Starting phenix.real_space_refine on Fri Mar 6 12:27:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s6k_24878/03_2026/7s6k_24878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s6k_24878/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s6k_24878/03_2026/7s6k_24878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s6k_24878/03_2026/7s6k_24878.map" model { file = "/net/cci-nas-00/data/ceres_data/7s6k_24878/03_2026/7s6k_24878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s6k_24878/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 21 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 dihedrals: 21 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.94, per 1000 atoms: 0.22 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: 2.77 Conformation dependent library (CDL) restraints added in 1.2 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: 1.61 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: 8.84 Time building geometry restraints manager: 3.57 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: 18757 17.50 - 34.99: 476 34.99 - 52.49: 96 52.49 - 69.98: 84 69.98 - 87.48: 15 Dihedral angle restraints: 19428 sinusoidal: 8145 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 19425 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: 0.06 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: 5.270 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 31.110 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 9.772 87.478 12042 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 covalent geometry : bond 0.02016 (31611) covalent geometry : angle 1.79258 (43014) SS BOND : bond 0.07151 ( 48) SS BOND : angle 2.51494 ( 96) hydrogen bonds : bond 0.16931 ( 1226) hydrogen bonds : angle 8.42026 ( 3354) link_BETA1-4 : bond 0.07077 ( 12) link_BETA1-4 : angle 5.31249 ( 36) link_NAG-ASN : bond 0.08365 ( 33) link_NAG-ASN : angle 2.56918 ( 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 : 1.085 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: 0.2085 time to fit residues: 229.9027 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 : 0.979 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.160891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112897 restraints weight = 52394.921| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.21 r_work: 0.3284 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2872 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= 0.183 Angle : 0.740 9.768 43245 Z= 0.391 Chirality : 0.048 0.365 4983 Planarity : 0.005 0.056 5499 Dihedral : 5.740 32.537 5130 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.78 % Allowed : 6.81 % Favored : 91.42 % 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: 1.77 (0.20), residues: 660 sheet: 0.72 (0.16), residues: 972 loop : -0.35 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 38 TYR 0.019 0.002 TYR E1067 PHE 0.025 0.002 PHE A 497 TRP 0.026 0.002 TRP L 35 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00401 (31611) covalent geometry : angle 0.71994 (43014) SS BOND : bond 0.00459 ( 48) SS BOND : angle 1.51322 ( 96) hydrogen bonds : bond 0.06129 ( 1226) hydrogen bonds : angle 6.62392 ( 3354) link_BETA1-4 : bond 0.00847 ( 12) link_BETA1-4 : angle 2.93018 ( 36) link_NAG-ASN : bond 0.00517 ( 33) link_NAG-ASN : angle 2.98960 ( 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 507 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 447 time to evaluate : 1.097 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: A 376 THR cc_start: 0.8838 (m) cc_final: 0.8303 (p) REVERT: A 984 LEU cc_start: 0.8204 (tp) cc_final: 0.7930 (tp) REVERT: A 1002 GLN cc_start: 0.8679 (tp40) cc_final: 0.8405 (tp40) REVERT: H 32 TYR cc_start: 0.7635 (m-80) cc_final: 0.7084 (m-80) REVERT: H 36 TRP cc_start: 0.8146 (m100) cc_final: 0.6939 (m100) REVERT: H 61 GLN cc_start: 0.8024 (tp40) cc_final: 0.7557 (pp30) REVERT: H 80 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5259 (ttm) REVERT: H 91 TYR cc_start: 0.7018 (p90) cc_final: 0.6740 (p90) REVERT: H 94 ARG cc_start: 0.7034 (ttm-80) cc_final: 0.6457 (ttm-80) REVERT: L 24 