0) cc_final: 0.7487 (t0) REVERT: B 179 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7967 (pp) REVERT: B 986 LYS cc_start: 0.8622 (ptmm) cc_final: 0.8386 (ptmm) REVERT: B 1017 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7799 (tt0) REVERT: C 111 ASP cc_start: 0.7872 (t0) cc_final: 0.7442 (t0) REVERT: C 177 MET cc_start: 0.8496 (ttp) cc_final: 0.8099 (ttm) REVERT: C 244 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8101 (pp) REVERT: C 1017 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7904 (tt0) REVERT: C 1076 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8120 (p) outliers start: 34 outliers final: 25 residues processed: 191 average time/residue: 0.1918 time to fit residues: 57.8384 Evaluate side-chains 174 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 262 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.083805 restraints weight = 40124.388| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.22 r_work: 0.2866 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 27636 Z= 0.254 Angle : 0.692 21.143 37716 Z= 0.341 Chirality : 0.049 0.339 4380 Planarity : 0.004 0.039 4764 Dihedral : 6.899 71.917 4965 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.60 % Allowed : 10.73 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.79 (0.14), residues: 3285 helix: 1.34 (0.20), residues: 747 sheet: 0.13 (0.18), residues: 858 loop : -1.83 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 214 TYR 0.021 0.002 TYR A 365 PHE 0.018 0.002 PHE B 515 TRP 0.009 0.002 TRP A 353 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00629 (27534) covalent geometry : angle 0.62234 (37455) SS BOND : bond 0.00818 ( 45) SS BOND : angle 2.47787 ( 90) hydrogen bonds : bond 0.06187 ( 1045) hydrogen bonds : angle 5.38285 ( 2883) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.26759 ( 45) link_NAG-ASN : bond 0.00683 ( 42) link_NAG-ASN : angle 4.84218 ( 126) *********************** 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 190 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8031 (pp) REVERT: A 574 ASP cc_start: 0.8768 (t70) cc_final: 0.8429 (t70) REVERT: A 786 LYS cc_start: 0.8254 (pttm) cc_final: 0.7412 (tppt) REVERT: A 882 ILE cc_start: 0.8863 (mt) cc_final: 0.8581 (mt) REVERT: A 979 ASP cc_start: 0.7961 (t0) cc_final: 0.7617 (t0) REVERT: A 1017 GLU cc_start: 0.8162 (tp30) cc_final: 0.7765 (tt0) REVERT: B 179 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7954 (pp) REVERT: B 986 LYS cc_start: 0.8619 (ptmm) cc_final: 0.8389 (ptmm) REVERT: C 244 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8086 (pp) REVERT: C 1002 GLN cc_start: 0.7426 (tp40) cc_final: 0.7134 (tt0) REVERT: C 1017 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7959 (tt0) REVERT: C 1076 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8351 (p) outliers start: 46 outliers final: 33 residues processed: 183 average time/residue: 0.1909 time to fit residues: 55.3994 Evaluate side-chains 177 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 188 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 6 optimal weight: 0.3980 chunk 240 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B1002 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088048 restraints weight = 39659.382| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.22 r_work: 0.2951 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27636 Z= 0.113 Angle : 0.607 20.812 37716 Z= 0.297 Chirality : 0.046 0.312 4380 Planarity : 0.003 0.036 4764 Dihedral : 6.573 69.904 4965 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.32 % Allowed : 11.04 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.58 (0.14), residues: 3285 helix: 1.54 (0.20), residues: 747 sheet: 0.34 (0.18), residues: 834 loop : -1.73 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1019 TYR 0.020 0.001 TYR B 365 PHE 0.021 0.001 PHE C 133 TRP 0.010 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00250 (27534) covalent geometry : angle 0.53182 (37455) SS BOND : bond 0.00650 ( 45) SS BOND : angle 2.37775 ( 90) hydrogen bonds : bond 0.04725 ( 1045) hydrogen bonds : angle 5.19813 ( 2883) link_BETA1-4 : bond 0.00426 ( 15) link_BETA1-4 : angle 1.19059 ( 45) link_NAG-ASN : bond 0.00787 ( 42) link_NAG-ASN : angle 4.63839 ( 126) *********************** 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 189 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7915 (pp) REVERT: A 574 ASP cc_start: 0.8775 (t70) cc_final: 0.8433 (t70) REVERT: A 786 LYS cc_start: 0.8278 (pttm) cc_final: 0.7408 (tppt) REVERT: A 1017 GLU cc_start: 0.8107 (tp30) cc_final: 0.7724 (tt0) REVERT: B 111 ASP cc_start: 0.8022 (t0) cc_final: 0.7493 (t0) REVERT: B 179 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8019 (pp) REVERT: B 986 LYS cc_start: 0.8541 (ptmm) cc_final: 0.8322 (ptmm) REVERT: B 1017 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7808 (tt0) REVERT: C 111 ASP cc_start: 0.7893 (t0) cc_final: 0.7465 (t0) REVERT: C 244 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8067 (pp) REVERT: C 1017 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7790 (tt0) outliers start: 38 outliers final: 28 residues processed: 183 average time/residue: 0.1852 time to fit residues: 53.6193 Evaluate side-chains 177 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 297 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.087077 restraints weight = 39768.586| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.23 r_work: 0.2936 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27636 Z= 0.142 Angle : 0.619 20.874 37716 Z= 0.303 Chirality : 0.046 0.280 4380 Planarity : 0.003 0.036 4764 Dihedral : 6.462 69.856 4965 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.39 % Allowed : 10.94 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.55 (0.14), residues: 3285 helix: 1.56 (0.20), residues: 747 sheet: 0.37 (0.18), residues: 834 loop : -1.71 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 214 TYR 0.020 0.001 TYR B 365 PHE 0.017 0.001 PHE C 133 TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00339 (27534) covalent geometry : angle 0.54489 (37455) SS BOND : bond 0.00667 ( 45) SS BOND : angle 2.50621 ( 90) hydrogen bonds : bond 0.04977 ( 1045) hydrogen bonds : angle 5.20328 ( 2883) link_BETA1-4 : bond 0.00374 ( 15) link_BETA1-4 : angle 1.18847 ( 45) link_NAG-ASN : bond 0.00720 ( 42) link_NAG-ASN : angle 4.61533 ( 126) ********************** 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 186 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8022 (pp) REVERT: A 574 ASP cc_start: 0.8778 (t70) cc_final: 0.8430 (t70) REVERT: A 786 LYS cc_start: 0.8389 (pttm) cc_final: 0.7646 (tppt) REVERT: A 1017 GLU cc_start: 0.8113 (tp30) cc_final: 0.7721 (tt0) REVERT: B 111 ASP cc_start: 0.8152 (t0) cc_final: 0.7564 (t0) REVERT: B 179 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8041 (pp) REVERT: B 986 LYS cc_start: 0.8540 (ptmm) cc_final: 0.8322 (ptmm) REVERT: B 1017 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7792 (tt0) REVERT: C 111 ASP cc_start: 0.7971 (t0) cc_final: 0.7546 (t0) REVERT: C 244 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8107 (pp) REVERT: C 1017 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7793 (tt0) outliers start: 40 outliers final: 34 residues processed: 179 average time/residue: 0.1766 time to fit residues: 50.6563 Evaluate side-chains 179 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 219 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 158 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 68 optimal weight: 0.0570 chunk 86 optimal weight: 2.9990 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 493 GLN A1002 GLN B1002 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088907 restraints weight = 39415.038| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.22 r_work: 0.2947 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 27636 Z= 0.108 Angle : 0.591 20.725 37716 Z= 0.289 Chirality : 0.045 0.284 4380 Planarity : 0.003 0.037 4764 Dihedral : 6.256 68.369 4965 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.22 % Allowed : 11.15 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3285 helix: 1.81 (0.20), residues: 726 sheet: 0.41 (0.18), residues: 846 loop : -1.68 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 214 TYR 0.020 0.001 TYR B1138 PHE 0.017 0.001 PHE C 133 TRP 0.009 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00242 (27534) covalent geometry : angle 0.51939 (37455) SS BOND : bond 0.00601 ( 45) SS BOND : angle 2.16935 ( 90) hydrogen bonds : bond 0.04464 ( 1045) hydrogen bonds : angle 5.12659 ( 2883) link_BETA1-4 : bond 0.00425 ( 15) link_BETA1-4 : angle 1.15235 ( 45) link_NAG-ASN : bond 0.00762 ( 42) link_NAG-ASN : angle 4.51847 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5122.21 seconds wall clock time: 88 minutes 49.95 seconds (5329.95 seconds total)