Starting phenix.real_space_refine on Fri Mar 6 12:34:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s6j_24877/03_2026/7s6j_24877.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s6j_24877/03_2026/7s6j_24877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s6j_24877/03_2026/7s6j_24877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s6j_24877/03_2026/7s6j_24877.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s6j_24877/03_2026/7s6j_24877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s6j_24877/03_2026/7s6j_24877.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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 144 5.16 5 C 19572 2.51 5 N 5106 2.21 5 O 5973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30795 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8392 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "B" Number of atoms: 8392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8392 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "E" Number of atoms: 8392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8392 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 772 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.12, per 1000 atoms: 0.23 Number of scatterers: 30795 At special positions: 0 Unit cell: (159.85, 170.2, 197.8, 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 144 16.00 O 5973 8.00 N 5106 7.00 C 19572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.20 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.10 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS E 383 " distance=2.20 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS E 985 " distance=2.20 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.07 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.10 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.01 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.05 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.07 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.04 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.02 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.09 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.01 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 709 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A 17 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 234 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B 17 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 234 " " NAG E1301 " - " ASN E 709 " " NAG E1302 " - " ASN E1134 " " NAG E1303 " - " ASN E 17 " " NAG E1304 " - " ASN E 149 " " NAG E1305 " - " ASN E 234 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN E 717 " " NAG Q 1 " - " ASN E 801 " " NAG R 1 " - " ASN E1098 " Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7260 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 63 sheets defined 21.4% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.644A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.792A 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: 3.723A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.708A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.348A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 3.910A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.967A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.935A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.645A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.793A 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: 3.723A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.708A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.347A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.910A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.967A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.936A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 150 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.644A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.792A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.723A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.708A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.348A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 963 removed outlier: 3.910A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 964 through 968 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.967A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR E 998 " --> pdb=" O ASP E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1147 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.936A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.597A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.436A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.650A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.351A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.506A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.184A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.958A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.958A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.607A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.234A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.484A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.767A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.848A pdb=" N THR H 33 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 18 through 24 Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.407A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS L 39 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.598A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.436A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.650A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.352A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.505A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.183A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.957A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.957A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.607A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.234A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.483A pdb=" N ALA B 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS E 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 703 " --> pdb=" O LYS E 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.598A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.598A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.766A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.848A pdb=" N THR C 33 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 18 through 24 Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.406A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS D 39 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.598A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS E 187 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 224 " --> pdb=" O SER E 205 