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7529 (tpt170) REVERT: L 32 TYR cc_start: 0.6665 (m-80) cc_final: 0.6073 (m-10) REVERT: B 140 PHE cc_start: 0.9119 (p90) cc_final: 0.8458 (p90) REVERT: B 351 TYR cc_start: 0.6369 (OUTLIER) cc_final: 0.5861 (t80) REVERT: B 376 THR cc_start: 0.8879 (m) cc_final: 0.8370 (p) REVERT: B 574 ASP cc_start: 0.8127 (t0) cc_final: 0.7851 (t0) REVERT: B 984 LEU cc_start: 0.8305 (tp) cc_final: 0.8045 (tp) REVERT: C 36 TRP cc_start: 0.7845 (m100) cc_final: 0.5986 (m100) REVERT: C 61 GLN cc_start: 0.8043 (tp40) cc_final: 0.7215 (pp30) REVERT: C 80 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.5255 (ttm) REVERT: C 83 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.7282 (ptt90) REVERT: C 90 TYR cc_start: 0.8500 (p90) cc_final: 0.8218 (p90) REVERT: E 376 THR cc_start: 0.8843 (m) cc_final: 0.8283 (p) REVERT: E 633 TRP cc_start: 0.5965 (t-100) cc_final: 0.5715 (t-100) REVERT: E 634 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.8069 (mtm-85) REVERT: E 984 LEU cc_start: 0.8299 (tp) cc_final: 0.8059 (tp) REVERT: E 992 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6630 (mm-40) REVERT: F 33 THR cc_start: 0.8561 (m) cc_final: 0.8121 (p) REVERT: F 61 GLN cc_start: 0.8147 (tp40) cc_final: 0.7387 (pp30) REVERT: F 80 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.4913 (tpp) REVERT: F 90 TYR cc_start: 0.8472 (p90) cc_final: 0.7791 (p90) REVERT: F 91 TYR cc_start: 0.7138 (p90) cc_final: 0.6762 (p90) REVERT: F 100 HIS cc_start: 0.8249 (p-80) cc_final: 0.7916 (p-80) REVERT: F 109 VAL cc_start: 0.8022 (t) cc_final: 0.7819 (t) REVERT: G 14 SER cc_start: 0.8013 (m) cc_final: 0.7648 (p) REVERT: G 32 TYR cc_start: 0.6661 (m-80) cc_final: 0.6015 (m-10) outliers start: 60 outliers final: 29 residues processed: 475 average time/residue: 0.2037 time to fit residues: 151.0262 Evaluate side-chains 378 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 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 811 LYS 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 249 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: 10.0000 chunk 57 optimal weight: 0.6980 chunk 220 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 384 optimal weight: 20.0000 chunk 254 optimal weight: 7.9990 chunk 299 optimal weight: 8.9990 chunk 343 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 784 GLN B 125 ASN B 165 ASN B 755 GLN E 137 ASN E 498 GLN E 564 GLN E 914 ASN E 992 GLN E1142 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.157123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099587 restraints weight = 52806.397| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.58 r_work: 0.3095 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31704 Z= 0.170 Angle : 0.655 10.605 43245 Z= 0.342 Chirality : 0.047 0.308 4983 Planarity : 0.005 0.073 5499 Dihedral : 5.394 35.335 5130 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.04 % Allowed : 8.67 % Favored : 89.28 % 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: 0.35 (0.13), residues: 3837 helix: 2.33 (0.20), residues: 618 sheet: 0.34 (0.15), residues: 1077 loop : -0.42 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 567 TYR 0.022 0.002 TYR B 904 PHE 0.022 0.002 PHE A 133 TRP 0.019 0.002 TRP F 36 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00388 (31611) covalent geometry : angle 0.63776 (43014) SS BOND : bond 0.00794 ( 48) SS BOND : angle 1.57839 ( 96) hydrogen bonds : bond 0.05250 ( 1226) hydrogen bonds : angle 6.15990 ( 3354) link_BETA1-4 : bond 0.00479 ( 12) link_BETA1-4 : angle 2.36609 ( 36) link_NAG-ASN : bond 0.00420 ( 33) link_NAG-ASN : angle 2.44597 ( 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 465 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 396 time to evaluate : 0.948 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 464 PHE cc_start: 0.8759 (m-80) cc_final: 0.8440 (m-80) REVERT: A 984 LEU cc_start: 0.7900 (tp) cc_final: 0.7500 (tp) REVERT: H 32 TYR cc_start: 0.7739 (m-80) cc_final: 0.7037 (m-80) REVERT: H 36 TRP cc_start: 0.8138 (m100) cc_final: 0.6952 (m100) REVERT: H 61 GLN cc_start: 0.8183 (tp40) cc_final: 0.7678 (pp30) REVERT: H 80 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.4823 (ttm) REVERT: H 94 ARG cc_start: 0.7030 (ttm-80) cc_final: 0.6462 (ttm170) REVERT: L 32 TYR cc_start: 0.6845 (m-80) cc_final: 0.6367 (m-10) REVERT: B 140 PHE cc_start: 0.9174 (p90) cc_final: 0.8398 (p90) REVERT: B 376 THR cc_start: 0.8809 (m) cc_final: 0.8211 (p) REVERT: B 403 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7242 (ttp80) REVERT: B 505 TYR cc_start: 0.8004 (m-80) cc_final: 0.7770 (m-80) REVERT: B 574 ASP cc_start: 0.8451 (t0) cc_final: 0.8209 (t0) REVERT: B 977 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7792 (mt) REVERT: B 984 LEU cc_start: 0.8206 (tp) cc_final: 0.7885 (tp) REVERT: B 1138 TYR cc_start: 0.8386 (t80) cc_final: 0.8096 (t80) REVERT: C 36 TRP cc_start: 0.7810 (m100) cc_final: 0.6206 (m100) REVERT: C 61 GLN cc_start: 0.8148 (tp40) cc_final: 0.7308 (pp30) REVERT: C 80 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.5298 (ttm) REVERT: C 90 TYR cc_start: 0.8392 (p90) cc_final: 0.8182 (p90) REVERT: C 91 TYR cc_start: 0.7154 (p90) cc_final: 0.6900 (p90) REVERT: D 37 GLN cc_start: 0.6907 (pp30) cc_final: 0.6517 (tm-30) REVERT: E 505 TYR cc_start: 0.8238 (m-80) cc_final: 0.7695 (m-80) REVERT: E 856 ASN cc_start: 0.8163 (p0) cc_final: 0.7900 (m-40) REVERT: E 978 ASN cc_start: 0.7903 (m-40) cc_final: 0.7694 (t0) REVERT: E 984 LEU cc_start: 0.8195 (tp) cc_final: 0.7845 (tp) REVERT: F 61 GLN cc_start: 0.8186 (tp40) cc_final: 0.7496 (pm20) REVERT: F 80 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.4737 (tpp) REVERT: F 90 TYR cc_start: 0.8403 (p90) cc_final: 0.8057 (p90) REVERT: F 100 HIS cc_start: 0.8232 (p-80) cc_final: 0.7979 (p-80) REVERT: G 14 SER cc_start: 0.7843 (m) cc_final: 0.7443 (p) REVERT: G 32 TYR cc_start: 0.6723 (m-80) cc_final: 0.6180 (m-10) outliers start: 69 outliers final: 45 residues processed: 435 average time/residue: 0.1868 time to fit residues: 130.1232 Evaluate side-chains 389 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 339 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 403 ARG 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 977 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 C residue 80 MET Chi-restraints excluded: chain D residue 5 THR 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 994 ASP 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: 1.9990 chunk 357 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 250 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 342 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 161 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 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 = 0.4156 r_free = 0.4156 target = 0.156681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098602 restraints weight = 52565.665| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.65 r_work: 0.3068 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31704 Z= 0.155 Angle : 0.618 10.369 43245 Z= 0.320 Chirality : 0.046 0.306 4983 Planarity : 0.004 0.041 5499 Dihedral : 5.288 38.472 5130 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.31 % Allowed : 9.44 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 3837 helix: 2.19 (0.20), residues: 645 sheet: 0.11 (0.15), residues: 1116 loop : -0.51 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 567 TYR 0.021 0.002 TYR B 904 PHE 0.030 0.002 PHE A 497 TRP 0.017 0.002 TRP F 36 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00356 (31611) covalent geometry : angle 0.60244 (43014) SS BOND : bond 0.00308 ( 48) SS BOND : angle 1.34373 ( 96) hydrogen bonds : bond 0.04817 ( 1226) hydrogen bonds : angle 5.92031 ( 3354) link_BETA1-4 : bond 0.00378 ( 12) link_BETA1-4 : angle 2.17980 ( 36) link_NAG-ASN : bond 0.00366 ( 33) link_NAG-ASN : angle 2.37366 ( 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 451 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 373 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7376 (tt) REVERT: A 634 ARG cc_start: 0.8774 (mtm-85) cc_final: 0.8336 (mtm-85) REVERT: A 856 ASN cc_start: 0.7978 (p0) cc_final: 0.7548 (m-40) REVERT: A 984 LEU cc_start: 