Starting phenix.real_space_refine on Sun Jul 5 22:52:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s6k_24878/07_2026/7s6k_24878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s6k_24878/07_2026/7s6k_24878.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7s6k_24878/07_2026/7s6k_24878.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s6k_24878/07_2026/7s6k_24878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s6k_24878/07_2026/7s6k_24878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s6k_24878/07_2026/7s6k_24878.map" model { file = "/net/cci-nas-00/data/ceres_data/7s6k_24878/07_2026/7s6k_24878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s6k_24878/07_2026/7s6k_24878.cif" } 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= -0.000 sd= 0.036 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 19641 2.51 5 N 5100 2.21 5 O 6018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30903 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 5 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: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 5 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: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 5 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.34, per 1000 atoms: 0.24 Number of scatterers: 30903 At special positions: 0 Unit cell: (151.8, 157.55, 205.85, 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 6018 8.00 N 5100 7.00 C 19641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 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=2.03 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 E 985 " distance=2.32 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS B 383 " distance=2.32 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 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 985 " - pdb=" SG CYS E 383 " distance=2.32 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 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.04 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 17 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 17 " " NAG E1301 " - " ASN E 616 " " NAG E1302 " - " ASN E 709 " " NAG E1303 " - " ASN E 343 " " NAG E1304 " - " ASN E 61 " " NAG E1305 " - " ASN E 282 " " NAG E1306 " - " ASN E1074 " " NAG E1307 " - " ASN E 17 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN E 717 " " NAG S 1 " - " ASN E 801 " " NAG T 1 " - " ASN E1098 " " NAG U 1 " - " ASN E1134 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7242 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 63 sheets defined 20.5% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.875A 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 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.250A 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 966 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'H' and resid 27 through 32 Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.875A 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 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.250A 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 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 52A through 55 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.875A 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 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.683A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.250A 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 966 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.650A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1147 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 52A through 55 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.968A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.397A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.815A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.482A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY A 142 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU A 154 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.548A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.377A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.937A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.938A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU A 516 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.838A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.027A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.686A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.187A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.780A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.506A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR H 33 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.395A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.969A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.397A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.816A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.482A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.550A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.377A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.937A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.938A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.837A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.027A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.687A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 788 through 790 removed outlier: 6.187A pdb=" N ILE B 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.780A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.505A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 33 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.394A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AE8, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.969A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN E 188 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE E 210 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG E 190 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR E 208 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE E 192 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS E 206 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE E 194 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR E 204 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN E 196 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS E 202 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.398A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.880A 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: 6.815A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE E 140 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU E 156 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY E 142 