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.436A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.650A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ARG E 246 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL E 143 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE E 140 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE E 157 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY E 142 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 83 through 85 removed outlier: 4.351A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN E 121 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.507A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL E 595 " --> pdb=" O SER E 316 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 324 through 326 removed outlier: 6.183A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 348 through 349 removed outlier: 6.957A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 348 through 349 removed outlier: 6.957A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.607A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AG1, first strand: chain 'E' and resid 654 through 660 removed outlier: 5.234A pdb=" N THR E 696 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN E 658 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AG5, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.767A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.847A pdb=" N THR F 33 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 18 through 24 Processing sheet with id=AG8, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.407A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS G 39 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) 1278 hydrogen bonds defined for protein. 3384 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: 7.96 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6384 1.32 - 1.46: 10902 1.46 - 1.60: 13980 1.60 - 1.74: 57 1.74 - 1.88: 177 Bond restraints: 31500 Sorted by residual: bond pdb=" NE ARG B 634 " pdb=" CZ ARG B 634 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 5.02e+01 bond pdb=" NE ARG A 634 " pdb=" CZ ARG A 634 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 4.98e+01 bond pdb=" NE ARG E 634 " pdb=" CZ ARG E 634 " ideal model delta sigma weight residual 1.326 1.403 -0.077 1.10e-02 8.26e+03 4.95e+01 bond pdb=" NE ARG C 95 " pdb=" CZ ARG C 95 " ideal model delta sigma weight residual 1.326 1.386 -0.060 1.10e-02 8.26e+03 3.01e+01 bond pdb=" NE ARG H 95 " pdb=" CZ ARG H 95 " ideal model delta sigma weight residual 1.326 1.386 -0.060 1.10e-02 8.26e+03 2.99e+01 ... (remaining 31495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 35916 2.29 - 4.57: 5699 4.57 - 6.86: 1031 6.86 - 9.15: 185 9.15 - 11.43: 27 Bond angle restraints: 42858 Sorted by residual: angle pdb=" N GLY F 106 " pdb=" CA GLY F 106 " pdb=" C GLY F 106 " ideal model delta sigma weight residual 111.70 123.12 -11.42 1.28e+00 6.10e-01 7.96e+01 angle pdb=" N GLY H 106 " pdb=" CA GLY H 106 " pdb=" C GLY H 106 " ideal model delta sigma weight residual 111.70 123.09 -11.39 1.28e+00 6.10e-01 7.92e+01 angle pdb=" N GLY C 106 " pdb=" CA GLY C 106 " pdb=" C GLY C 106 " ideal model delta sigma weight residual 111.70 123.04 -11.34 1.28e+00 6.10e-01 7.85e+01 angle pdb=" C ASN E 81 " pdb=" N PRO E 82 " pdb=" CA PRO E 82 " ideal model delta sigma weight residual 120.31 128.69 -8.38 9.80e-01 1.04e+00 7.32e+01 angle pdb=" C ASN B 81 " pdb=" N PRO B 82 " pdb=" CA PRO B 82 " ideal model delta sigma weight residual 120.31 128.69 -8.38 9.80e-01 1.04e+00 7.31e+01 ... (remaining 42853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 18529 17.68 - 35.35: 491 35.35 - 53.03: 141 53.03 - 70.71: 75 70.71 - 88.38: 9 Dihedral angle restraints: 19245 sinusoidal: 7932 harmonic: 11313 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 160.00 -67.00 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 159.98 -66.98 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS E 617 " pdb=" SG CYS E 617 " pdb=" SG CYS E 649 " pdb=" CB CYS E 649 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 ... (remaining 19242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3457 0.102 - 0.204: 1173 0.204 - 0.306: 201 0.306 - 0.408: 71 0.408 - 0.510: 30 Chirality restraints: 4932 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.21e+02 ... (remaining 4929 not shown) Planarity restraints: 5526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.073 2.00e-02 2.50e+03 7.62e-02 7.25e+01 pdb=" CG ASN E 234 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.118 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.073 2.00e-02 2.50e+03 7.61e-02 7.23e+01 pdb=" CG ASN A 234 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.117 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.073 2.00e-02 2.50e+03 7.60e-02 7.23e+01 pdb=" CG ASN B 234 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.118 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.093 2.00e-02 2.50e+03 ... (remaining 5523 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 12580 2.90 - 3.40: 28437 3.40 - 3.90: 53403 3.90 - 4.40: 61951 4.40 - 4.90: 99959 Nonbonded interactions: 256330 Sorted by model distance: nonbonded pdb=" N ASN B 185 " pdb=" O ASN B 185 " model vdw 2.401 2.496 nonbonded pdb=" N ASN A 185 " pdb=" O ASN A 185 " model vdw 2.402 2.496 nonbonded pdb=" N ASN E 185 " pdb=" O ASN E 185 " model vdw 2.402 2.496 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.413 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.414 3.120 ... (remaining 256325 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.280 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.020 0.168 31584 Z= 1.078 Angle : 1.813 12.210 43059 Z= 1.214 Chirality : 0.110 0.510 4932 Planarity : 0.009 0.050 5502 Dihedral : 9.983 88.383 11832 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.12), residues: 3852 helix: 0.23 (0.18), residues: 648 sheet: 0.76 (0.17), residues: 945 loop : -0.15 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 95 TYR 0.093 0.009 TYR E 37 PHE 0.050 0.006 PHE E 55 TRP 0.063 0.011 TRP E 64 HIS 0.012 0.003 HIS C 100G Details of bonding type rmsd covalent geometry : bond 0.02012 (31500) covalent geometry : angle 1.80257 (42858) SS BOND : bond 0.04557 ( 51) SS BOND : angle 3.01230 ( 102) hydrogen bonds : bond 0.16377 ( 1236) hydrogen bonds : angle 8.83199 ( 3384) link_BETA1-4 : bond 0.07600 ( 9) link_BETA1-4 : angle 6.06770 ( 27) link_NAG-ASN : bond 0.08478 ( 24) link_NAG-ASN : angle 2.36971 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 581 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.3964 (m-80) cc_final: 0.3184 (m-80) REVERT: A 177 MET cc_start: 0.7446 (mtp) cc_final: 0.6773 (mtm) REVERT: A 205 SER cc_start: 0.8229 (p) cc_final: 0.7625 (p) REVERT: A 269 TYR cc_start: 0.7191 (m-80) cc_final: 0.6716 (m-80) REVERT: A 338 PHE cc_start: 0.7487 (m-80) cc_final: 0.7284 (m-80) REVERT: A 342 PHE cc_start: 0.7601 (m-80) cc_final: 0.7273 (m-80) REVERT: A 428 ASP cc_start: 0.8499 (t0) cc_final: 0.8175 (p0) REVERT: A 456 PHE cc_start: 0.6884 (m-80) cc_final: 0.4995 (m-80) REVERT: H 54 LEU cc_start: 0.7411 (mt) cc_final: 0.6815 (mt) REVERT: H 68 THR cc_start: 0.5518 (p) cc_final: 0.4555 (p) REVERT: H 80 MET cc_start: 0.1473 (ttp) cc_final: 0.0482 (ppp) REVERT: L 4 MET cc_start: 0.4435 (mmm) cc_final: 0.3858 (mmm) REVERT: B 160 TYR cc_start: 0.4066 (m-80) cc_final: 0.3258 (m-80) REVERT: B 177 MET cc_start: 0.7386 (mtp) cc_final: 0.6630 (mtm) REVERT: B 201 PHE cc_start: 0.7807 (t80) cc_final: 0.7478 (t80) REVERT: B 335 LEU cc_start: 0.8742 (mt) cc_final: 0.8459 (tp) REVERT: B 402 ILE cc_start: 0.8030 (pt) cc_final: 0.7650 (pt) REVERT: B 428 ASP cc_start: 0.8272 (t0) cc_final: 0.7956 (p0) REVERT: B 456 PHE cc_start: 0.7045 (m-80) cc_final: 0.4988 (m-80) REVERT: C 48 MET cc_start: 0.6766 (mtm) cc_final: 0.6513 (mtt) REVERT: C 54 LEU cc_start: 0.7391 (mt) cc_final: 0.6752 (mp) REVERT: C 68 THR cc_start: 0.5648 (p) cc_final: 0.4954 (p) REVERT: C 80 MET cc_start: 0.0703 (ttp) cc_final: 0.0419 (ppp) REVERT: D 4 MET cc_start: 0.4422 (mmm) cc_final: 0.3864 (mmm) REVERT: E 61 ASN cc_start: 0.7034 (m-40) cc_final: 0.6493 (p0) REVERT: E 160 TYR cc_start: 0.3888 (m-80) cc_final: 0.2944 (m-80) REVERT: E 177 MET cc_start: 0.7347 (mtp) cc_final: 0.6954 (mtm) REVERT: E 456 PHE cc_start: 0.7021 (m-80) cc_final: 0.5130 (m-80) REVERT: E 461 LEU cc_start: 0.8732 (mt) cc_final: 0.8458 (mt) REVERT: F 54 LEU cc_start: 0.7640 (mt) cc_final: 0.7167 (mp) REVERT: F 68 THR cc_start: 0.5281 (p) cc_final: 0.4749 (p) REVERT: F 80 MET cc_start: 0.1100 (ttp) cc_final: 0.0192 (ppp) REVERT: G 4 MET cc_start: 0.4270 (mmm) cc_final: 0.3786 (mmm) outliers start: 6 outliers final: 3 residues processed: 587 average time/residue: 0.2149 time to fit residues: 194.9384 Evaluate side-chains 236 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 233 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 81 ASN A 218 GLN A 360 ASN A 655 HIS A 804 GLN A 907 ASN A 913 GLN A1119 ASN L 38 GLN B 49 HIS B 81 ASN B 218 GLN B 360 ASN B 655 HIS B 907 ASN B 913 GLN B1119 ASN D 38 GLN E 49 HIS E 81 ASN E 218 GLN E 360 ASN E 613 GLN E 655 HIS E 907 ASN E 913 GLN E1119 ASN F 39 GLN F 61 GLN G 37 GLN G 38 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.137888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086655 restraints weight = 69275.946| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.73 r_work: 0.3004 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 31584 Z= 0.262 Angle : 0.811 9.380 43059 Z= 0.424 Chirality : 0.051 0.322 4932 Planarity : 0.005 0.046 5502 Dihedral : 6.976 59.971 4896 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.21 % Allowed : 5.82 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 3852 helix: 1.59 (0.20), residues: 645 sheet: 0.16 (0.16), residues: 1041 loop : -0.70 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 214 TYR 0.034 0.003 TYR F 102 PHE 0.030 0.003 PHE H 100H TRP 0.030 0.002 TRP A 64 HIS 0.008 0.002 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00612 (31500) covalent geometry : angle 0.79070 (42858) SS BOND : bond 0.00845 ( 51) SS BOND : angle 2.00671 ( 102) hydrogen bonds : bond 0.05867 ( 1236) hydrogen bonds : angle 7.02319 ( 3384) link_BETA1-4 : bond 0.00511 ( 9) link_BETA1-4 : angle 3.84893 ( 27) link_NAG-ASN : bond 0.00607 ( 24) link_NAG-ASN : angle 3.17462 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.4054 (m-80) cc_final: 0.3066 (m-80) REVERT: A 177 MET cc_start: 0.7304 (mtp) cc_final: 0.6994 (mtm) REVERT: A 192 PHE cc_start: 0.8124 (m-10) cc_final: 0.7873 (m-10) REVERT: A 269 TYR cc_start: 0.7645 (m-80) cc_final: 0.6994 (m-80) REVERT: A 338 PHE cc_start: 0.7617 (m-80) cc_final: 0.7169 (m-80) REVERT: A 342 PHE cc_start: 0.7932 (m-80) cc_final: 0.7424 (m-80) REVERT: A 378 LYS cc_start: 0.8157 (tmtm) cc_final: 0.7940 (tmtt) REVERT: A 428 ASP cc_start: 0.8888 (t0) cc_final: 0.8442 (p0) REVERT: A 456 PHE cc_start: 0.7169 (m-80) cc_final: 0.6848 (m-80) REVERT: H 80 MET cc_start: 0.1499 (ttp) cc_final: 0.0478 (ppp) REVERT: H 90 TYR cc_start: 0.5823 (p90) cc_final: 0.5524 (p90) REVERT: L 4 MET cc_start: 0.5968 (mmm) cc_final: 0.5106 (mpp) REVERT: B 153 MET cc_start: 0.8687 (tpp) cc_final: 0.8338 (ptm) REVERT: B 160 TYR cc_start: 0.4285 (m-80) cc_final: 0.3027 (m-80) REVERT: B 177 MET cc_start: 0.7393 (mtp) cc_final: 0.6871 (mtm) REVERT: B 192 PHE cc_start: 0.7917 (m-10) cc_final: 0.7593 (m-10) REVERT: B 201 PHE cc_start: 0.7752 (t80) cc_final: 0.7492 (t80) REVERT: B 342 PHE cc_start: 0.7680 (m-80) cc_final: 0.7465 (m-80) REVERT: B 456 PHE cc_start: 0.7155 (m-80) cc_final: 0.6795 (m-80) REVERT: B 529 LYS cc_start: 0.8001 (pptt) cc_final: 0.7660 (pptt) REVERT: C 80 MET cc_start: 0.1008 (ttp) cc_final: 0.0087 (ppp) REVERT: C 90 TYR cc_start: 0.5920 (p90) cc_final: 0.5553 (p90) REVERT: D 4 MET cc_start: 0.6048 (mmm) cc_final: 0.5115 (mpp) REVERT: D 32 TYR cc_start: 0.6135 (m-80) cc_final: 0.5855 (m-80) REVERT: D 50 ASP cc_start: 0.7788 (t0) cc_final: 0.7527 (t70) REVERT: D 91 PRO cc_start: 0.6706 (Cg_exo) cc_final: 0.6479 (Cg_endo) REVERT: E 153 MET cc_start: 0.8683 (tpp) cc_final: 0.8308 (ptm) REVERT: E 160 TYR cc_start: 0.3934 (m-80) cc_final: 0.2958 (m-80) REVERT: E 192 PHE cc_start: 0.7718 (m-80) cc_final: 0.7397 (m-80) REVERT: E 205 SER cc_start: 0.8058 (p) cc_final: 0.7301 (t) REVERT: E 338 PHE cc_start: 0.7107 (m-80) cc_final: 0.6811 (m-80) REVERT: E 402 ILE cc_start: 0.7744 (pt) cc_final: 0.7197 (pt) REVERT: E 456 PHE cc_start: 0.7100 (m-80) cc_final: 0.6754 (m-80) REVERT: E 461 LEU cc_start: 0.8723 (mt) cc_final: 0.8420 (mt) REVERT: E 517 LEU cc_start: 0.7119 (mt) cc_final: 0.6303 (mp) REVERT: F 80 MET cc_start: 0.1560 (ttp) cc_final: 0.0376 (ppp) REVERT: F 90 TYR cc_start: 0.5925 (p90) cc_final: 0.5484 (p90) REVERT: G 4 MET cc_start: 0.6119 (mmm) cc_final: 0.5709 (mpp) outliers start: 41 outliers final: 25 residues processed: 310 average time/residue: 0.1824 time to fit residues: 93.2560 Evaluate side-chains 239 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 226 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 329 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 0.0980 chunk 301 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 354 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 381 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN H 39 GLN L 90 GLN B 914 ASN C 39 GLN D 90 GLN E 914 ASN G 38 GLN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.139606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087632 restraints weight = 69403.300| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.23 r_work: 0.3095 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31584 Z= 0.135 Angle : 0.649 9.929 43059 Z= 0.336 Chirality : 0.046 0.257 4932 Planarity : 0.004 0.040 5502 Dihedral : 6.307 58.069 4896 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.48 % Allowed : 6.91 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.01 (0.13), residues: 3852 helix: 1.93 (0.20), residues: 666 sheet: 0.28 (0.16), residues: 1014 loop : -0.75 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.040 0.002 TYR D 