Starting phenix.real_space_refine on Sun Jul 5 10:19:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wgv_32490/07_2026/7wgv_32490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgv_32490/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wgv_32490/07_2026/7wgv_32490.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wgv_32490/07_2026/7wgv_32490.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wgv_32490/07_2026/7wgv_32490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgv_32490/07_2026/7wgv_32490.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wgv_32490/07_2026/7wgv_32490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgv_32490/07_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-6108/lib/python3.11/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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 11 Time building chain proxies: 5.91, per 1000 atoms: 0.22 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 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: 1.10 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: 7.68 Time building geometry restraints manager: 3.28 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: 14423 17.99 - 35.98: 1132 35.98 - 53.98: 195 53.98 - 71.97: 66 71.97 - 89.96: 42 Dihedral angle restraints: 15858 sinusoidal: 6228 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 15855 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 28.140 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 14.167 89.961 9537 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/Z covalent geometry : bond 0.01732 / 0.87 (27534) covalent geometry : angle 1.28662 / 0.48 (37455) SS BOND : bond 0.00732 / 0.54 ( 45) SS BOND : angle 2.52331 / 1.83 ( 90) hydrogen bonds : bond 0.12189 / 8.00 ( 1045) hydrogen bonds : angle 6.30149 / 4.44 ( 2883) link_BETA1-4 : bond 0.00293 / 0.17 ( 15) link_BETA1-4 : angle 0.88873 / 0.64 ( 45) link_NAG-ASN : bond 0.00831 / 0.55 ( 42) link_NAG-ASN : angle 4.87237 / 4.14 ( 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 : 1.035 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: 0.1947 time to fit residues: 65.5258 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 : 1.031 ------------------------------------------------------------------------------- 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... ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A 895 GLN A 935 GLN A 957 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094614 restraints weight = 40084.627| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.05 r_work: 0.3004 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27636 Z= 0.144 Angle : 0.658 20.243 37716 Z= 0.310 Chirality : 0.047 0.413 4380 Planarity : 0.004 0.033 4764 Dihedral : 7.258 89.410 3642 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.45 % Allowed : 4.79 % Favored : 94.76 % 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: 1.84 (0.20), residues: 735 sheet: 0.29 (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 B1138 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/Z covalent geometry : bond 0.00332 / 0.14 (27534) covalent geometry : angle 0.58191 / 0.29 (37455) SS BOND : bond 0.00616 / 0.45 ( 45) SS BOND : angle 1.83692 / 1.36 ( 90) hydrogen bonds : bond 0.05015 / 3.28 ( 1045) hydrogen bonds : angle 5.45357 / 3.82 ( 2883) link_BETA1-4 : bond 0.00444 / 0.25 ( 15) link_BETA1-4 : angle 1.15446 / 0.79 ( 45) link_NAG-ASN : bond 0.00741 / 0.50 ( 42) link_NAG-ASN : angle 5.09893 / 4.31 ( 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 164 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.970 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: 0.8097 (t0) cc_final: 0.7577 (t0) REVERT: B 606 ASN cc_start: 0.8133 (m-40) cc_final: 0.7331 (p0) REVERT: B 817 PHE cc_start: 0.6799 (t80) cc_final: 0.6518 (t80) REVERT: C 111 ASP cc_start: 0.7782 (t0) cc_final: 0.7337 (t0) REVERT: C 177 MET cc_start: 0.8192 (ttp) cc_final: 0.7774 (ttm) REVERT: C 443 SER cc_start: 0.9103 (t) cc_final: 0.8791 (p) REVERT: C 731 MET cc_start: 0.8920 (ptm) cc_final: 0.8688 (ptp) REVERT: C 781 VAL cc_start: 0.7332 (t) cc_final: 0.7007 (t) outliers start: 13 outliers final: 5 residues processed: 160 average time/residue: 0.1855 time to fit residues: 47.1116 Evaluate side-chains 133 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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: 8.9990 chunk 146 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 172 optimal weight: 0.0040 chunk 40 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN B 493 GLN C 895 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 = 0.3519 r_free = 0.3519 target = 0.118291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089844 restraints weight = 39716.999| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.24 r_work: 0.2937 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27636 Z= 0.132 Angle : 0.615 20.391 37716 Z= 0.296 Chirality : 0.046 0.368 4380 Planarity : 0.003 0.033 4764 Dihedral : 6.838 89.135 3642 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.45 % Allowed : 6.42 % Favored : 93.12 % 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: 1.76 (0.20), residues: 738 sheet: 0.40 (0.18), residues: 789 loop : -1.73 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.020 0.001 TYR B1138 PHE 0.016 0.001 PHE B 133 TRP 0.007 0.001 TRP B 152 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (27534) covalent geometry : angle 0.53901 / 0.28 (37455) SS BOND : bond 0.00543 / 0.39 ( 45) SS BOND : angle 2.07805 / 1.57 ( 90) hydrogen bonds : bond 0.04811 / 3.15 ( 1045) hydrogen bonds : angle 5.27490 / 3.70 ( 2883) link_BETA1-4 : bond 0.00399 / 0.22 ( 15) link_BETA1-4 : angle 1.11990 / 0.78 ( 45) link_NAG-ASN : bond 0.00741 / 0.50 ( 42) link_NAG-ASN : angle 4.81659 / 4.16 ( 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 165 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7527 (m-80) cc_final: 0.7219 (m-10) REVERT: A 1017 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7645 (tt0) REVERT: A 1050 MET cc_start: 0.8242 (ptp) cc_final: 0.8031 (ptm) REVERT: B 111 ASP cc_start: 0.8120 (t0) cc_final: 0.7602 (t0) REVERT: B 606 ASN cc_start: 0.8125 (m-40) cc_final: 0.7307 (p0) REVERT: C 111 ASP cc_start: 0.7813 (t0) cc_final: 0.7359 (t0) REVERT: C 177 MET cc_start: 0.8337 (ttp) cc_final: 0.7944 (ttm) REVERT: C 443 SER cc_start: 0.9096 (t) cc_final: 0.8780 (p) REVERT: C 781 VAL cc_start: 0.7240 (t) cc_final: 0.6923 (t) outliers start: 13 outliers final: 7 residues processed: 160 average time/residue: 0.1996 time to fit residues: 50.0833 Evaluate side-chains 138 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 34 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 241 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 148 ASN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.083115 restraints weight = 40045.998| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.20 r_work: 0.2855 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 27636 Z= 0.289 Angle : 0.759 21.290 37716 Z= 0.374 Chirality : 0.051 0.379 4380 Planarity : 0.004 0.043 4764 Dihedral : 7.148 87.747 3642 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.15 % Allowed : 8.51 % Favored : 90.35 % 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: -0.95 (0.14), residues: 3285 helix: 1.22 (0.20), residues: 744 sheet: 0.10 (0.17), residues: 819 loop : -1.93 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 102 TYR 0.022 0.002 TYR A 365 PHE 0.031 0.003 PHE B 906 TRP 0.011 0.002 TRP A 353 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.29 (27534) covalent geometry : angle 0.68693 / 0.36 (37455) SS BOND : bond 0.00739 / 0.52 ( 45) SS BOND : angle 2.73605 / 1.96 ( 90) hydrogen bonds : bond 0.06955 / 4.58 ( 1045) hydrogen bonds : angle 5.58816 / 3.92 ( 2883) link_BETA1-4 : bond 0.00409 / 0.23 ( 15) link_BETA1-4 : angle 1.22497 / 0.82 ( 45) link_NAG-ASN : bond 0.00667 / 0.45 ( 42) link_NAG-ASN : angle 5.13214 / 4.50 ( 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 183 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.8761 (t70) cc_final: 0.8347 (t70) REVERT: A 786 LYS cc_start: 0.8037 (pttm) cc_final: 0.7195 (tppt) REVERT: A 994 ASP cc_start: 0.8020 (m-30) cc_final: 0.7526 (t0) REVERT: B 179 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7956 (pp) REVERT: B 606 ASN cc_start: 0.8111 (m-40) cc_final: 0.7870 (m-40) REVERT: B 900 MET cc_start: 0.8558 (mtt) cc_final: 0.8297 (mtp) REVERT: B 1002 GLN cc_start: 0.7550 (tp40) cc_final: 0.7331 (tp40) REVERT: C 118 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8294 (tt) REVERT: C 346 ARG cc_start: 0.8249 (tpt90) cc_final: 0.8032 (mmm160) REVERT: C 443 SER cc_start: 0.9106 (t) cc_final: 0.8856 (p) REVERT: C 1002 GLN cc_start: 0.7533 (tp40) cc_final: 0.7172 (tp40) outliers start: 33 outliers final: 17 residues processed: 178 average time/residue: 0.1887 time to fit residues: 52.2789 Evaluate side-chains 155 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ASP 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 291 CYS Chi-restraints excluded: chain B residue 662 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 118 LEU 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 