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU E 154 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 83 through 85 removed outlier: 13.482A pdb=" N PHE E 238 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ASN E 137 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N THR E 240 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU E 242 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE E 140 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU E 156 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY E 142 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU E 154 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.550A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 324 through 326 removed outlier: 6.376A pdb=" N GLU E 324 " --> pdb=" O ASN E 540 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY E 566 " --> pdb=" O ASP E 574 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 348 through 349 removed outlier: 6.938A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.938A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU E 516 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL E 395 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER E 514 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA E 397 " --> pdb=" O VAL E 512 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL E 512 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER E 399 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E 510 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL E 401 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR E 508 " --> pdb=" O VAL E 401 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.648A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.838A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN E1106 " --> pdb=" O GLU E1111 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU E1111 " --> pdb=" O GLN E1106 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 718 through 728 removed outlier: 6.028A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.687A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.780A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AG6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.506A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 33 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.395A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 1256 hydrogen bonds defined for protein. 3354 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: 9.54 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5305 1.31 - 1.45: 10202 1.45 - 1.59: 15840 1.59 - 1.73: 87 1.73 - 1.87: 177 Bond restraints: 31611 Sorted by residual: bond pdb=" CB PHE F 100H" pdb=" CG PHE F 100H" ideal model delta sigma weight residual 1.502 1.352 0.150 2.30e-02 1.89e+03 4.28e+01 bond pdb=" CB PHE H 100H" pdb=" CG PHE H 100H" ideal model delta sigma weight residual 1.502 1.352 0.150 2.30e-02 1.89e+03 4.24e+01 bond pdb=" CB PHE C 100H" pdb=" CG PHE C 100H" ideal model delta sigma weight residual 1.502 1.353 0.149 2.30e-02 1.89e+03 4.19e+01 bond pdb=" CZ2 TRP A 152 " pdb=" CH2 TRP A 152 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.12e+01 bond pdb=" CZ2 TRP B 152 " pdb=" CH2 TRP B 152 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.10e+01 ... (remaining 31606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.10: 42858 7.10 - 14.21: 153 14.21 - 21.31: 0 21.31 - 28.41: 0 28.41 - 35.52: 3 Bond angle restraints: 43014 Sorted by residual: angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 160.08 -35.52 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG R 1 " pdb=" N2 NAG R 1 " pdb=" C7 NAG R 1 " ideal model delta sigma weight residual 124.56 160.06 -35.50 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG N 1 " pdb=" N2 NAG N 1 " pdb=" C7 NAG N 1 " ideal model delta sigma weight residual 124.56 160.04 -35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N GLY A 261 " pdb=" CA GLY A 261 " pdb=" C GLY A 261 " ideal model delta sigma weight residual 112.14 100.54 11.60 1.29e+00 6.01e-01 8.09e+01 angle pdb=" N GLY E 261 " pdb=" CA GLY E 261 " pdb=" C GLY E 261 " ideal model delta sigma weight residual 112.14 100.54 11.60 1.29e+00 6.01e-01 8.08e+01 ... (remaining 43009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 17848 17.50 - 34.99: 446 34.99 - 52.49: 90 52.49 - 69.98: 84 69.98 - 87.48: 15 Dihedral angle restraints: 18483 sinusoidal: 7200 harmonic: 11283 Sorted by residual: dihedral pdb=" CB CYS B 985 " pdb=" SG CYS B 985 " pdb=" SG CYS E 383 " pdb=" CB CYS E 383 " ideal model delta sinusoidal sigma weight residual 93.00 19.08 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 383 " pdb=" SG CYS A 383 " pdb=" SG CYS E 985 " pdb=" CB CYS E 985 " ideal model delta sinusoidal sigma weight residual 93.00 19.09 73.91 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 985 " pdb=" SG CYS A 985 " pdb=" SG CYS B 383 " pdb=" CB CYS B 383 " ideal model delta sinusoidal sigma weight residual 93.00 19.09 73.91 1 1.00e+01 1.00e-02 6.94e+01 ... (remaining 18480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3466 0.098 - 0.197: 1144 0.197 - 0.295: 226 0.295 - 0.394: 87 0.394 - 0.492: 60 Chirality restraints: 4983 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.41e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+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 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 4980 not shown) Planarity restraints: 5532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.075 2.00e-02 2.50e+03 8.14e-02 8.28e+01 pdb=" CG ASN A1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.132 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E1134 " 0.075 2.00e-02 2.50e+03 8.13e-02 8.26e+01 pdb=" CG ASN E1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN E1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E1134 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " 0.075 2.00e-02 2.50e+03 8.13e-02 8.25e+01 pdb=" CG ASN B1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.096 2.00e-02 2.50e+03 ... (remaining 5529 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 12195 2.89 - 3.40: 28473 3.40 - 3.90: 53262 3.90 - 4.40: 61444 4.40 - 4.90: 99552 Nonbonded interactions: 254926 Sorted by model distance: nonbonded pdb=" N TYR B 351 " pdb=" N ALA B 352 " model vdw 2.392 2.560 nonbonded pdb=" N TYR E 351 " pdb=" N ALA E 352 " model vdw 2.393 2.560 nonbonded pdb=" N TYR A 351 " pdb=" N ALA A 352 " model vdw 2.393 2.560 nonbonded pdb=" NZ LYS B 854 " pdb=" OD2 ASP E 614 " model vdw 2.395 3.120 nonbonded pdb=" NZ LYS A 854 " pdb=" OD2 ASP B 614 " model vdw 2.395 3.120 ... (remaining 254921 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: 0.09 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.270 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.021 