36 PHE 0.019 0.001 PHE A 329 TRP 0.016 0.002 TRP L 35 HIS 0.003 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00293 (31500) covalent geometry : angle 0.63022 (42858) SS BOND : bond 0.00274 ( 51) SS BOND : angle 1.48938 ( 102) hydrogen bonds : bond 0.04649 ( 1236) hydrogen bonds : angle 6.39979 ( 3384) link_BETA1-4 : bond 0.00584 ( 9) link_BETA1-4 : angle 3.58454 ( 27) link_NAG-ASN : bond 0.00500 ( 24) link_NAG-ASN : angle 2.71871 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.3699 (m-80) cc_final: 0.2914 (m-80) REVERT: A 177 MET cc_start: 0.7301 (mtp) cc_final: 0.7064 (mtm) REVERT: A 269 TYR cc_start: 0.7630 (m-80) cc_final: 0.7084 (m-80) REVERT: A 338 PHE cc_start: 0.7622 (m-80) cc_final: 0.7212 (m-80) REVERT: A 342 PHE cc_start: 0.7865 (m-80) cc_final: 0.7628 (m-80) REVERT: A 456 PHE cc_start: 0.6985 (m-80) cc_final: 0.6643 (m-80) REVERT: A 516 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: H 2 VAL cc_start: 0.7584 (t) cc_final: 0.7213 (p) REVERT: H 80 MET cc_start: 0.1090 (ttp) cc_final: 0.0030 (ppp) REVERT: H 90 TYR cc_start: 0.5768 (p90) cc_final: 0.5447 (p90) REVERT: L 4 MET cc_start: 0.6109 (mmm) cc_final: 0.5026 (mpp) REVERT: L 32 TYR cc_start: 0.5951 (m-80) cc_final: 0.5395 (m-80) REVERT: B 52 GLN cc_start: 0.8170 (tt0) cc_final: 0.7951 (tt0) REVERT: B 153 MET cc_start: 0.8717 (tpp) cc_final: 0.8335 (ptm) REVERT: B 160 TYR cc_start: 0.3969 (m-80) cc_final: 0.2991 (m-80) REVERT: B 177 MET cc_start: 0.7308 (mtp) cc_final: 0.6832 (mtm) REVERT: B 192 PHE cc_start: 0.8007 (m-10) cc_final: 0.7745 (m-10) REVERT: B 269 TYR cc_start: 0.7637 (m-80) cc_final: 0.7424 (m-80) REVERT: B 342 PHE cc_start: 0.7684 (m-80) cc_final: 0.7406 (m-80) REVERT: B 456 PHE cc_start: 0.7211 (m-80) cc_final: 0.6859 (m-80) REVERT: B 529 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7742 (pptt) REVERT: B 988 GLU cc_start: 0.8003 (mp0) cc_final: 0.7800 (pm20) REVERT: C 48 MET cc_start: 0.7791 (mmm) cc_final: 0.7429 (mmm) REVERT: C 80 MET cc_start: 0.1022 (ttp) cc_final: 0.0545 (ppp) REVERT: D 4 MET cc_start: 0.5994 (mmm) cc_final: 0.4678 (mpp) REVERT: D 32 TYR cc_start: 0.6290 (m-80) cc_final: 0.5999 (m-80) REVERT: D 46 LEU cc_start: 0.4924 (OUTLIER) cc_final: 0.4437 (mt) REVERT: E 52 GLN cc_start: 0.8268 (tt0) cc_final: 0.8060 (tt0) REVERT: E 81 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6590 (t0) REVERT: E 153 MET cc_start: 0.8753 (tpp) cc_final: 0.8550 (tpp) REVERT: E 160 TYR cc_start: 0.4005 (m-80) cc_final: 0.3286 (m-80) REVERT: E 201 PHE cc_start: 0.7780 (t80) cc_final: 0.7336 (t80) REVERT: E 205 SER cc_start: 0.8045 (p) cc_final: 0.7788 (p) REVERT: E 269 TYR cc_start: 0.7759 (m-80) cc_final: 0.7550 (m-80) REVERT: E 338 PHE cc_start: 0.6949 (m-80) cc_final: 0.6653 (m-80) REVERT: E 456 PHE cc_start: 0.7078 (m-80) cc_final: 0.6684 (m-80) REVERT: E 461 LEU cc_start: 0.8667 (mt) cc_final: 0.8398 (mt) REVERT: E 495 TYR cc_start: 0.6229 (t80) cc_final: 0.5997 (t80) REVERT: F 80 MET cc_start: 0.0859 (ttp) cc_final: -0.0028 (ppp) REVERT: G 4 MET cc_start: 0.6155 (mmm) cc_final: 0.5162 (mpp) outliers start: 50 outliers final: 22 residues processed: 288 average time/residue: 0.1747 time to fit residues: 84.2637 Evaluate side-chains 229 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 382 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 282 optimal weight: 10.0000 chunk 270 optimal weight: 7.9990 chunk 303 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 355 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 341 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 146 HIS A 544 ASN A 907 ASN A 913 GLN L 38 GLN B 907 ASN B 913 GLN C 100GHIS D 38 GLN E 66 HIS E 907 ASN E 913 GLN F 100GHIS ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.137831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081008 restraints weight = 69182.489| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.83 r_work: 0.3081 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31584 Z= 0.178 Angle : 0.648 11.604 43059 Z= 0.333 Chirality : 0.046 0.250 4932 Planarity : 0.004 0.040 5502 Dihedral : 6.223 58.143 4896 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.68 % Allowed : 7.47 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 3852 helix: 1.94 (0.20), residues: 663 sheet: 0.02 (0.15), residues: 1092 loop : -0.85 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1014 TYR 0.022 0.002 TYR B1067 PHE 0.017 0.002 PHE A 329 TRP 0.017 0.002 TRP H 47 HIS 0.006 0.001 HIS E1058 Details of bonding type rmsd covalent geometry : bond 0.00420 (31500) covalent geometry : angle 0.62996 (42858) SS BOND : bond 0.00270 ( 51) SS BOND : angle 1.59929 ( 102) hydrogen bonds : bond 0.04634 ( 1236) hydrogen bonds : angle 6.17412 ( 3384) link_BETA1-4 : bond 0.00527 ( 9) link_BETA1-4 : angle 3.27616 ( 27) link_NAG-ASN : bond 0.00435 ( 24) link_NAG-ASN : angle 2.67100 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7424 (mtp) cc_final: 0.7103 (mtm) REVERT: A 192 PHE cc_start: 0.8234 (m-10) cc_final: 0.8008 (m-10) REVERT: A 269 TYR cc_start: 0.8011 (m-80) cc_final: 0.7559 (m-80) REVERT: A 338 PHE cc_start: 0.7759 (m-80) cc_final: 0.7242 (m-80) REVERT: A 342 PHE cc_start: 0.7898 (m-80) cc_final: 0.7596 (m-80) REVERT: A 456 PHE cc_start: 0.7106 (m-80) cc_final: 0.6830 (m-80) REVERT: A 516 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: A 950 ASP cc_start: 0.8884 (t70) cc_final: 0.8624 (t0) REVERT: H 2 VAL cc_start: 0.7559 (t) cc_final: 0.7171 (p) REVERT: H 80 MET cc_start: 0.0821 (ttp) cc_final: 0.0258 (tmm) REVERT: L 4 MET cc_start: 0.6207 (mmm) cc_final: 0.5195 (mpp) REVERT: L 32 TYR cc_start: 0.5927 (m-80) cc_final: 0.5452 (m-80) REVERT: B 153 MET cc_start: 0.8842 (tpp) cc_final: 0.8606 (tpp) REVERT: B 160 TYR cc_start: 0.4189 (m-80) cc_final: 0.3095 (m-80) REVERT: B 177 MET cc_start: 0.7324 (mtp) cc_final: 0.6874 (mtm) REVERT: B 192 PHE cc_start: 0.8203 (m-80) cc_final: 0.7917 (m-10) REVERT: B 201 PHE cc_start: 0.8068 (t80) cc_final: 0.7717 (t80) REVERT: B 269 TYR cc_start: 0.7968 (m-80) cc_final: 0.7704 (m-80) REVERT: B 338 PHE cc_start: 0.7181 (m-80) cc_final: 0.6969 (m-80) REVERT: B 342 PHE cc_start: 0.7674 (m-80) cc_final: 0.7408 (m-80) REVERT: B 456 PHE cc_start: 0.7345 (m-80) cc_final: 0.7051 (m-80) REVERT: B 529 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7830 (pptt) REVERT: B 988 GLU cc_start: 0.8118 (mp0) cc_final: 0.7870 (pm20) REVERT: C 48 MET cc_start: 0.7542 (mmm) cc_final: 0.7319 (mmm) REVERT: C 80 MET cc_start: 0.1048 (ttp) cc_final: 0.0506 (ppp) REVERT: D 4 MET cc_start: 0.6012 (mmm) cc_final: 0.4846 (mpp) REVERT: D 32 TYR cc_start: 0.6323 (m-80) cc_final: 0.6037 (m-80) REVERT: D 46 LEU cc_start: 0.4994 (OUTLIER) cc_final: 0.4531 (mt) REVERT: E 153 MET cc_start: 0.8793 (tpp) cc_final: 0.8588 (tpp) REVERT: E 160 TYR cc_start: 0.3769 (m-80) cc_final: 0.2964 (m-80) REVERT: E 198 ASP cc_start: 0.6881 (t0) cc_final: 0.6652 (t0) REVERT: E 201 PHE cc_start: 0.8100 (t80) cc_final: 0.7611 (t80) REVERT: E 269 TYR cc_start: 0.8047 (m-80) cc_final: 0.7796 (m-80) REVERT: E 338 PHE