870 ILE Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 187 optimal weight: 2.9990 chunk 100 optimal weight: 0.0770 chunk 323 optimal weight: 0.0060 chunk 281 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 327 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN A 957 GLN C 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.088175 restraints weight = 39463.873| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.22 r_work: 0.2948 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 27636 Z= 0.112 Angle : 0.613 20.801 37716 Z= 0.297 Chirality : 0.046 0.330 4380 Planarity : 0.003 0.037 4764 Dihedral : 6.626 80.483 3642 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.11 % Allowed : 9.27 % Favored : 89.62 % 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: -0.59 (0.14), residues: 3285 helix: 1.55 (0.20), residues: 741 sheet: 0.29 (0.17), residues: 840 loop : -1.71 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.019 0.001 TYR B 365 PHE 0.019 0.001 PHE B 133 TRP 0.009 0.001 TRP C 104 HIS 0.003 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (27534) covalent geometry : angle 0.53717 / 0.28 (37455) SS BOND : bond 0.00621 / 0.45 ( 45) SS BOND : angle 2.37062 / 1.81 ( 90) hydrogen bonds : bond 0.04846 / 3.18 ( 1045) hydrogen bonds : angle 5.23583 / 3.67 ( 2883) link_BETA1-4 : bond 0.00422 / 0.23 ( 15) link_BETA1-4 : angle 1.10696 / 0.76 ( 45) link_NAG-ASN : bond 0.00763 / 0.52 ( 42) link_NAG-ASN : angle 4.73448 / 4.18 ( 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 191 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7885 (pp) REVERT: A 574 ASP cc_start: 0.8793 (t70) cc_final: 0.8366 (t70) REVERT: A 786 LYS cc_start: 0.8157 (pttm) cc_final: 0.7353 (tppt) REVERT: A 882 ILE cc_start: 0.8645 (mt) cc_final: 0.8392 (mt) REVERT: A 957 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: A 1017 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7681 (tt0) REVERT: B 111 ASP cc_start: 0.8015 (t0) cc_final: 0.7581 (t0) REVERT: B 214 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7547 (ttm110) REVERT: B 900 MET cc_start: 0.8391 (mtt) cc_final: 0.8138 (mtp) REVERT: B 986 LYS cc_start: 0.8621 (ptmm) cc_final: 0.8346 (ptmm) REVERT: B 1017 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7820 (tt0) REVERT: C 346 ARG cc_start: 0.8374 (tpt90) cc_final: 0.8137 (mmm160) REVERT: C 792 PRO cc_start: 0.9026 (Cg_exo) cc_final: 0.8793 (Cg_endo) REVERT: C 1017 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7956 (tt0) REVERT: C 1076 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8165 (p) outliers start: 32 outliers final: 17 residues processed: 182 average time/residue: 0.1813 time to fit residues: 51.6902 Evaluate side-chains 161 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1050 MET 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 291 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 964 LYS 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 662 CYS 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: 7.9990 chunk 300 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 935 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 = 0.3452 r_free = 0.3452 target = 0.113208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.084544 restraints weight = 40040.131| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.23 r_work: 0.2875 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27636 Z= 0.231 Angle : 0.684 21.042 37716 Z= 0.334 Chirality : 0.048 0.363 4380 Planarity : 0.004 0.037 4764 Dihedral : 6.727 77.858 3642 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.28 % Allowed : 10.10 % Favored : 88.61 % 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: -0.76 (0.14), residues: 3285 helix: 1.38 (0.20), residues: 747 sheet: 0.19 (0.18), residues: 852 loop : -1.83 (0.13), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.021 0.002 TYR B 365 PHE 0.016 0.002 PHE B 194 TRP 0.008 0.001 TRP C 353 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.23 (27534) covalent geometry : angle 0.61270 / 0.32 (37455) SS BOND : bond 0.00738 / 0.53 ( 45) SS BOND : angle 2.39816 / 1.71 ( 90) hydrogen bonds : bond 0.06022 / 3.97 ( 1045) hydrogen bonds : angle 5.37917 / 3.79 ( 2883) link_BETA1-4 : bond 0.00317 / 0.17 ( 15) link_BETA1-4 : angle 1.14291 / 0.78 ( 45) link_NAG-ASN : bond 0.00708 / 0.47 ( 42) link_NAG-ASN : angle 4.88998 / 4.32 ( 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 183 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8009 (pp) REVERT: A 574 ASP cc_start: 0.8775 (t70) cc_final: 0.8390 (t70) REVERT: A 786 LYS cc_start: 0.8190 (pttm) cc_final: 