0.285 31704 Z= 1.074 Angle : 1.802 35.518 43245 Z= 1.194 Chirality : 0.114 0.492 4983 Planarity : 0.008 0.036 5499 Dihedral : 9.971 87.478 11097 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.43 (0.13), residues: 3837 helix: 0.44 (0.19), residues: 648 sheet: 1.25 (0.16), residues: 933 loop : -0.12 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 50 TYR 0.047 0.008 TYR B 38 PHE 0.035 0.006 PHE B 329 TRP 0.040 0.011 TRP C 36 HIS 0.008 0.003 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.02016 / 1.06 (31611) covalent geometry : angle 1.79258 / 1.19 (43014) SS BOND : bond 0.07151 / 3.61 ( 48) SS BOND : angle 2.51494 / 1.68 ( 96) hydrogen bonds : bond 0.16931 / 11.08 ( 1226) hydrogen bonds : angle 8.42026 / 5.86 ( 3354) link_BETA1-4 : bond 0.07077 / 4.62 ( 12) link_BETA1-4 : angle 5.31249 / 3.47 ( 36) link_NAG-ASN : bond 0.08365 / 5.53 ( 33) link_NAG-ASN : angle 2.56918 / 1.73 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 717 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8403 (p90) cc_final: 0.8092 (p90) REVERT: A 395 VAL cc_start: 0.8817 (t) cc_final: 0.8588 (t) REVERT: A 1031 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8275 (mt-10) REVERT: H 32 TYR cc_start: 0.7387 (m-80) cc_final: 0.6856 (m-80) REVERT: L 32 TYR cc_start: 0.5904 (m-80) cc_final: 0.5558 (m-10) REVERT: B 140 PHE cc_start: 0.8332 (p90) cc_final: 0.8091 (p90) REVERT: B 473 TYR cc_start: 0.6994 (t80) cc_final: 0.6741 (t80) REVERT: B 764 ASN cc_start: 0.7825 (t0) cc_final: 0.7540 (t0) REVERT: B 1031 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8132 (mt-10) REVERT: C 32 TYR cc_start: 0.7427 (m-80) cc_final: 0.7209 (m-80) REVERT: D 35 TRP cc_start: 0.5166 (m100) cc_final: 0.4912 (m100) REVERT: F 32 TYR cc_start: 0.7332 (m-80) cc_final: 0.6888 (m-80) REVERT: F 33 THR cc_start: 0.8209 (m) cc_final: 0.7999 (p) REVERT: F 109 VAL cc_start: 0.7206 (t) cc_final: 0.6710 (t) outliers start: 0 outliers final: 0 residues processed: 717 average time/residue: 0.2298 time to fit residues: 252.9815 Evaluate side-chains 368 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 188 ASN A 207 HIS A 532 ASN A 784 GLN A 914 ASN A 935 GLN A 955 ASN B 474 GLN B 532 ASN B 784 GLN B 907 ASN B 914 ASN B 955 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN E 30 ASN E 784 GLN E 914 ASN E 955 ASN E 992 GLN E1119 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.160917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112898 restraints weight = 52389.293| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.20 r_work: 0.3288 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31704 Z= 0.177 Angle : 0.736 10.296 43245 Z= 0.387 Chirality : 0.048 0.340 4983 Planarity : 0.005 0.061 5499 Dihedral : 5.394 20.580 4185 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.81 % Allowed : 6.72 % Favored : 91.47 % 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: 0.42 (0.13), residues: 3837 helix: 1.75 (0.20), residues: 660 sheet: 0.75 (0.16), residues: 966 loop : -0.36 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 567 TYR 0.020 0.002 TYR B1067 PHE 0.024 0.002 PHE A 497 TRP 0.024 0.002 TRP G 35 HIS 0.009 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (31611) covalent geometry : angle 0.71701 / 0.38 (43014) SS BOND : bond 0.00459 / 0.28 ( 48) SS BOND : angle 1.51589 / 1.07 ( 96) hydrogen bonds : bond 0.06022 / 4.02 ( 1226) hydrogen bonds : angle 6.60795 / 4.60 ( 3354) link_BETA1-4 : bond 0.00600 / 0.41 ( 12) link_BETA1-4 : angle 2.59663 / 1.56 ( 36) link_NAG-ASN : bond 0.00472 / 0.33 ( 33) link_NAG-ASN : angle 2.92190 / 1.93 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 456 time to evaluate : 1.237 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 376 THR cc_start: 0.8835 (m) cc_final: 0.8299 (p) REVERT: A 752 LEU cc_start: 0.9202 (mt) cc_final: 0.8997 (mt) REVERT: A 984 LEU cc_start: 0.8184 (tp) cc_final: 0.7908 (tp) REVERT: A 1002 GLN cc_start: 0.8708 (tp40) cc_final: 0.8433 (tp40) REVERT: H 32 TYR cc_start: 0.7667 (m-80) cc_final: 0.7014 (m-80) REVERT: H 36 TRP cc_start: 0.8155 (m100) cc_final: 0.6986 (m100) REVERT: H 61 GLN cc_start: 0.8030 (tp40) cc_final: 0.7567 (pp30) REVERT: H 80 MET cc_start: 0.6140 (OUTLIER) cc_final: 0.4923 (tpp) REVERT: H 91 TYR cc_start: 0.7096 (p90) cc_final: 0.6808 (p90) REVERT: H 94 ARG cc_start: 0.7029 (ttm-80) cc_final: 0.6796 (ttm170) REVERT: L 24 ARG cc_start: 0.7757 (mmm160) cc_final: 0.7526 (tpt170) REVERT: L 32 TYR cc_start: 0.6728 (m-80) cc_final: 0.6125 (m-10) REVERT: B 140 PHE cc_start: 0.9125 (p90) cc_final: 0.8457 (p90) REVERT: B 351 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5827 (t80) REVERT: B 376 THR cc_start: 0.8869 (m) cc_final: 0.8355 (p) REVERT: B 574 ASP cc_start: 0.8162 (t0) cc_final: 0.7884 (t0) REVERT: B 984 LEU cc_start: 0.8285 (tp) cc_final: 0.8015 (tp) REVERT: C 36 TRP cc_start: 0.7855 (m100) cc_final: 0.5885 (m100) REVERT: C 61 GLN cc_start: 0.8043 (tp40) cc_final: 0.7225 (pp30) REVERT: C 80 MET cc_start: 0.5652 (OUTLIER) cc_final: 0.5323 (ttt) REVERT: C 83 ARG cc_start: 0.7532 (mmm-85) cc_final: 0.7287 (ptt90) REVERT: D 35 TRP cc_start: 0.5759 (m100) cc_final: 0.5510 (m100) REVERT: E 376 THR cc_start: 0.8834 (m) cc_final: 0.8270 (p) REVERT: E 984 LEU cc_start: 0.8287 (tp) cc_final: 0.8041 (tp) REVERT: E 992 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6690 (mm-40) REVERT: F 32 TYR cc_start: 0.7322 (m-80) cc_final: 0.6926 (m-80) REVERT: F 33 THR cc_start: 0.8561 (m) cc_final: 0.8186 (p) REVERT: F 61 GLN cc_start: 0.8111 (tp40) cc_final: 0.7345 (pp30) REVERT: F 80 MET cc_start: 0.5769 (OUTLIER) cc_final: 0.4942 (tpp) REVERT: F 90 TYR cc_start: 0.8485 (p90) cc_final: 0.7793 (p90) REVERT: F 91 TYR cc_start: 0.7139 (p90) cc_final: 0.6778 (p90) REVERT: F 109 VAL cc_start: 0.8017 (t) cc_final: 0.7811 (t) REVERT: G 14 SER cc_start: 0.7890 (m) cc_final: 0.7501 (p) REVERT: G 32 TYR cc_start: 0.6676 (m-80) cc_final: 0.6039 (m-10) outliers start: 61 outliers final: 28 residues processed: 485 average time/residue: 0.2078 time to fit residues: 157.8613 Evaluate side-chains 379 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 346 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 702 GLU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 80 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 384 optimal weight: 20.0000 chunk 254 optimal weight: 20.0000 chunk 299 optimal weight: 0.9990 chunk 343 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN A 784 GLN A 935 GLN B 125 ASN B 165 ASN E 137 ASN E 498 GLN E 564 GLN E 755 GLN E 914 ASN E1142 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100GHIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.158128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.114183 restraints weight = 52524.876| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.45 r_work: 