cc_start: 0.7054 (m-80) cc_final: 0.6815 (m-80) REVERT: E 456 PHE cc_start: 0.7075 (m-80) cc_final: 0.6787 (m-80) REVERT: E 461 LEU cc_start: 0.8712 (mt) cc_final: 0.8488 (mt) REVERT: E 495 TYR cc_start: 0.6639 (t80) cc_final: 0.5732 (t80) REVERT: E 558 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8504 (tmtt) REVERT: F 80 MET cc_start: 0.0977 (ttp) cc_final: 0.0644 (ppp) REVERT: G 4 MET cc_start: 0.6299 (mmm) cc_final: 0.3706 (mpp) outliers start: 57 outliers final: 37 residues processed: 263 average time/residue: 0.1712 time to fit residues: 76.0507 Evaluate side-chains 234 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 102 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 320 optimal weight: 0.0770 chunk 345 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 245 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 377 optimal weight: 20.0000 chunk 224 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 804 GLN B1048 HIS E 66 HIS E 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.137992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083031 restraints weight = 69312.382| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.10 r_work: 0.3065 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31584 Z= 0.148 Angle : 0.613 8.022 43059 Z= 0.315 Chirality : 0.046 0.262 4932 Planarity : 0.004 0.043 5502 Dihedral : 6.007 56.568 4896 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.89 % Allowed : 7.91 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 3852 helix: 2.08 (0.20), residues: 663 sheet: 0.02 (0.16), residues: 1059 loop : -0.89 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.046 0.002 TYR D 86 PHE 0.018 0.001 PHE A 329 TRP 0.017 0.001 TRP A 258 HIS 0.004 0.001 HIS E1058 Details of bonding type rmsd covalent geometry : bond 0.00344 (31500) covalent geometry : angle 0.59540 (42858) SS BOND : bond 0.00226 ( 51) SS BOND : angle 1.43495 ( 102) hydrogen bonds : bond 0.04321 ( 1236) hydrogen bonds : angle 6.00960 ( 3384) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 3.19513 ( 27) link_NAG-ASN : bond 0.00404 ( 24) link_NAG-ASN : angle 2.64316 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6981 (tt) REVERT: A 160 TYR cc_start: 0.3994 (m-80) cc_final: 0.3256 (m-80) REVERT: A 177 MET cc_start: 0.7417 (mtp) cc_final: 0.7063 (mtm) REVERT: A 192 PHE cc_start: 0.8224 (m-10) cc_final: 0.7872 (m-10) REVERT: A 198 ASP cc_start: 0.6760 (t0) cc_final: 0.6510 (t0) REVERT: A 269 TYR cc_start: 0.8077 (m-80) cc_final: 0.7527 (m-80) REVERT: A 338 PHE cc_start: 0.7862 (m-80) cc_final: 0.7501 (m-80) REVERT: A 342 PHE cc_start: 0.8064 (m-80) cc_final: 0.7826 (m-80) REVERT: A 354 ASN cc_start: 0.9027 (t0) cc_final: 0.8799 (t0) REVERT: A 456 PHE cc_start: 0.7123 (m-80) cc_final: 0.6751 (m-80) REVERT: A 516 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: A 517 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6462 (mp) REVERT: A 762 GLN cc_start: 0.8931 (mt0) cc_final: 0.8667 (mt0) REVERT: A 950 ASP cc_start: 0.8824 (t70) cc_final: 0.8623 (t0) REVERT: H 90 TYR cc_start: 0.5487 (p90) cc_final: 0.4941 (p90) REVERT: L 4 MET cc_start: 0.6209 (mmm) cc_final: 0.4964 (mpp) REVERT: L 32 TYR cc_start: 0.6027 (m-80) cc_final: 0.5573 (m-80) REVERT: B 153 MET cc_start: 0.8919 (tpp) cc_final: 0.8673 (tpp) REVERT: B 160 TYR cc_start: 0.4161 (m-80) cc_final: 0.3037 (m-80) REVERT: B 177 MET cc_start: 0.7256 (mtp) cc_final: 0.6844 (mtm) REVERT: B 192 PHE cc_start: 0.8213 (m-80) cc_final: 0.7892 (m-10) REVERT: B 201 PHE cc_start: 0.8089 (t80) cc_final: 0.7617 (t80) REVERT: B 269 TYR cc_start: 0.8035 (m-80) cc_final: 0.7686 (m-80) REVERT: B 456 PHE cc_start: 0.7409 (m-80) cc_final: 0.6355 (m-80) REVERT: B 495 TYR cc_start: 0.8180 (t80) cc_final: 0.7359 (t80) REVERT: B 529 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7833 (pptt) REVERT: B 988 GLU cc_start: 0.8061 (mp0) cc_final: 0.7736 (pm20) REVERT: C 80 MET cc_start: 0.0983 (ttp) cc_final: 0.0595 (tmm) REVERT: D 4 MET cc_start: 0.6030 (mmm) cc_final: 0.4788 (mpp) REVERT: D 32 TYR cc_start: 0.6218 (m-80) cc_final: 0.5926 (m-80) REVERT: D 47 LEU cc_start: 0.7270 (mt) cc_final: 0.6255 (pt) REVERT: D 86 TYR cc_start: 0.5765 (OUTLIER) cc_final: 0.5322 (t80) REVERT: E 81 ASN cc_start: 0.7211 (OUTLIER) cc_final: 0.6815 (t0) REVERT: E 269 TYR cc_start: 0.8090 (m-80) cc_final: 0.7715 (m-80) REVERT: E 338 PHE cc_start: 0.7064 (m-80) cc_final: 0.6748 (m-80) REVERT: E 456 PHE cc_start: 0.7208 (m-80) cc_final: 0.6636 (m-80) REVERT: E 461 LEU cc_start: 0.8684 (mt) cc_final: 0.8429 (mt) REVERT: E 495 TYR cc_start: 0.6649 (t80) cc_final: 0.6391 (t80) REVERT: E 558 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8471 (tmtt) REVERT: F 80 MET cc_start: 0.0494 (ttp) cc_final: 0.0203 (tmm) REVERT: G 4 MET cc_start: 0.5466 (mmm) cc_final: 0.4608 (mtp) outliers start: 64 outliers final: 39 residues processed: 258 average time/residue: 0.1688 time to fit residues: 74.1902 Evaluate side-chains 244 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 237 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 345 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 333 optimal weight: 0.6980 chunk 113 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 353 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1048 HIS E 66 HIS E1048 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.136695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085432 restraints weight = 69317.144| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.58 r_work: 0.2994 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31584 Z= 0.199 Angle : 0.641 9.069 43059 Z= 0.328 Chirality : 0.047 0.301 4932 Planarity : 0.004 0.043 5502 Dihedral : 6.107 58.002 4896 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.92 % Allowed : 8.44 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.28 (0.13), residues: 3852 helix: 1.98 (0.20), residues: 663 sheet: -0.09 (0.15), residues: 1089 loop : -0.95 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.029 0.002 TYR H 79 PHE 0.017 0.002 PHE A 329 TRP 0.018 0.002 TRP E 258 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00475 (31500) covalent geometry : angle 0.62326 (42858) SS BOND : bond 0.00422 ( 51) SS BOND : angle 1.55740 ( 102) hydrogen bonds : bond 0.04562 ( 1236) hydrogen bonds : angle 6.00201 ( 3384) link_BETA1-4 : bond 0.00397 ( 9) link_BETA1-4 : angle 3.17260 ( 27) link_NAG-ASN : bond 0.00397 ( 24) link_NAG-ASN : angle 2.65134 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 213 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.8317 (mt) cc_final: 0.7912 (pt) REVERT: A 177 MET cc_start: 0.7322 (mtp) cc_final: 0.7055 (mtm) REVERT: A 192 PHE cc_start: 0.8179 (m-10) cc_final: 0.7773 (m-10) REVERT: A 269 TYR cc_start: 0.8020 (m-80) cc_final: 0.7531 (m-80) REVERT: A 338 PHE cc_start: 0.7840 (m-80) cc_final: 0.7547 (m-80) REVERT: A 342 PHE cc_start: 0.8014 (m-80) cc_final: 0.7797 (m-80) REVERT: A 354 ASN cc_start: 0.9033 (t0) cc_final: 0.8766 (t0) REVERT: A 456 PHE cc_start: 0.7446 (m-80) cc_final: 0.7068 (m-80) REVERT: A 516 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: A 762 GLN cc_start: 0.8873 (mt0) cc_final: 0.8598 (mt0) REVERT: A 950 ASP cc_start: 0.8655 (t70) cc_final: 0.8448 (t0) REVERT: H 21 SER cc_start: 0.6377 (OUTLIER) cc_final: 0.5398 (t) REVERT: H 79 TYR cc_start: 0.7492 (t80) cc_final: 0.6917 (t80) REVERT: H 80 MET cc_start: 0.2210 (ppp) cc_final: 0.0634 (tmm) REVERT: L 4 MET cc_start: 0.6258 (mmm) cc_final: 0.5248 (mpp) REVERT: L 32 TYR cc_start: 0.6014 (m-80) cc_final: 0.5575 (m-80) REVERT: B 153 MET cc_start: 0.8850 (tpp) cc_final: 0.8601 (tpp) REVERT: B 160 TYR cc_start: 0.4300 (m-80) cc_final: 0.3059 (m-80) REVERT: B 177 MET cc_start: 0.7337 (mtp) cc_final: 0.6944 (mtm) REVERT: B 192 PHE cc_start: 0.8119 (m-80) cc_final: 0.7757 (m-10) REVERT: B 200 TYR cc_start: 0.7377 (m-80) cc_final: 0.7095 (m-80) REVERT: B 201 PHE cc_start: 0.8204 (t80) cc_final: 0.7688 (t80) REVERT: B 269 TYR cc_start: 0.7990 (m-80) cc_final: 0.7587 (m-80) REVERT: B 456 PHE cc_start: 0.7240 (m-80) cc_final: 0.6922 (m-80) REVERT: B 495 TYR cc_start: 0.8206 (t80) cc_final: 0.7386 (t80) REVERT: B 529 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7922 (pptt) REVERT: B 988 GLU cc_start: 0.7863 (mp0) cc_final: 0.7584 (pm20) REVERT: C 80 MET cc_start: 0.0837 (ttp) cc_final: 0.0486 (tmm) REVERT: D 4 MET cc_start: 0.6043 (mmm) cc_final: 0.4944 (mpp) REVERT: D 32 TYR cc_start: 0.6263 (m-80) cc_final: 0.5944 (m-80) REVERT: D 47 LEU cc_start: 0.6858 (mt) cc_final: 0.6041 (pt) REVERT: D 86 TYR cc_start: 0.5732 (OUTLIER) cc_final: 0.5159 (t80) REVERT: E 81 ASN cc_start: 0.7254 (OUTLIER) cc_final: 0.6899 (t0) REVERT: E 201 PHE cc_start: 0.8096 (t80) cc_final: 0.7517 (t80) REVERT: E 269 TYR cc_start: 0.7972 (m-80) cc_final: 0.7596 (m-80) REVERT: E 461 LEU cc_start: 0.8679 (mt) cc_final: 0.8426 (mt) REVERT: E 495 TYR cc_start: 0.6661 (t80) cc_final: 0.6389 (t80) REVERT: E 558 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8579 (tmtt) REVERT: F 80 MET cc_start: 0.0387 (ttp) cc_final: 0.0011 (tmm) REVERT: G 4 MET cc_start: 0.5509 (mmm) cc_final: 0.4521 (mtt) outliers start: 65 outliers final: 45 residues processed: 253 average time/residue: 0.1653 time to fit residues: 71.6109 Evaluate side-chains 246 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 46 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 319 optimal weight: 0.9990 chunk 386 optimal weight: 9.9990 chunk 345 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 306 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 439 ASN E 66 HIS E 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.137619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084536 restraints weight = 69081.498| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.30 r_work: 0.3052 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31584 Z= 0.140 Angle : 0.629 16.921 43059 Z= 0.316 Chirality : 0.046 0.268 4932 Planarity : 0.004 0.042 5502 Dihedral : 5.993 56.215 4894 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.59 % Allowed : 9.03 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.24 (0.13), residues: 3852 helix: 2.14 (0.20), residues: 663 sheet: -0.10 (0.16), residues: 1074 loop : -0.95 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.067 0.002 TYR G 86 PHE 0.020 0.001 PHE E 338 TRP 0.016 0.001 TRP C 47 HIS 0.003 0.001 HIS E1058 Details of bonding type rmsd covalent geometry : bond 0.00322 (31500) covalent geometry : angle 0.60326 (42858) SS BOND : bond 0.00261 ( 51) SS BOND : angle 1.38976 ( 102) hydrogen bonds : bond 0.04245 ( 1236) hydrogen bonds : angle 5.88742 ( 3384) link_BETA1-4 : bond 0.00456 ( 9) link_BETA1-4 : angle 3.10676 ( 27) link_NAG-ASN : bond 0.00420 ( 24) link_NAG-ASN : angle 3.71477 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.3756 (m-80) cc_final: 0.3135 (m-80) REVERT: A 176 LEU cc_start: 0.8300 (mt) cc_final: 0.7938 (pt) REVERT: A 177 MET cc_start: 0.7333 (mtp) cc_final: 0.7061 (mtm) REVERT: A 192 PHE cc_start: 0.8170 (m-10) cc_final: 0.7794 (m-80) REVERT: A 198 ASP cc_start: 0.6672 (t0) cc_final: 0.6451 (t0) REVERT: A 258 TRP cc_start: 0.6417 (p-90) cc_final: 0.4893 (p-90) REVERT: A 269 TYR cc_start: 0.7906 (m-80) cc_final: 0.7487 (m-80) REVERT: A 338 PHE cc_start: 0.7841 (m-80) cc_final: 0.7544 (m-80) REVERT: A 354 ASN cc_start: 0.9007 (t0) cc_final: 0.8747 (t0) REVERT: A 456 PHE cc_start: 0.7342 (m-80) cc_final: 0.6715 (m-80) REVERT: A 516 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: A 517 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6448 (mp) REVERT: A 762 GLN cc_start: 0.8789 (mt0) cc_final: 0.8529 (mt0) REVERT: H 21 SER cc_start: 0.6505 (OUTLIER) cc_final: 0.5457 (t) REVERT: H 79 TYR cc_start: 0.7430 (t80) cc_final: 0.6869 (t80) REVERT: H 80 MET cc_start: 0.1900 (ppp) cc_final: 0.0537 (tmm) REVERT: L 4 MET cc_start: 0.6146 (mmm) cc_final: 0.4991 (mpp) REVERT: L 32 TYR cc_start: 0.6039 (m-80) cc_final: 0.5600 (m-80) REVERT: B 153 MET cc_start: 0.8834 (tpp) cc_final: 0.8598 (tpp) REVERT: B 160 TYR cc_start: 0.4122 (m-80) cc_final: 0.2981 (m-80) REVERT: B 177 MET cc_start: 0.7346 (mtp) cc_final: 0.6936 (mtm) REVERT: B 192 PHE cc_start: 0.8111 (m-80) cc_final: 0.7662 (m-10) REVERT: B 201 PHE cc_start: 0.8077 (t80) cc_final: 0.7600 (t80) REVERT: B 269 TYR cc_start: 0.7936 (m-80) cc_final: 0.7521 (m-80) REVERT: B 456 PHE cc_start: 0.7174 (m-80) cc_final: 0.6833 (m-80) REVERT: B 495 TYR cc_start: 0.8150 (t80) cc_final: 0.7373 (t80) REVERT: B 529 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7921 (pptt) REVERT: C 80 MET cc_start: 0.0843 (ttp) cc_final: 0.0475 (tmm) REVERT: D 4 MET cc_start: 0.5929 (mmm) cc_final: 0.4575 (mpp) REVERT: D 32 TYR cc_start: 0.6313 (m-80) cc_final: 0.6009 (m-80) REVERT: D 47 LEU cc_start: 0.6956 (mt) cc_final: 0.6274 (pt) REVERT: D 86 TYR cc_start: 0.5622 (OUTLIER) cc_final: 0.5392 (t80) REVERT: E 81 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6779 (t0) REVERT: E 153 MET cc_start: 0.8661 (tpp) cc_final: 0.8381 (ptm) REVERT: E 201 PHE cc_start: 0.8103 (t80) cc_final: 0.7589 (t80) REVERT: E 223 LEU cc_start: 0.7692 (mt) cc_final: 0.7384 (mt) REVERT: E 269 TYR cc_start: 0.7915 (m-80) cc_final: 0.7505 (m-80) REVERT: E 338 PHE cc_start: 0.7375 (m-80) cc_final: 0.7065 (m-80) REVERT: E 456 PHE cc_start: 0.7403 (m-80) cc_final: 0.7127 (m-80) REVERT: E 461 LEU cc_start: 0.8640 (mt) cc_final: 0.8412 (mt) REVERT: E 495 TYR cc_start: 0.6637 (t80) cc_final: 0.6346 (t80) REVERT: E 558 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8608 (tmtt) REVERT: F 80 MET cc_start: 0.0745 (ttp) cc_final: 0.0455 (tmm) REVERT: G 4 MET cc_start: 0.5428 (mmm) cc_final: 0.4358 (mtt) outliers start: 54 outliers final: 41 residues processed: 237 average time/residue: 0.1708 time to fit residues: 69.0387 Evaluate side-chains 242 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 306 optimal weight: 20.0000 chunk 276 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 2 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 chunk 287 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN E 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.136429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085786 restraints weight = 69142.200| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.67 r_work: 0.2994 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31584 Z= 0.189 Angle : 0.648 13.086 43059 Z= 0.327 Chirality : 0.047 0.251 4932 Planarity : 0.004 0.044 5502 Dihedral : 6.181 57.939 4894 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.65 % Allowed : 8.92 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.38 (0.13), residues: 3852 helix: 1.87 (0.20), residues: 684 sheet: -0.17 (0.15), residues: 1098 loop : -1.04 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 50 TYR 0.023 0.002 TYR G 86 PHE 0.017 0.002 PHE A 329 TRP 0.022 0.002 TRP C 47 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00448 (31500) covalent geometry : angle 0.62652 (42858) SS BOND : bond 0.00286 ( 51) SS BOND : angle 1.54673 ( 102) hydrogen bonds : bond 0.04511 ( 1236) hydrogen bonds : angle 5.92282 ( 3384) link_BETA1-4 : bond 0.00448 ( 9) link_BETA1-4 : angle 3.06744 ( 27) link_NAG-ASN : bond 0.00351 ( 24) link_NAG-ASN : angle 3.22522 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8792 (tpp) cc_final: 0.8431 (tpp) REVERT: A 176 LEU cc_start: 0.8265 (mt) cc_final: 0.7894 (pt) REVERT: A 177 MET cc_start: 0.7430 (mtp) cc_final: 0.7161 (mtm) REVERT: A 192 PHE cc_start: 0.8317 (m-10) cc_final: 0.7940 (m-80) REVERT: A 269 TYR cc_start: 0.8006 (m-80) cc_final: 0.7619 (m-80) REVERT: A 338 PHE cc_start: 0.7946 (m-80) cc_final: 0.7528 (m-80) REVERT: A 354 ASN cc_start: 0.9062 (t0) cc_final: 0.8806 (t0) REVERT: A 456 PHE cc_start: 0.7144 (m-80) cc_final: 0.6926 (m-80) REVERT: A 516 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: A 517 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6422 (mp) REVERT: A 762 GLN cc_start: 0.8834 (mt0) cc_final: 0.8562 (mt0) REVERT: A 1002 GLN cc_start: 0.8623 (tp40) cc_final: 0.8173 (tt0) REVERT: H 21 SER cc_start: 0.6423 (OUTLIER) cc_final: 0.5360 (t) REVERT: H 79 TYR cc_start: 0.7506 (t80) cc_final: 0.6951 (t80) REVERT: H 80 MET cc_start: 0.1826 (ppp) cc_final: 0.0183 (tmm) REVERT: L 4 MET cc_start: 0.6068 (mmm) cc_final: 0.4865 (mpp) REVERT: L 32 TYR cc_start: 0.6363 (m-80) cc_final: 0.5931 (m-80) REVERT: B 40 ASP cc_start: 0.8158 (t0) cc_final: 0.7938 (t0) REVERT: B 153 MET cc_start: 0.8786 (tpp) cc_final: 0.8564 (tpp) REVERT: B 176 LEU cc_start: 0.8187 (mt) cc_final: 0.7748 (pt) REVERT: B 177 MET cc_start: 0.7278 (mtp) cc_final: 0.6819 (mtm) REVERT: B 201 PHE cc_start: 0.8299 (t80) cc_final: 0.7836 (t80) REVERT: B 269 TYR cc_start: 0.8011 (m-80) cc_final: 0.7616 (m-80) REVERT: B 456 PHE cc_start: 0.7241 (m-80) cc_final: 0.6863 (m-80) REVERT: B 495 TYR cc_start: 0.8169 (t80) cc_final: 0.7457 (t80) REVERT: B 529 LYS cc_start: 0.8348 (pptt) cc_final: 0.8005 (pptt) REVERT: C 58 MET cc_start: 0.5834 (pmm) cc_final: 0.5280 (pmm) REVERT: C 80 MET cc_start: 0.0872 (ttp) cc_final: 0.0494 (tmm) REVERT: D 4 MET cc_start: 0.5974 (mmm) cc_final: 0.5647 (mpp) REVERT: D 32 TYR cc_start: 0.6356 (m-80) cc_final: 0.6062 (m-80) REVERT: D 47 LEU cc_start: 0.7068 (mt) cc_final: 0.6300 (pt) REVERT: D 86 TYR cc_start: 0.5802 (OUTLIER) cc_final: 0.5582 (t80) REVERT: E 153 MET cc_start: 0.8717 (tpp) cc_final: 0.8355 (ptm) REVERT: E 269 TYR cc_start: 0.7871 (m-80) cc_final: 0.7665 (m-80) REVERT: E 461 LEU cc_start: 0.8698 (mt) cc_final: 0.8498 (mt) REVERT: E 558 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8736 (tmtt) REVERT: F 80 MET cc_start: 0.0482 (ttp) cc_final: 0.0163 (tmm) REVERT: G 4 MET cc_start: 0.5376 (mmm) cc_final: 0.4455 (mtt) outliers start: 56 outliers final: 45 residues processed: 242 average time/residue: 0.1699 time to fit residues: 69.8312 Evaluate side-chains 239 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 84 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 373 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 280 optimal weight: 9.9990 chunk 149 optimal weight: 0.0570 chunk 312 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.137064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.086755 restraints weight = 69100.301| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.60 r_work: 0.3015 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31584 Z= 0.154 Angle : 0.627 13.622 43059 Z= 0.317 Chirality : 0.046 0.256 4932 Planarity : 0.004 0.044 5502 Dihedral : 6.104 59.930 4894 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.71 % Allowed : 8.95 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 3852 helix: 1.97 (0.20), residues: 684 sheet: -0.12 (0.15), residues: 1077 loop : -1.03 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.030 0.002 TYR B 636 PHE 0.025 0.001 PHE B 318 TRP 0.019 0.002 TRP A 258 HIS 0.018 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00361 (31500) covalent geometry : angle 0.60632 (42858) SS BOND : bond 0.00278 ( 51) SS BOND : angle 1.38627 ( 102) hydrogen bonds : bond 0.04266 ( 1236) hydrogen bonds : angle 5.84201 ( 3384) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 3.05466 ( 27) link_NAG-ASN : bond 0.00321 ( 24) link_NAG-ASN : angle 3.15528 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8855 (tpp) cc_final: 0.8515 (tpp) REVERT: A 160 TYR cc_start: 0.3829 (m-80) cc_final: 0.3124 (m-80) REVERT: A 176 LEU cc_start: 0.8332 (mt) cc_final: 0.7975 (pt) REVERT: A 177 MET cc_start: 0.7420 (mtp) cc_final: 0.7122 (mtm) REVERT: A 192 PHE cc_start: 0.8224 (m-10) cc_final: 0.7891 (m-80) REVERT: A 269 TYR cc_start: 0.7964 (m-80) cc_final: 0.7516 (m-80) REVERT: A 338 PHE cc_start: 0.7970 (m-80) cc_final: 0.7516 (m-80) REVERT: A 354 ASN cc_start: 0.9042 (t0) cc_final: 0.8796 (t0) REVERT: A 456 PHE cc_start: 0.7203 (m-80) cc_final: 0.6875 (m-80) REVERT: A 516 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 517 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6521 (mp) REVERT: A 1002 GLN cc_start: 0.8607 (tp40) cc_final: 0.8125 (tt0) REVERT: H 48 MET cc_start: 0.7423 (mpp) cc_final: 0.5880 (ptm) REVERT: H 79 TYR cc_start: 0.7477 (t80) cc_final: 0.7099 (t80) REVERT: H 80 MET cc_start: 0.1840 (ppp) cc_final: 0.0115 (tmm) REVERT: L 4 MET cc_start: 0.5991 (mmm) cc_final: 0.4684 (mpp) REVERT: L 32 TYR cc_start: 0.6273 (m-80) cc_final: 0.5771 (m-80) REVERT: B 40 ASP cc_start: 0.8128 (t0) cc_final: 0.7881 (t0) REVERT: B 153 MET cc_start: 0.8883 (tpp) cc_final: 0.8641 (tpp) REVERT: B 176 LEU cc_start: 0.8235 (mt) cc_final: 0.7824 (pt) REVERT: B 177 MET cc_start: 0.7270 (mtp) cc_final: 0.6768 (mtm) REVERT: B 192 PHE cc_start: 0.8135 (m-10) cc_final: 0.7698 (m-10) REVERT: B 201 PHE cc_start: 0.8225 (t80) cc_final: 0.7818 (t80) REVERT: B 269 TYR cc_start: 0.7997 (m-80) cc_final: 0.7523 (m-80) REVERT: B 456 PHE cc_start: 0.7205 (m-80) cc_final: 0.6880 (m-80) REVERT: B 495 TYR cc_start: 0.8101 (t80) cc_final: 0.7355 (t80) REVERT: B 529 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7989 (pptt) REVERT: C 80 MET cc_start: 0.0791 (ttp) cc_final: 0.0459 (tmm) REVERT: D 4 MET