0.7342 (tppt) REVERT: B 111 ASP cc_start: 0.8090 (t0) cc_final: 0.7590 (t0) REVERT: B 179 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7944 (pp) REVERT: B 214 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7593 (ttm110) REVERT: B 900 MET cc_start: 0.8404 (mtt) cc_final: 0.8127 (mtp) REVERT: B 986 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8437 (ptmm) REVERT: C 244 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8132 (pp) REVERT: C 346 ARG cc_start: 0.8369 (tpt90) cc_final: 0.8162 (mmm160) REVERT: C 792 PRO cc_start: 0.8998 (Cg_exo) cc_final: 0.8763 (Cg_endo) REVERT: C 1002 GLN cc_start: 0.7433 (tp40) cc_final: 0.7145 (tt0) REVERT: C 1076 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8303 (p) outliers start: 37 outliers final: 26 residues processed: 179 average time/residue: 0.1779 time to fit residues: 50.2415 Evaluate side-chains 171 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS 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 1050 MET 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 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 581 THR 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: 0.0870 chunk 118 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 108 optimal weight: 0.0060 chunk 48 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 228 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN B1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.089955 restraints weight = 39245.446| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.21 r_work: 0.2979 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1801 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= 0.104 Angle : 0.588 20.736 37716 Z= 0.285 Chirality : 0.045 0.354 4380 Planarity : 0.003 0.036 4764 Dihedral : 6.231 66.850 3642 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.25 % Allowed : 10.31 % 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: -0.49 (0.14), residues: 3285 helix: 1.68 (0.20), residues: 741 sheet: 0.36 (0.18), residues: 846 loop : -1.69 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.019 0.001 TYR B 365 PHE 0.010 0.001 PHE A 133 TRP 0.012 0.001 TRP C 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (27534) covalent geometry : angle 0.51941 / 0.27 (37455) SS BOND : bond 0.00580 / 0.42 ( 45) SS BOND : angle 1.75727 / 1.31 ( 90) hydrogen bonds : bond 0.04384 / 2.88 ( 1045) hydrogen bonds : angle 5.09439 / 3.57 ( 2883) link_BETA1-4 : bond 0.00460 / 0.25 ( 15) link_BETA1-4 : angle 1.07960 / 0.75 ( 45) link_NAG-ASN : bond 0.00799 / 0.54 ( 42) link_NAG-ASN : angle 4.55325 / 4.06 ( 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 191 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7917 (pp) REVERT: A 574 ASP cc_start: 0.8801 (t70) cc_final: 0.8435 (t70) REVERT: A 786 LYS cc_start: 0.8218 (pttm) cc_final: 0.7369 (tppt) REVERT: A 1017 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7586 (tt0) REVERT: A 1019 ARG cc_start: 0.7823 (tmm160) cc_final: 0.7356 (ttp-110) REVERT: B 32 PHE cc_start: 0.7534 (m-80) cc_final: 0.7329 (m-80) REVERT: B 111 ASP cc_start: 0.8179 (t0) cc_final: 0.7604 (t0) REVERT: B 179 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7971 (pp) REVERT: B 900 MET cc_start: 0.8344 (mtt) cc_final: 0.8112 (mtp) REVERT: B 986 LYS cc_start: 0.8509 (ptmm) cc_final: 0.8247 (ptmm) REVERT: B 1017 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7730 (tt0) REVERT: C 111 ASP cc_start: 0.7869 (t0) cc_final: 0.7472 (t0) REVERT: C 177 MET cc_start: 0.8502 (ttp) cc_final: 0.8122 (ttm) REVERT: C 233 ILE cc_start: 0.8286 (mt) cc_final: 0.8023 (tt) REVERT: C 346 ARG cc_start: 0.8375 (tpt90) cc_final: 0.8173 (mmm160) REVERT: C 1017 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7898 (tt0) REVERT: C 1076 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8128 (p) outliers start: 36 outliers final: 22 residues processed: 186 average time/residue: 0.1728 time to fit residues: 51.0136 Evaluate side-chains 172 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 662 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1050 MET 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 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 581 THR 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 291 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 743 CYS 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: 3.9990 chunk 239 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 106 optimal weight: 0.0570 chunk 253 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.084027 restraints weight = 40084.071| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.21 