0.7943 (tp) cc_final: 0.7535 (tp) REVERT: H 32 TYR cc_start: 0.7826 (m-80) cc_final: 0.7205 (m-80) REVERT: H 36 TRP cc_start: 0.8090 (m100) cc_final: 0.6978 (m100) REVERT: H 61 GLN cc_start: 0.8355 (tp40) cc_final: 0.7626 (pp30) REVERT: H 66 ARG cc_start: 0.7440 (mtm110) cc_final: 0.7198 (mtm110) REVERT: H 80 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.4705 (ttm) REVERT: H 94 ARG cc_start: 0.6937 (ttm-80) cc_final: 0.6694 (tmm-80) REVERT: L 32 TYR cc_start: 0.7036 (m-80) cc_final: 0.6649 (m-10) REVERT: L 48 ILE cc_start: 0.6101 (mt) cc_final: 0.5815 (mp) REVERT: B 140 PHE cc_start: 0.9166 (p90) cc_final: 0.8385 (p90) REVERT: B 402 ILE cc_start: 0.8832 (pt) cc_final: 0.8624 (pt) REVERT: B 505 TYR cc_start: 0.8097 (m-80) cc_final: 0.7880 (m-80) REVERT: B 574 ASP cc_start: 0.8532 (t0) cc_final: 0.8322 (t0) REVERT: B 984 LEU cc_start: 0.8176 (tp) cc_final: 0.7819 (tp) REVERT: B 1138 TYR cc_start: 0.8482 (t80) cc_final: 0.8228 (t80) REVERT: C 36 TRP cc_start: 0.7678 (m100) cc_final: 0.5845 (m100) REVERT: C 61 GLN cc_start: 0.8239 (tp40) cc_final: 0.7462 (pp30) REVERT: C 80 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.5344 (ttm) REVERT: C 91 TYR cc_start: 0.7154 (p90) cc_final: 0.6870 (p90) REVERT: E 442 ASP cc_start: 0.6641 (m-30) cc_final: 0.6020 (m-30) REVERT: E 856 ASN cc_start: 0.7930 (p0) cc_final: 0.7634 (m-40) REVERT: E 984 LEU cc_start: 0.8186 (tp) cc_final: 0.7767 (tp) REVERT: F 61 GLN cc_start: 0.8181 (tp40) cc_final: 0.7522 (pm20) REVERT: F 80 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.4932 (tpp) REVERT: F 90 TYR cc_start: 0.8362 (p90) cc_final: 0.7739 (p90) REVERT: G 14 SER cc_start: 0.7852 (m) cc_final: 0.7440 (p) REVERT: G 32 TYR cc_start: 0.6843 (m-80) cc_final: 0.6361 (m-10) REVERT: G 37 GLN cc_start: 0.6613 (pp30) cc_final: 0.6314 (tm-30) outliers start: 78 outliers final: 57 residues processed: 416 average time/residue: 0.1833 time to fit residues: 122.7482 Evaluate side-chains 388 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 327 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 329 PHE 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 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 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 28 THR 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 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 524 VAL Chi-restraints excluded: chain E residue 564 GLN Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 761 THR 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: 8.9990 chunk 0 optimal weight: 10.0000 chunk 363 optimal weight: 0.0170 chunk 49 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 343 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 375 optimal weight: 10.0000 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 655 HIS B 907 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 165 ASN E 564 GLN E 655 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.152818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094543 restraints weight = 52908.477| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.66 r_work: 0.2988 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 31704 Z= 0.271 Angle : 0.683 10.189 43245 Z= 0.355 Chirality : 0.049 0.300 4983 Planarity : 0.005 0.041 5499 Dihedral : 5.457 37.965 5130 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 3.02 % Allowed : 9.44 % Favored : 87.54 % 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: -0.14 (0.13), residues: 3837 helix: 1.86 (0.20), residues: 645 sheet: -0.07 (0.15), residues: 1161 loop : -0.72 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 634 TYR 0.033 0.002 TYR B 904 PHE 0.028 0.002 PHE B 497 TRP 0.020 0.002 TRP A 633 HIS 0.007 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00653 (31611) covalent geometry : angle 0.66845 (43014) SS BOND : bond 0.00378 ( 48) SS BOND : angle 1.44377 ( 96) hydrogen bonds : bond 0.05530 ( 1226) hydrogen bonds : angle 5.98604 ( 3354) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 2.14177 ( 36) link_NAG-ASN : bond 0.00396 ( 33) link_NAG-ASN : angle 2.38951 ( 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 