cc_start: 0.5641 (mmm) cc_final: 0.4222 (mpp) REVERT: D 32 TYR cc_start: 0.6317 (m-80) cc_final: 0.6029 (m-80) REVERT: D 47 LEU cc_start: 0.7080 (mt) cc_final: 0.6302 (pt) REVERT: D 86 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.5564 (t80) REVERT: E 153 MET cc_start: 0.8802 (tpp) cc_final: 0.8390 (ptm) REVERT: E 201 PHE cc_start: 0.8192 (t80) cc_final: 0.7731 (t80) REVERT: E 269 TYR cc_start: 0.7896 (m-80) cc_final: 0.7681 (m-80) REVERT: E 276 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8988 (tt) REVERT: E 338 PHE cc_start: 0.7426 (m-80) cc_final: 0.7083 (m-80) REVERT: E 461 LEU cc_start: 0.8668 (mt) cc_final: 0.8443 (mt) REVERT: E 495 TYR cc_start: 0.7134 (t80) cc_final: 0.6701 (t80) REVERT: E 558 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8756 (tmtt) REVERT: F 80 MET cc_start: 0.0602 (ttp) cc_final: 0.0232 (tmm) REVERT: G 4 MET cc_start: 0.5521 (mmm) cc_final: 0.4784 (mtt) outliers start: 58 outliers final: 51 residues processed: 240 average time/residue: 0.1773 time to fit residues: 71.6645 Evaluate side-chains 248 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 148 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 337 optimal weight: 0.9980 chunk 255 optimal weight: 30.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 644 GLN E 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.138129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084803 restraints weight = 68769.160| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.12 r_work: 0.3085 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31584 Z= 0.124 Angle : 0.606 13.896 43059 Z= 0.306 Chirality : 0.045 0.253 4932 Planarity : 0.004 0.046 5502 Dihedral : 5.836 59.599 4894 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.45 % Allowed : 9.36 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.21 (0.13), residues: 3852 helix: 2.14 (0.20), residues: 684 sheet: -0.03 (0.16), residues: 1056 loop : -0.98 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.025 0.001 TYR E 37 PHE 0.017 0.001 PHE A 329 TRP 0.043 0.002 TRP A 258 HIS 0.006 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00283 (31500) covalent geometry : angle 0.58595 (42858) SS BOND : bond 0.00257 ( 51) SS BOND : angle 1.24844 ( 102) hydrogen bonds : bond 0.03966 ( 1236) hydrogen bonds : angle 5.71724 ( 3384) link_BETA1-4 : bond 0.00437 ( 9) link_BETA1-4 : angle 3.04279 ( 27) link_NAG-ASN : bond 0.00312 ( 24) link_NAG-ASN : angle 3.04260 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.6372 (tp) cc_final: 0.6068 (tp) REVERT: A 153 MET cc_start: 0.8902 (tpp) cc_final: 0.8525 (tpp) REVERT: A 160 TYR cc_start: 0.3869 (m-80) cc_final: 0.3143 (m-80) REVERT: A 176 LEU cc_start: 0.8286 (mt) cc_final: 0.7945 (pt) REVERT: A 177 MET cc_start: 0.7511 (mtp) cc_final: 0.7182 (mtm) REVERT: A 192 PHE cc_start: 0.8316 (m-10) cc_final: 0.8036 (m-80) REVERT: A 269 TYR cc_start: 0.8069 (m-80) cc_final: 0.7739 (m-80) REVERT: A 338 PHE cc_start: 0.8044 (m-80) cc_final: 0.7536 (m-80) REVERT: A 354 ASN cc_start: 0.9014 (t0) cc_final: 0.8810 (t0) REVERT: A 456 PHE cc_start: 0.7088 (m-80) cc_final: 0.6834 (m-80) REVERT: A 516 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: A 517 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6619 (mp) REVERT: H 79 TYR cc_start: 0.7478 (t80) cc_final: 0.7098 (t80) REVERT: H 80 MET cc_start: 0.1813 (ppp) cc_final: 0.0265 (tmm) REVERT: L 4 MET cc_start: 0.6288 (mmm) cc_final: 0.5886 (mpp) REVERT: L 32 TYR cc_start: 0.6174 (m-80) cc_final: 0.5732 (m-80) REVERT: B 40 ASP cc_start: 0.8165 (t0) cc_final: 0.7914 (t0) REVERT: B 153 MET cc_start: 0.8904 (tpp) cc_final: 0.8648 (tpp) REVERT: B 176 LEU cc_start: 0.8200 (mt) cc_final: 0.7818 (pt) REVERT: B 177 MET cc_start: 0.7298 (mtp) cc_final: 0.6752 (mtm) REVERT: B 192 PHE cc_start: 0.8235 (m-10) cc_final: 0.7806 (m-10) REVERT: B 201 PHE cc_start: 0.8242 (t80) cc_final: 0.7934 (t80) REVERT: B 269 TYR cc_start: 0.8165 (m-80) cc_final: 0.7732 (m-80) REVERT: B 456 PHE cc_start: 0.7164 (m-80) cc_final: 0.6819 (m-80) REVERT: B 495 TYR cc_start: 0.8087 (t80) cc_final: 0.7353 (t80) REVERT: B 529 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8042 (pptt) REVERT: B 1002 GLN cc_start: 0.8804 (tp40) cc_final: 0.8401 (tt0) REVERT: C 48 MET cc_start: 0.7924 (mmp) cc_final: 0.7649 (mmp) REVERT: C 80 MET cc_start: 0.0749 (ttp) cc_final: 0.0383 (tmm) REVERT: D 4 MET cc_start: 0.5585 (mmm) cc_final: 0.4104 (mpp) REVERT: D 32 TYR cc_start: 0.6331 (m-80) cc_final: 0.6095 (m-80) REVERT: D 47 LEU cc_start: 0.7108 (mt) cc_final: 0.6312 (pt) REVERT: E 153 MET cc_start: 0.8820 (tpp) cc_final: 0.8419 (ptm) REVERT: E 201 PHE cc_start: 0.8208 (t80) cc_final: 0.7911 (t80) REVERT: E 276 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8996 (tt) REVERT: E 338 PHE cc_start: 0.7510 (m-80) cc_final: 0.7066 (m-80) REVERT: E 461 LEU cc_start: 0.8653 (mt) cc_final: 0.8444 (mt) REVERT: E 495 TYR cc_start: 0.7076 (t80) cc_final: 0.6462 (t80) REVERT: E 558 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8797 (tmtt) REVERT: F 80 MET cc_start: 0.0609 (ttp) cc_final: 0.0232 (tmm) REVERT: F 94 ARG cc_start: 0.6983 (ttp80) cc_final: 0.6640 (tmm-80) REVERT: G 4 MET cc_start: 0.5642 (mmm) cc_final: 0.4855 (mtt) outliers start: 49 outliers final: 37 residues processed: 250 average time/residue: 0.1794 time to fit residues: 74.5396 Evaluate side-chains 237 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 186 optimal weight: 9.9990 chunk 343 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 111 optimal weight: 9.9990 chunk 251 optimal weight: 30.0000 chunk 205 optimal weight: 0.8980 chunk 344 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 299 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN E 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.138023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084567 restraints weight = 69196.929| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.19 r_work: 0.3072 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31584 Z= 0.129 Angle : 0.619 15.126 43059 Z= 0.308 Chirality : 0.046 0.247 4932 Planarity : 0.004 0.046 5502 Dihedral : 5.663 56.526 4894 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.42 % Allowed : 9.80 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.18 (0.13), residues: 3852 helix: 2.20 (0.20), residues: 684 sheet: -0.03 (0.16), residues: 1062 loop : -0.97 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 94 TYR 0.042 0.002 TYR D 86 PHE 0.023 0.001 PHE E 192 TRP 0.032 0.002 TRP A 258 HIS 0.003 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00297 (31500) covalent geometry : angle 0.60043 (42858) SS BOND : bond 0.00255 ( 51) SS BOND : angle 1.23431 ( 102) hydrogen bonds : bond 0.03962 ( 1236) hydrogen bonds : angle 5.70316 ( 3384) link_BETA1-4 : bond 0.00421 ( 9) link_BETA1-4 : angle 3.01718 ( 27) link_NAG-ASN : bond 0.00304 ( 24) link_NAG-ASN : angle 2.95216 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9596.48 seconds wall clock time: 164 minutes 15.92 seconds (9855.92 seconds total)