0.3186 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31704 Z= 0.173 Angle : 0.662 11.007 43245 Z= 0.345 Chirality : 0.047 0.273 4983 Planarity : 0.004 0.061 5499 Dihedral : 5.067 20.472 4185 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.13 % Allowed : 8.35 % Favored : 89.52 % 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: 0.32 (0.13), residues: 3837 helix: 2.27 (0.20), residues: 618 sheet: 0.32 (0.15), residues: 1077 loop : -0.43 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 567 TYR 0.023 0.002 TYR B 904 PHE 0.023 0.002 PHE A 497 TRP 0.021 0.002 TRP G 35 HIS 0.006 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (31611) covalent geometry : angle 0.64732 / 0.34 (43014) SS BOND : bond 0.00368 / 0.22 ( 48) SS BOND : angle 1.53017 / 1.20 ( 96) hydrogen bonds : bond 0.05290 / 3.54 ( 1226) hydrogen bonds : angle 6.15232 / 4.28 ( 3354) link_BETA1-4 : bond 0.00519 / 0.36 ( 12) link_BETA1-4 : angle 2.02731 / 1.23 ( 36) link_NAG-ASN : bond 0.00450 / 0.30 ( 33) link_NAG-ASN : angle 2.34779 / 1.53 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 391 time to evaluate : 1.224 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 464 PHE cc_start: 0.8735 (m-80) cc_final: 0.8424 (m-80) REVERT: A 984 LEU cc_start: 0.8008 (tp) cc_final: 0.7622 (tp) REVERT: H 32 TYR cc_start: 0.7643 (m-80) cc_final: 0.7259 (m-80) REVERT: H 36 TRP cc_start: 0.8077 (m100) cc_final: 0.6940 (m100) REVERT: H 61 GLN cc_start: 0.8092 (tp40) cc_final: 0.7575 (pp30) REVERT: H 80 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5069 (ttm) REVERT: L 32 TYR cc_start: 0.6769 (m-80) cc_final: 0.6352 (m-10) REVERT: B 140 PHE cc_start: 0.9131 (p90) cc_final: 0.8418 (p90) REVERT: B 351 TYR cc_start: 0.6138 (t80) cc_final: 0.5937 (t80) REVERT: B 376 THR cc_start: 0.8920 (m) cc_final: 0.8369 (p) REVERT: B 574 ASP cc_start: 0.8439 (t0) cc_final: 0.8213 (t0) REVERT: B 984 LEU cc_start: 0.8267 (tp) cc_final: 0.7985 (tp) REVERT: C 36 TRP cc_start: 0.7856 (m100) cc_final: 0.6220 (m100) REVERT: C 61 GLN cc_start: 0.8059 (tp40) cc_final: 0.7253 (pp30) REVERT: C 80 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5198 (ttm) REVERT: C 91 TYR cc_start: 0.7085 (p90) cc_final: 0.6850 (p90) REVERT: E 505 TYR cc_start: 0.8034 (m-80) cc_final: 0.7541 (m-80) REVERT: E 984 LEU cc_start: 0.8284 (tp) cc_final: 0.7942 (tp) REVERT: F 32 TYR cc_start: 0.7427 (m-80) cc_final: 0.6998 (m-80) REVERT: F 61 GLN cc_start: 0.8073 (tp40) cc_final: 0.7422 (pm20) REVERT: F 80 MET cc_start: 0.5824 (OUTLIER) cc_final: 0.4958 (tpp) REVERT: F 90 TYR cc_start: 0.8294 (p90) cc_final: 0.7868 (p90) REVERT: G 14 SER cc_start: 0.7863 (m) cc_final: 0.7403 (p) REVERT: G 24 ARG cc_start: 0.8060 (tmt-80) cc_final: 0.7773 (tmt-80) REVERT: G 32 TYR cc_start: 0.6685 (m-80) cc_final: 0.6172 (m-10) REVERT: G 35 TRP cc_start: 0.5312 (m100) cc_final: 0.5039 (m100) outliers start: 72 outliers final: 45 residues processed: 431 average time/residue: 0.2059 time to fit residues: 141.7693 Evaluate side-chains 386 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 338 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 564 GLN Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 702 GLU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain E residue 1141 LEU Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 335 optimal weight: 0.0000 chunk 357 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 142 optimal weight: 0.0060 chunk 250 optimal weight: 20.0000 chunk 181 optimal weight: 8.9990 chunk 342 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 161 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN E 125 ASN E 755 GLN E 914 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.158022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101691 restraints weight = 52213.376| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.80 r_work: 0.3121 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31704 Z= 0.117 Angle : 0.595 9.312 43245 Z= 0.309 Chirality : 0.045 0.260 4983 Planarity : 0.004 0.040 5499 Dihedral : 4.767 19.816 4185 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.92 % Allowed : 10.07 % Favored : 88.01 % 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: 0.27 (0.13), residues: 3837 helix: 2.31 (0.20), residues: 645 sheet: 0.18 (0.15), residues: 1107 loop : -0.47 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 634 TYR 0.021 0.001 TYR C 32 PHE 0.030 0.002 PHE A 497 TRP 0.015 0.002 TRP L 35 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (31611) covalent geometry : angle 0.58088 / 0.31 (43014) SS BOND : bond 0.00299 / 0.17 ( 48) SS BOND : angle 1.33037 / 1.05 ( 96) hydrogen bonds : bond 0.04466 / 2.99 ( 1226) hydrogen bonds : angle 5.86975 / 4.09 ( 3354) link_BETA1-4 : bond 0.00463 / 0.31 ( 12) link_BETA1-4 : angle 1.78980 / 1.08 ( 36) link_NAG-ASN : bond 0.00378 / 0.26 ( 33) link_NAG-ASN : angle 2.23405 / 1.44 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 381 time to evaluate : 1.154 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 335 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7365 (tt) REVERT: A 449 TYR cc_start: 0.8307 (m-80) cc_final: 0.7860 (m-80) REVERT: A 856 ASN cc_start: 0.8002 (p0) cc_final: 0.7557 (m-40) REVERT: A 984 LEU cc_start: 0.7923 (tp) cc_final: 0.7491 (tp) REVERT: A 1005 GLN cc_start: 0.8436 (tt0) cc_final: 0.8180 (mt0) REVERT: H 32 TYR cc_start: 0.7686 (m-80) cc_final: 0.7274 (m-80) REVERT: H 36 TRP cc_start: 0.8022 (m100) cc_final: 0.7107 (m100) REVERT: H 61 GLN cc_start: 0.8321 (tp40) cc_final: 0.7641 (pp30) REVERT: H 80 MET cc_start: 0.5882 (OUTLIER) cc_final: 0.5029 (ttm) REVERT: L 32 TYR cc_start: 0.7022 (m-80) cc_final: 0.6642 (m-10) REVERT: L 48 ILE cc_start: 0.6081 (mt) cc_final: 0.5789 (mp) REVERT: B 140 PHE cc_start: 0.9263 (p90) cc_final: 0.8434 (p90) REVERT: B 402 ILE cc_start: 0.8740 (pt) cc_final: 0.8494 (pt) REVERT: B 403 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6955 (ttp80) REVERT: B 574 ASP cc_start: 0.8480 (t0) cc_final: 0.8243 (t0) REVERT: B 984 LEU cc_start: 0.8157 (tp) cc_final: 0.7778 (tp) REVERT: B 1050 MET cc_start: 0.8893 (ptm) cc_final: 0.8569 (ptm) REVERT: C 36 TRP cc_start: 0.7724 (m100) cc_final: 0.5859 (m100) REVERT: C 61 GLN cc_start: 0.8323 (tp40) cc_final: 0.7582 (pp30) REVERT: C 91 TYR cc_start: 0.7126 (p90) cc_final: 0.6867 (p90) REVERT: C 100 PHE cc_start: 0.6652 (m-80) cc_final: 0.6451 (m-80) REVERT: E 442 ASP cc_start: 0.6553 (m-30) cc_final: 0.5902 (m-30) REVERT: E 984 LEU cc_start: 0.8148 (tp) cc_final: 0.7774 (tp) REVERT: F 32 TYR cc_start: 0.7561 (m-80) cc_final: 0.7233 (m-80) REVERT: F 36 TRP cc_start: 0.8166 (m100) cc_final: 0.7577 (m100) REVERT: F 61 GLN cc_start: 0.8187 (tp40) cc_final: 0.7534 (pm20) REVERT: F 80 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.4875 (tpp) REVERT: F 90 TYR cc_start: 0.8298 (p90) cc_final: 0.7937 (p90) REVERT: G 14 SER cc_start: 0.7853 (m) cc_final: 0.7445 (p) REVERT: G 32 TYR cc_start: 0.6904 (m-80) cc_final: 0.6490 (m-10) outliers start: 65 outliers final: 38 residues processed: 410 average time/residue: 0.1915 time to fit residues: 125.2577 Evaluate side-chains 377 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 335 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 856 ASN Chi-restraints excluded: chain E residue 914 ASN Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 238 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 363 optimal weight: 0.0570 chunk 49 optimal weight: 9.9990 chunk 67 optimal weight: 0.0060 chunk 343 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 375 optimal weight: 4.9990 overall best weight: 1.