r_work: 0.2870 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 27636 Z= 0.247 Angle : 0.695 21.019 37716 Z= 0.341 Chirality : 0.049 0.310 4380 Planarity : 0.004 0.041 4764 Dihedral : 6.547 70.778 3642 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.32 % Allowed : 10.62 % Favored : 88.06 % 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: -0.73 (0.14), residues: 3285 helix: 1.40 (0.20), residues: 747 sheet: 0.16 (0.18), residues: 858 loop : -1.80 (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 0.019 0.002 PHE B 515 TRP 0.011 0.002 TRP B 64 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.25 (27534) covalent geometry : angle 0.62803 / 0.32 (37455) SS BOND : bond 0.00819 / 0.59 ( 45) SS BOND : angle 2.41099 / 1.70 ( 90) hydrogen bonds : bond 0.06177 / 4.08 ( 1045) hydrogen bonds : angle 5.36406 / 3.77 ( 2883) link_BETA1-4 : bond 0.00315 / 0.17 ( 15) link_BETA1-4 : angle 1.16073 / 0.78 ( 45) link_NAG-ASN : bond 0.00696 / 0.47 ( 42) link_NAG-ASN : angle 4.75889 / 4.26 ( 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 182 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8036 (pp) REVERT: A 574 ASP cc_start: 0.8778 (t70) cc_final: 0.8407 (t70) REVERT: A 786 LYS cc_start: 0.8251 (pttm) cc_final: 0.7415 (tppt) REVERT: A 979 ASP cc_start: 0.7960 (t0) cc_final: 0.7603 (t0) REVERT: A 1017 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7753 (tt0) REVERT: B 111 ASP cc_start: 0.8068 (t0) cc_final: 0.7565 (t0) REVERT: B 179 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8025 (pp) REVERT: B 900 MET cc_start: 0.8443 (mtt) cc_final: 0.8198 (mtp) REVERT: B 986 LYS cc_start: 0.8640 (ptmm) cc_final: 0.8420 (ptmm) REVERT: C 1002 GLN cc_start: 0.7395 (tp40) cc_final: 0.7131 (tp40) REVERT: C 1017 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8002 (tt0) REVERT: C 1076 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8289 (p) outliers start: 38 outliers final: 30 residues processed: 176 average time/residue: 0.1725 time to fit residues: 48.1585 Evaluate side-chains 174 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1050 MET 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 1002 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 188 optimal weight: 0.0870 chunk 215 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 257 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 299 optimal weight: 7.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.086911 restraints weight = 39778.741| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.23 r_work: 0.2931 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1985 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= 0.133 Angle : 0.628 20.913 37716 Z= 0.306 Chirality : 0.046 0.317 4380 Planarity : 0.003 0.036 4764 Dihedral : 6.383 70.012 3642 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.39 % Allowed : 10.76 % Favored : 87.85 % 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: -0.59 (0.14), residues: 3285 helix: 1.51 (0.20), residues: 744 sheet: 0.30 (0.18), residues: 846 loop : -1.71 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 214 TYR 0.021 0.001 TYR B 365 PHE 0.023 0.001 PHE C 133 TRP 0.008 0.001 TRP C 104 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (27534) covalent geometry : angle 0.55553 / 0.29 (37455) SS BOND : bond 0.00638 / 0.47 ( 45) SS BOND : angle 2.48131 / 1.87 ( 90) hydrogen bonds : bond 0.05096 / 3.36 ( 1045) hydrogen bonds : angle 5.23807 / 3.68 ( 2883) link_BETA1-4 : bond 0.00374 / 0.20 ( 15) link_BETA1-4 : angle 1.08533 / 0.74 ( 45) link_NAG-ASN : bond 0.00735 / 0.50 ( 42) link_NAG-ASN : angle 4.65479 / 4.17 ( 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 184 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 574 ASP cc_start: 0.8789 (t70) cc_final: 0.8439 (t70) REVERT: A 786 LYS cc_start: 0.8370 (pttm) cc_final: 0.7644 (tppt) REVERT: A 1017 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7710 (tt0) REVERT: B 111 ASP cc_start: 0.8021 (t0) cc_final: 0.7593 (t0) REVERT: B 179 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8003 (pp) REVERT: B 900 MET cc_start: 0.8313 (mtt) cc_final: 0.8068 (mtp) REVERT: B 986 LYS cc_start: 0.8464 (ptmm) cc_final: 0.8209 (ptmm) REVERT: B 1017 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7802 (tt0) REVERT: C 244 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8069 (pp) REVERT: C 1017 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7846 (tt0) REVERT: C 1076 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8253 (p) outliers start: 40 outliers final: 32 residues processed: 179 average time/residue: 