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 HIS ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN E 655 HIS E 914 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.154557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.104402 restraints weight = 52832.284| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.26 r_work: 0.3120 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 31704 Z= 0.216 Angle : 0.639 10.500 43245 Z= 0.332 Chirality : 0.047 0.262 4983 Planarity : 0.004 0.041 5499 Dihedral : 4.806 20.984 4185 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 2.75 % Allowed : 9.38 % Favored : 87.86 % 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: 0.08 (0.13), residues: 3837 helix: 2.04 (0.20), residues: 648 sheet: 0.11 (0.15), residues: 1110 loop : -0.60 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 634 TYR 0.026 0.002 TYR B 904 PHE 0.026 0.002 PHE A 497 TRP 0.017 0.002 TRP C 36 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (31611) covalent geometry : angle 0.62589 / 0.33 (43014) SS BOND : bond 0.00367 / 0.20 ( 48) SS BOND : angle 1.50775 / 1.02 ( 96) hydrogen bonds : bond 0.05064 / 3.35 ( 1226) hydrogen bonds : angle 5.85734 / 4.10 ( 3354) link_BETA1-4 : bond 0.00315 / 0.21 ( 12) link_BETA1-4 : angle 1.72748 / 1.07 ( 36) link_NAG-ASN : bond 0.00318 / 0.22 ( 33) link_NAG-ASN : angle 2.21692 / 1.46 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 354 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7078 (mp) cc_final: 0.6556 (tt) REVERT: A 226 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7561 (mp) REVERT: A 335 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7415 (tt) REVERT: A 856 ASN cc_start: 0.7862 (p0) cc_final: 0.7511 (m-40) REVERT: A 984 LEU cc_start: 0.7993 (tp) cc_final: 0.7582 (tp) REVERT: H 36 TRP cc_start: 0.7986 (m100) cc_final: 0.7224 (m100) REVERT: H 61 GLN cc_start: 0.8282 (tp40) cc_final: 0.7617 (pp30) REVERT: H 80 MET cc_start: 0.5412 (OUTLIER) cc_final: 0.4749 (ttm) REVERT: L 4 MET cc_start: 0.3936 (tmm) cc_final: 0.3703 (tmm) REVERT: L 32 TYR cc_start: 0.6992 (m-80) cc_final: 0.6722 (m-80) REVERT: L 48 ILE cc_start: 0.6093 (mt) cc_final: 0.5834 (mp) REVERT: B 140 PHE cc_start: 0.9204 (p90) cc_final: 0.8349 (p90) REVERT: B 226 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7720 (mp) REVERT: B 351 TYR cc_start: 0.5422 (t80) cc_final: 0.5020 (t80) REVERT: B 402 ILE cc_start: 0.8927 (pt) cc_final: 0.8688 (pt) REVERT: B 403 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6843 (ttp80) REVERT: B 984 LEU cc_start: 0.8251 (tp) cc_final: 0.7899 (tp) REVERT: C 36 TRP cc_start: 0.7785 (m100) cc_final: 0.6108 (m100) REVERT: C 61 GLN cc_start: 0.8433 (tp40) cc_final: 0.7635 (pp30) REVERT: C 91 TYR cc_start: 0.6896 (p90) cc_final: 0.6666 (p90) REVERT: C 100 PHE cc_start: 0.6819 (m-80) cc_final: 0.6480 (m-80) REVERT: E 442 ASP cc_start: 0.6315 (m-30) cc_final: 0.6034 (m-30) REVERT: E 565 PHE cc_start: 0.7269 (t80) cc_final: 0.7019 (t80) REVERT: E 979 ASP cc_start: 0.8350 (t0) cc_final: 0.8136 (t0) REVERT: E 984 LEU cc_start: 0.8209 (tp) cc_final: 0.7836 (tp) REVERT: F 36 TRP cc_start: 0.8088 (m100) cc_final: 0.6251 (m100) REVERT: F 61 GLN cc_start: 0.8183 (tp40) cc_final: 0.7529 (pp30) REVERT: F 80 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.4909 (tpp) REVERT: F 90 TYR cc_start: 0.8374 (p90) cc_final: 0.8032 (p90) REVERT: G 14 SER cc_start: 0.7870 (m) cc_final: 0.7403 (p) REVERT: G 32 TYR cc_start: 0.6879 (m-80) cc_final: 0.6508 (m-10) outliers start: 93 outliers final: 64 residues processed: 412 average time/residue: 0.1869 time to fit residues: 125.2402 Evaluate side-chains 389 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 319 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 702 GLU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 856 ASN Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 966 LEU Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 363 optimal weight: 0.0770 chunk 209 optimal weight: 0.5980 chunk 306 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 238 optimal weight: 20.0000 chunk 124 optimal weight: 0.2980 chunk 116 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN E 913 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.156309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.106302 restraints weight = 52238.467| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.24 r_work: 0.3179 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31704 Z= 0.117 Angle : 0.580 9.033 43245 Z= 0.300 Chirality : 0.045 0.252 4983 Planarity : 0.004 0.051 5499 Dihedral : 4.592 20.347 4185 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 2.25 % Allowed : 10.48 % Favored : 87.27 % 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 (0.14), residues: 3837 helix: 2.56 (0.21), residues: 624 sheet: 0.05 (0.15), residues: 1119 loop : -0.53 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 94 TYR 0.023 0.001 TYR C 32 PHE 0.026 0.001 PHE B 565 TRP 0.018 0.001 TRP F 47 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (31611) covalent geometry : angle 0.56763 / 0.30 (43014) SS BOND : bond 0.00301 / 0.17 ( 48) SS BOND : angle 1.25429 / 0.88 ( 96) hydrogen bonds : bond 0.04239 / 2.81 ( 1226) hydrogen bonds : angle 5.64446 / 3.95 ( 3354) link_BETA1-4 : bond 0.00454 / 0.31 ( 12) link_BETA1-4 : angle 1.59317 / 0.96 ( 36) link_NAG-ASN : bond 0.00353 / 0.24 ( 33) link_NAG-ASN : angle 2.07004 / 1.33 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 352 time to evaluate : 1.011 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 335 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7448 (tt) REVERT: A 358 ILE cc_start: 0.8733 (mt) cc_final: 0.8526 (mm) REVERT: A 464 PHE cc_start: 0.8849 (m-80) cc_final: 0.8419 (m-80) REVERT: A 856 ASN cc_start: 0.7700 (p0) cc_final: 0.7398 (m-40) REVERT: A 979 ASP cc_start: 0.8178 (t0) cc_final: 0.7902 (t0) REVERT: A 984 LEU cc_start: 0.7856 (tp) cc_final: 0.7397 (tp) REVERT: A 1001 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 1005 GLN cc_start: 0.8273 (tt0) cc_final: 0.8028 (mt0) REVERT: H 36 TRP cc_start: 0.7921 (m100) cc_final: 0.7259 (m100) REVERT: H 61 GLN cc_start: 0.8225 (tp40) cc_final: 0.7594 (pp30) REVERT: H 66 ARG cc_start: 0.7435 (mtm110) cc_final: 0.7041 (mtm110) REVERT: H 80 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.5338 (ttm) REVERT: L 4 MET cc_start: 0.4069 (tmm) cc_final: 0.3777 (tmm) REVERT: L 32 TYR cc_start: 0.6902 (m-80) cc_final: 0.6630 (m-80) REVERT: L 48 ILE cc_start: 0.6235 (mt) cc_final: 0.5997 (mp) REVERT: B 140 PHE cc_start: 0.9194 (p90) cc_final: 0.8365 (p90) REVERT: B 177 MET cc_start: 0.6678 (tpp) cc_final: 0.6323 (mtt) REVERT: B 755 GLN cc_start: 0.8781 (tt0) cc_final: 0.8370 (tm-30) REVERT: B 977 LEU cc_start: 0.7950 (mp) cc_final: 0.7698 (mt) REVERT: B 984 LEU cc_start: 0.8169 (tp) cc_final: 0.7760 (tp) REVERT: B 1050 MET cc_start: 0.8802 (ptm) cc_final: 0.8493 (ptm) REVERT: C 36 TRP cc_start: 0.7719 (m100) cc_final: 0.6010 (m100) REVERT: C 61 GLN cc_start: 0.8388 (tp40) cc_final: 0.7701 (pp30) REVERT: C 91 TYR cc_start: 0.6865 (p90) cc_final: 0.6644 (p90) REVERT: E 177 MET cc_start: 0.6583 (tpp) cc_final: 0.6156 (mtt) REVERT: E 646 ARG cc_start: 0.8757 (tpp80) cc_final: 0.8411 (tpt170) REVERT: E 983 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7223 (mtm110) REVERT: E 984 LEU cc_start: 0.8109 (tp) cc_final: 0.7748 (tp) REVERT: F 36 TRP cc_start: 0.8035 (m100) cc_final: 0.6233 (m100) REVERT: F 61 GLN cc_start: 0.8063 (tp40) cc_final: 0.7488 (pp30) REVERT: F 80 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.5048 (tpp) REVERT: G 14 SER cc_start: 0.7857 (m) cc_final: 0.7394 (p) REVERT: G 32 TYR cc_start: 0.7017 (m-80) cc_final: 0.6630 (m-10) outliers start: 76 outliers final: 47 residues processed: 395 average time/residue: 0.1920 time to fit residues: 122.7416 Evaluate side-chains 379 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 328 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 70 optimal weight: 0.7980 chunk 157 optimal weight: 0.0970 chunk 369 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 359 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 251 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN E 856 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.156370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105817 restraints weight = 52539.594| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.23 r_work: 0.3149 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31704 Z= 0.144 Angle : 0.586 8.851 43245 Z= 0.303 Chirality : 0.045 0.250 4983 Planarity : 0.004 0.043 5499 Dihedral : 4.569 27.656 4185 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.26 % Rotamer: Outliers : 2.19 % Allowed : 10.81 % Favored : 87.00 % 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: 0.19 (0.14), residues: 3837 helix: 2.57 (0.20), residues: 624 sheet: 0.10 (0.15), residues: 1095 loop : -0.60 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.033 0.002 TYR B 351 PHE 0.025 0.002 PHE E 497 TRP 0.021 0.002 TRP F 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (31611) covalent geometry : angle 0.57367 / 0.30 (43014) SS BOND : bond 0.00462 / 0.24 ( 48) SS BOND : angle 1.55744 / 1.08 ( 96) hydrogen bonds : bond 0.04348 / 2.89 ( 1226) hydrogen bonds : angle 5.58144 / 3.91 ( 3354) link_BETA1-4 : bond 0.00409 / 0.29 ( 12) link_BETA1-4 : angle 1.58281 / 0.98 ( 36) link_NAG-ASN : bond 0.00285 / 0.19 ( 33) link_NAG-ASN : angle 1.89998 / 1.21 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 337 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7307 (tt) REVERT: A 464 PHE cc_start: 0.8892 (m-80) cc_final: 0.8460 (m-80) REVERT: A 856 ASN cc_start: 0.7831 (p0) cc_final: 0.7503 (m-40) REVERT: A 979 ASP cc_start: 0.8253 (t0) cc_final: 0.7972 (t0) REVERT: A 984 LEU cc_start: 0.7878 (tp) cc_final: 0.7395 (tp) REVERT: A 1001 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8588 (mt) REVERT: A 1005 GLN cc_start: 0.8404 (tt0) cc_final: 0.8126 (mt0) REVERT: H 32 TYR cc_start: 0.7499 (m-80) cc_final: 0.7226 (m-80) REVERT: H 36 TRP cc_start: 0.7895 (m100) cc_final: 0.7276 (m100) REVERT: H 66 ARG cc_start: 0.7458 (mtm110) cc_final: 0.7137 (mtm110) REVERT: H 100 GLN cc_start: 0.6102 (mp10) cc_final: 0.5610 (pm20) REVERT: L 32 TYR cc_start: 0.6974 (m-80) cc_final: 0.6709 (m-80) REVERT: L 48 ILE cc_start: 0.6465 (mt) cc_final: 0.6228 (mp) REVERT: B 140 PHE cc_start: 0.9220 (p90) cc_final: 0.8366 (p90) REVERT: B 177 MET cc_start: 0.6673 (tpp) cc_final: 0.6332 (mtt) REVERT: B 378 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7959 (mmtt) REVERT: B 755 GLN cc_start: 0.8824 (tt0) cc_final: 0.8414 (tm-30) REVERT: B 977 LEU cc_start: 0.8175 (mp) cc_final: 0.7924 (mt) REVERT: B 984 LEU cc_start: 0.7658 (tp) cc_final: 0.7275 (tp) REVERT: C 36 TRP cc_start: 0.7557 (m100) cc_final: 0.6085 (m100) REVERT: C 91 TYR cc_start: 0.6863 (p90) cc_final: 0.6599 (p90) REVERT: C 100 PHE cc_start: 0.6566 (m-80) cc_final: 0.6293 (m-10) REVERT: D 48 ILE cc_start: 0.7374 (mm) cc_final: 0.7042 (mm) REVERT: E 177 MET cc_start: 0.6451 (tpp) cc_final: 0.5985 (mtt) REVERT: E 449 TYR cc_start: 0.8350 (m-80) cc_final: 0.7905 (m-80) REVERT: E 646 ARG cc_start: 0.8765 (tpp80) cc_final: 0.8418 (tpp-160) REVERT: E 904 TYR cc_start: 0.8687 (m-10) cc_final: 0.8472 (m-10) REVERT: E 984 LEU cc_start: 0.8146 (tp) cc_final: 0.7748 (tp) REVERT: F 36 TRP cc_start: 0.8076 (m100) cc_final: 0.6230 (m100) REVERT: F 61 GLN cc_start: 0.8075 (tp40) cc_final: 0.7498 (pp30) REVERT: F 80 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.5476 (ttm) REVERT: G 14 SER cc_start: 0.7846 (m) cc_final: 0.7399 (p) REVERT: G 24 ARG cc_start: 0.7644 (tmt-80) cc_final: 0.7373 (tmt-80) REVERT: G 32 TYR cc_start: 0.6947 (m-80) cc_final: 0.6586 (m-10) outliers start: 74 outliers final: 56 residues processed: 380 average time/residue: 0.1999 time to fit residues: 123.0498 Evaluate side-chains 377 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 318 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 856 ASN Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 966 LEU Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 380 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 381 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 360 optimal weight: 0.6980 chunk 156 optimal weight: 0.4980 chunk 163 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 chunk 29 optimal weight: 0.0570 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 914 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.156382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.108789 restraints weight = 52620.543| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.47 r_work: 0.3140 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31704 Z= 0.137 Angle : 0.587 13.129 43245 Z= 0.301 Chirality : 0.045 0.248 4983 Planarity : 0.004 0.043 5499 Dihedral : 4.537 27.094 4185 