0.1831 time to fit residues: 51.4561 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 : 0.974 ------------------------------------------------------------------------------- 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 826 VAL Chi-restraints excluded: chain A residue 1050 MET 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 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 1050 MET Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 297 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.086783 restraints weight = 39797.399| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.23 r_work: 0.2931 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 27636 Z= 0.144 Angle : 0.630 20.903 37716 Z= 0.306 Chirality : 0.046 0.285 4380 Planarity : 0.003 0.037 4764 Dihedral : 6.296 69.891 3642 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.35 % Allowed : 10.69 % Favored : 87.95 % 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: -0.59 (0.14), residues: 3285 helix: 1.55 (0.20), residues: 747 sheet: 0.28 (0.18), residues: 858 loop : -1.74 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 214 TYR 0.021 0.001 TYR B 365 PHE 0.018 0.001 PHE C 133 TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (27534) covalent geometry : angle 0.55741 / 0.29 (37455) SS BOND : bond 0.00690 / 0.50 ( 45) SS BOND : angle 2.53409 / 1.92 ( 90) hydrogen bonds : bond 0.05103 / 3.36 ( 1045) hydrogen bonds : angle 5.22934 / 3.68 ( 2883) link_BETA1-4 : bond 0.00362 / 0.19 ( 15) link_BETA1-4 : angle 1.08557 / 0.74 ( 45) link_NAG-ASN : bond 0.00723 / 0.49 ( 42) link_NAG-ASN : angle 4.62136 / 4.14 ( 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 182 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8029 (pp) REVERT: A 574 ASP cc_start: 0.8795 (t70) cc_final: 0.8447 (t70) REVERT: A 786 LYS cc_start: 0.8384 (pttm) cc_final: 0.7653 (tppt) REVERT: A 1017 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7668 (tt0) REVERT: B 111 ASP cc_start: 0.8001 (t0) cc_final: 0.7572 (t0) REVERT: B 179 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7998 (pp) REVERT: B 900 MET cc_start: 0.8367 (mtt) cc_final: 0.8119 (mtp) REVERT: B 986 LYS cc_start: 0.8571 (ptmm) cc_final: 0.8333 (ptmm) REVERT: B 1017 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7833 (tt0) REVERT: C 111 ASP cc_start: 0.7984 (t0) cc_final: 0.7558 (t0) REVERT: C 244 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8044 (pp) REVERT: C 1017 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7836 (tt0) REVERT: C 1076 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8230 (p) outliers start: 39 outliers final: 32 residues processed: 176 average time/residue: 0.1762 time to fit residues: 48.7219 Evaluate side-chains 178 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 826 VAL Chi-restraints excluded: chain A residue 1050 MET 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 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 1092 GLU Chi-restraints excluded: chain B residue 1132 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 219 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 27 optimal weight: 0.3980 chunk 231 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 86 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN B1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090097 restraints weight = 39359.490| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.21 r_work: 0.2981 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.002 0.075 27636 Z= 0.104 Angle : 0.586 20.616 37716 Z= 0.285 Chirality : 0.045 0.283 4380 Planarity : 0.003 0.036 4764 Dihedral : 5.911 66.962 3642 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.25 % Allowed : 10.76 % Favored : 87.99 % 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: -0.41 (0.14), residues: 3285 helix: 1.89 (0.20), residues: 726 sheet: 0.39 (0.18), residues: 846 loop : -1.66 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 214 TYR 0.019 0.001 TYR B 365 PHE 0.017 0.001 PHE C 133 TRP 0.008 0.001 TRP C 436 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (27534) covalent geometry : angle 0.51730 / 0.27 (37455) SS BOND : bond 0.00608 / 0.44 ( 45) SS BOND : angle 2.09088 / 1.60 ( 90) hydrogen bonds : bond 0.04263 / 2.79 ( 1045) hydrogen bonds : angle 5.08036 / 3.58 ( 2883) link_BETA1-4 : bond 0.00431 / 0.23 ( 15) link_BETA1-4 : angle 1.06614 / 0.74 ( 45) link_NAG-ASN : bond 0.00775 / 0.52 ( 42) link_NAG-ASN : angle 4.44972 / 3.99 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4886.15 seconds wall clock time: 85 minutes 7.38 seconds (5107.38 seconds total)