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 1.92 % Allowed : 11.34 % Favored : 86.74 % 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 (0.14), residues: 3837 helix: 2.54 (0.20), residues: 642 sheet: 0.08 (0.15), residues: 1113 loop : -0.63 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 634 TYR 0.037 0.001 TYR B 351 PHE 0.024 0.001 PHE H 29 TRP 0.016 0.002 TRP F 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (31611) covalent geometry : angle 0.57655 / 0.30 (43014) SS BOND : bond 0.00313 / 0.18 ( 48) SS BOND : angle 1.34879 / 0.93 ( 96) hydrogen bonds : bond 0.04273 / 2.84 ( 1226) hydrogen bonds : angle 5.51929 / 3.87 ( 3354) link_BETA1-4 : bond 0.00359 / 0.25 ( 12) link_BETA1-4 : angle 1.54154 / 0.96 ( 36) link_NAG-ASN : bond 0.00253 / 0.17 ( 33) link_NAG-ASN : angle 1.87837 / 1.20 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 325 time to evaluate : 1.064 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 226 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7648 (mp) REVERT: A 335 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7387 (tt) REVERT: A 464 PHE cc_start: 0.8868 (m-80) cc_final: 0.8440 (m-80) REVERT: A 856 ASN cc_start: 0.7848 (p0) cc_final: 0.7524 (m-40) REVERT: A 982 SER cc_start: 0.8432 (m) cc_final: 0.8121 (p) REVERT: A 1001 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8610 (mt) REVERT: A 1005 GLN cc_start: 0.8413 (tt0) cc_final: 0.8140 (mt0) REVERT: H 32 TYR cc_start: 0.7498 (m-80) cc_final: 0.7282 (m-80) REVERT: H 36 TRP cc_start: 0.7815 (m100) cc_final: 0.7196 (m100) REVERT: H 66 ARG cc_start: 0.7374 (mtm110) cc_final: 0.6959 (mtm110) REVERT: H 100 GLN cc_start: 0.5995 (mp10) cc_final: 0.5599 (pm20) REVERT: L 4 MET cc_start: 0.4053 (tmm) cc_final: 0.3630 (tmm) REVERT: L 32 TYR cc_start: 0.6939 (m-80) cc_final: 0.6699 (m-80) REVERT: L 48 ILE cc_start: 0.6193 (mt) cc_final: 0.5732 (mp) REVERT: B 140 PHE cc_start: 0.9224 (p90) cc_final: 0.8397 (p90) REVERT: B 177 MET cc_start: 0.6646 (tpp) cc_final: 0.6337 (mtt) REVERT: B 346 ARG cc_start: 0.7748 (mmp80) cc_final: 0.7428 (tpt170) REVERT: B 378 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7959 (mmtt) REVERT: B 755 GLN cc_start: 0.8853 (tt0) cc_final: 0.8440 (tm-30) REVERT: B 977 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 984 LEU cc_start: 0.7730 (tp) cc_final: 0.7306 (tp) REVERT: C 36 TRP cc_start: 0.7765 (m100) cc_final: 0.6154 (m100) REVERT: C 100 GLN cc_start: 0.5780 (mp10) cc_final: 0.5475 (pm20) REVERT: C 100 PHE cc_start: 0.6774 (m-80) cc_final: 0.6553 (m-10) REVERT: D 4 MET cc_start: 0.3961 (tmm) cc_final: 0.3753 (tmm) REVERT: D 48 ILE cc_start: 0.7416 (mm) cc_final: 0.7046 (mm) REVERT: E 177 MET cc_start: 0.6443 (tpp) cc_final: 0.6014 (mtt) REVERT: E 449 TYR cc_start: 0.8309 (m-80) cc_final: 0.7855 (m-80) REVERT: E 565 PHE cc_start: 0.7300 (t80) cc_final: 0.7018 (t80) REVERT: E 646 ARG cc_start: 0.8857 (tpp80) cc_final: 0.8493 (tpp-160) REVERT: E 755 GLN cc_start: 0.8743 (tt0) cc_final: 0.8412 (tm-30) REVERT: E 984 LEU cc_start: 0.8205 (tp) cc_final: 0.7800 (tp) REVERT: F 61 GLN cc_start: 0.8022 (tp40) cc_final: 0.7563 (pp30) REVERT: F 80 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5068 (tpp) REVERT: F 101 ASP cc_start: 0.6105 (p0) cc_final: 0.5844 (p0) REVERT: G 4 MET cc_start: 0.3823 (tmm) cc_final: 0.3459 (tmm) REVERT: G 14 SER cc_start: 0.7713 (m) cc_final: 0.7253 (p) REVERT: G 32 TYR cc_start: 0.6717 (m-80) cc_final: 0.6356 (m-10) outliers start: 65 outliers final: 54 residues processed: 363 average time/residue: 0.1947 time to fit residues: 114.6363 Evaluate side-chains 370 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 311 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 90 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 153 optimal weight: 0.2980 chunk 366 optimal weight: 9.9990 chunk 278 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.155840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099725 restraints weight = 52537.870| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.59 r_work: 0.3062 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31704 Z= 0.143 Angle : 0.594 11.034 43245 Z= 0.304 Chirality : 0.045 0.247 4983 Planarity : 0.004 0.043 5499 Dihedral : 4.524 26.350 4185 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.13 % Rotamer: Outliers : 1.92 % Allowed : 11.43 % Favored : 86.65 % 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: 0.09 (0.14), residues: 3837 helix: 2.26 (0.20), residues: 681 sheet: 0.08 (0.15), residues: 1134 loop : -0.71 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 38 TYR 0.044 0.002 TYR B 351 PHE 0.019 0.002 PHE E 855 TRP 0.025 0.002 TRP H 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (31611) covalent geometry : angle 0.58364 / 0.30 (43014) SS BOND : bond 0.00387 / 0.28 ( 48) SS BOND : angle 1.27871 / 0.88 ( 96) hydrogen bonds : bond 0.04314 / 2.87 ( 1226) hydrogen bonds : angle 5.48296 / 3.86 ( 3354) link_BETA1-4 : bond 0.00358 / 0.24 ( 12) link_BETA1-4 : angle 1.51806 / 0.94 ( 36) link_NAG-ASN : bond 0.00227 / 0.15 ( 33) link_NAG-ASN : angle 1.85760 / 1.19 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 320 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6404 (mtt) cc_final: 0.6089 (mtt) REVERT: A 226 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7764 (mp) REVERT: A 335 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7400 (tt) REVERT: A 505 TYR cc_start: 0.8161 (m-80) cc_final: 0.7733 (m-80) REVERT: A 755 GLN cc_start: 0.8902 (tt0) cc_final: 0.8624 (tm-30) REVERT: A 856 ASN cc_start: 0.7917 (p0) cc_final: 0.7576 (m-40) REVERT: A 1001 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8654 (mt) REVERT: A 1005 GLN cc_start: 0.8545 (tt0) cc_final: 0.8276 (mt0) REVERT: H 66 ARG cc_start: 0.7375 (mtm110) cc_final: 0.7084 (mtm110) REVERT: L 32 TYR cc_start: 0.6996 (m-80) cc_final: 0.6682 (m-80) REVERT: L 38 GLN cc_start: 0.3924 (OUTLIER) cc_final: 0.3540 (mp10) REVERT: L 48 ILE cc_start: 0.6247 (mt) cc_final: 0.6036 (mp) REVERT: B 140 PHE cc_start: 0.9266 (p90) cc_final: 0.8336 (p90) REVERT: B 177 MET cc_start: 0.6800 (tpp) cc_final: 0.6377 (mtt) REVERT: B 378 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7973 (mmtt) REVERT: B 977 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7971 (mt) REVERT: B 984 LEU cc_start: 0.7627 (tp) cc_final: 0.7141 (tp) REVERT: C 36 TRP cc_start: 0.7712 (m100) cc_final: 0.5867 (m100) REVERT: C 100 GLN cc_start: 0.5785 (mp10) cc_final: 0.5492 (pm20) REVERT: C 100 PHE cc_start: 0.6704 (m-80) cc_final: 0.6417 (m-10) REVERT: D 4 MET cc_start: 0.3891 (tmm) cc_final: 0.3681 (tmm) REVERT: D 48 ILE cc_start: 0.7559 (mm) cc_final: 0.7296 (mm) REVERT: E 177 MET cc_start: 0.6520 (tpp) cc_final: 0.6051 (mtt) REVERT: E 449 TYR cc_start: 0.8367 (m-80) cc_final: 0.7921 (m-80) REVERT: E 565 PHE cc_start: 0.7342 (t80) cc_final: 0.7053 (t80) REVERT: E 646 ARG cc_start: 0.8918 (tpp80) cc_final: 0.8627 (tpt170) REVERT: E 755 GLN cc_start: 0.8846 (tt0) cc_final: 0.8595 (tm-30) REVERT: E 977 LEU cc_start: 0.7807 (mp) cc_final: 0.7531 (mt) REVERT: F 61 GLN cc_start: 0.8129 (tp40) cc_final: 0.7625 (pp30) REVERT: F 66 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7028 (ttp-110) REVERT: F 80 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.4940 (tpp) REVERT: G 14 SER cc_start: 0.7732 (m) cc_final: 0.7362 (p) REVERT: G 32 TYR cc_start: 0.6826 (m-80) cc_final: 0.6421 (m-10) outliers start: 65 outliers final: 52 residues processed: 359 average time/residue: 0.1916 time to fit residues: 111.4793 Evaluate side-chains 357 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 299 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 161 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 344 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 253 optimal weight: 20.0000 chunk 76 optimal weight: 0.0020 chunk 101 optimal weight: 0.2980 chunk 142 optimal weight: 6.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.155769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096982 restraints weight = 51795.520| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.48 r_work: 0.3102 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 31704 Z= 0.120 Angle : 0.591 13.819 43245 Z= 0.301 Chirality : 0.045 0.244 4983 Planarity : 0.004 0.043 5499 Dihedral : 4.447 25.420 4185 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 1.69 % Allowed : 11.81 % Favored : 86.50 % 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: 0.08 (0.14), residues: 3837 helix: 2.27 (0.20), residues: 681 sheet: 0.03 (0.15), residues: 1128 loop : -0.68 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 38 TYR 0.040 0.001 TYR B 351 PHE 0.026 0.001 PHE E 759 TRP 0.016 0.001 TRP C 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (31611) covalent geometry : angle 0.57953 / 0.30 (43014) SS BOND : bond 0.00272 / 0.14 ( 48) SS BOND : angle 1.53398 / 1.02 ( 96) hydrogen bonds : bond 0.04123 / 2.74 ( 1226) hydrogen bonds : angle 5.40052 / 3.80 ( 3354) link_BETA1-4 : bond 0.00393 / 0.27 ( 12) link_BETA1-4 : angle 1.49294 / 0.93 ( 36) link_NAG-ASN : bond 0.00262 / 0.17 ( 33) link_NAG-ASN : angle 1.82001 / 1.15 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7674 Ramachandran restraints generated. 3837 Oldfield, 0 Emsley, 3837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 1.013 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 335 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7365 (tt) REVERT: A 449 TYR cc_start: 0.8489 (m-80) cc_final: 0.8084 (m-80) REVERT: A 505 TYR cc_start: 0.8113 (m-80) cc_final: 0.7704 (m-80) REVERT: A 755 GLN cc_start: 0.8867 (tt0) cc_final: 0.8548 (tm-30) REVERT: A 856 ASN cc_start: 0.7818 (p0) cc_final: 0.7491 (m-40) REVERT: A 1001 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8617 (mt) REVERT: A 1005 GLN cc_start: 0.8514 (tt0) cc_final: 0.8247 (mt0) REVERT: H 36 TRP cc_start: 0.8003 (m100) cc_final: 0.6947 (m100) REVERT: H 66 ARG cc_start: 0.7374 (mtm110) cc_final: 0.7066 (mtm110) REVERT: L 4 MET cc_start: 0.3377 (tmm) cc_final: 0.2611 (tmm) REVERT: L 32 TYR cc_start: 0.7024 (m-80) cc_final: 0.6724 (m-80) REVERT: L 38 GLN cc_start: 0.4186 (OUTLIER) cc_final: 0.3755 (mp10) REVERT: L 48 ILE cc_start: 0.6188 (mt) cc_final: 0.5963 (mp) REVERT: B 140 PHE cc_start: 0.9260 (p90) cc_final: 0.8366 (p90) REVERT: B 177 MET cc_start: 0.6748 (tpp) cc_final: 0.6358 (mtt) REVERT: B 241 LEU cc_start: 0.7793 (mt) cc_final: 0.7546 (mp) REVERT: B 378 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7951 (mmtt) REVERT: B 755 GLN cc_start: 0.8999 (tt0) cc_final: 0.8562 (tm-30) REVERT: B 855 PHE cc_start: 0.6599 (p90) cc_final: 0.6392 (p90) REVERT: B 977 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7936 (mt) REVERT: B 979 ASP cc_start: 0.8432 (t0) cc_final: 0.8117 (t0) REVERT: B 984 LEU cc_start: 0.7495 (tp) cc_final: 0.6960 (tp) REVERT: C 36 TRP cc_start: 0.7562 (m100) cc_final: 0.6051 (m100) REVERT: C 100 GLN cc_start: 0.5835 (mp10) cc_final: 0.5563 (pm20) REVERT: C 100 PHE cc_start: 0.6547 (m-80) cc_final: 0.6300 (m-10) REVERT: D 48 ILE cc_start: 0.7509 (mm) cc_final: 0.7232 (mm) REVERT: E 177 MET cc_start: 0.6326 (tpp) cc_final: 0.5876 (mtt) REVERT: E 449 TYR cc_start: 0.8348 (m-80) cc_final: 0.7905 (m-80) REVERT: E 565 PHE cc_start: 0.7206 (t80) cc_final: 0.6908 (t80) REVERT: E 646 ARG cc_start: 0.8905 (tpp80) cc_final: 0.8615 (tpt170) REVERT: E 755 GLN cc_start: 0.8881 (tt0) cc_final: 0.8573 (tm-30) REVERT: E 984 LEU cc_start: 0.7428 (tp) cc_final: 0.7086 (tp) REVERT: F 61 GLN cc_start: 0.8129 (tp40) cc_final: 0.7666 (pp30) REVERT: F 80 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.4213 (tpp) REVERT: G 4 MET cc_start: 0.3800 (tmm) cc_final: 0.3231 (tmm) REVERT: G 14 SER cc_start: 0.7774 (m) cc_final: 0.7421 (p) REVERT: G 32 TYR cc_start: 0.6693 (m-80) cc_final: 0.6280 (m-10) outliers start: 57 outliers final: 48 residues processed: 358 average time/residue: 0.1892 time to fit residues: 108.9532 Evaluate side-chains 361 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1092 GLU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 319 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 207 optimal weight: 0.0980 chunk 320 optimal weight: 0.1980 chunk 352 optimal weight: 0.6980 chunk 280 optimal weight: 9.9990 chunk 313 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.155029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097111 restraints weight = 52258.893| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.51 r_work: 0.3047 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 31704 Z= 0.163 Angle : 0.615 11.331 43245 Z= 0.314 Chirality : 0.045 0.248 4983 Planarity : 0.004 0.042 5499 Dihedral : 4.509 25.834 4185 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.93 % Favored : 95.00 % Rotamer: Outliers : 1.81 % Allowed : 11.90 % Favored : 86.29 % 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: 0.03 (0.14), residues: 3837 helix: 2.21 (0.20), residues: 681 sheet: -0.02 (0.15), residues: 1167 loop : -0.71 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 38 TYR 0.044 0.002 TYR E 351 PHE 0.027 0.002 PHE F 29 TRP 0.023 0.002 TRP H 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (31611) covalent geometry : angle 0.60486 / 0.31 (43014) SS BOND : bond 0.00261 / 0.15 ( 48) SS BOND : angle 1.41499 / 0.94 ( 96) hydrogen bonds : bond 0.04423 / 2.94 ( 1226) hydrogen bonds : angle 5.44606 / 3.84 ( 3354) link_BETA1-4 : bond 0.00306 / 0.20 ( 12) link_BETA1-4 : angle 1.52742 / 0.96 ( 36) link_NAG-ASN : bond 0.00211 / 0.14 ( 33) link_NAG-ASN : angle 1.83628 / 1.17 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9822.97 seconds wall clock time: 168 minutes 20.63 seconds (10100.63 seconds total)