450 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 348 time to evaluate : 1.074 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: 0.8286 (OUTLIER) cc_final: 0.7844 (mp) REVERT: A 335 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7352 (tt) REVERT: A 856 ASN cc_start: 0.8077 (p0) cc_final: 0.7691 (m-40) REVERT: A 984 LEU cc_start: 0.7959 (tp) cc_final: 0.7528 (tp) REVERT: H 32 TYR cc_start: 0.7852 (m-80) cc_final: 0.7612 (m-80) REVERT: H 36 TRP cc_start: 0.8040 (m100) cc_final: 0.7035 (m100) REVERT: H 61 GLN cc_start: 0.8353 (tp40) cc_final: 0.7679 (pp30) REVERT: H 80 MET cc_start: 0.5458 (OUTLIER) cc_final: 0.4904 (ttp) REVERT: L 32 TYR cc_start: 0.7076 (m-80) cc_final: 0.6759 (m-10) REVERT: L 48 ILE cc_start: 0.6155 (mt) cc_final: 0.5940 (mp) REVERT: B 140 PHE cc_start: 0.9257 (p90) cc_final: 0.8377 (p90) REVERT: B 226 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 634 ARG cc_start: 0.8669 (mtm180) cc_final: 0.8058 (mtm180) REVERT: B 984 LEU cc_start: 0.8262 (tp) cc_final: 0.7916 (tp) REVERT: B 1138 TYR cc_start: 0.8608 (t80) cc_final: 0.8335 (t80) REVERT: C 36 TRP cc_start: 0.7688 (m100) cc_final: 0.6041 (m100) REVERT: C 61 GLN cc_start: 0.8353 (tp40) cc_final: 0.7475 (pp30) REVERT: C 91 TYR cc_start: 0.7009 (p90) cc_final: 0.6763 (p90) REVERT: E 131 CYS cc_start: 0.4997 (OUTLIER) cc_final: 0.4431 (m) REVERT: E 133 PHE cc_start: 0.8205 (m-80) cc_final: 0.7989 (m-80) REVERT: E 442 ASP cc_start: 0.6576 (m-30) cc_final: 0.6359 (m-30) REVERT: E 565 PHE cc_start: 0.7456 (t80) cc_final: 0.7113 (t80) REVERT: E 856 ASN cc_start: 0.7837 (p0) cc_final: 0.7633 (m-40) REVERT: E 973 ILE cc_start: 0.8909 (pt) cc_final: 0.8501 (pt) REVERT: E 984 LEU cc_start: 0.8374 (tp) cc_final: 0.8035 (tp) REVERT: E 1005 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8175 (tt0) REVERT: F 61 GLN cc_start: 0.8176 (tp40) cc_final: 0.7453 (pp30) REVERT: F 80 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.4907 (tpp) REVERT: F 90 TYR cc_start: 0.8389 (p90) cc_final: 0.7980 (p90) REVERT: G 14 SER cc_start: 0.7850 (m) cc_final: 0.7437 (p) REVERT: G 32 TYR cc_start: 0.7134 (m-80) cc_final: 0.6693 (m-10) REVERT: G 37 GLN cc_start: 0.6616 (pp30) cc_final: 0.6307 (tm-30) outliers start: 102 outliers final: 70 residues processed: 414 average time/residue: 0.1804 time to fit residues: 121.8065 Evaluate side-chains 390 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 314 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 A residue 1094 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 90 TYR Chi-restraints excluded: chain L residue 29 VAL 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 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR 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 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 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 28 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 LEU 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 208 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 376 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 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 761 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 985 CYS Chi-restraints excluded: chain E residue 994 ASP 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 38 GLN 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: 5.9990 chunk 100 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 363 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 chunk 306 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 238 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN ** 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 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 = 0.4133 r_free = 0.4133 target = 0.154959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.105674 restraints weight = 52528.912| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.29 r_work: 0.3128 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31704 Z= 0.142 Angle : 0.599 10.977 43245 Z= 0.309 Chirality : 0.045 0.286 4983 Planarity : 0.004 0.043 5499 Dihedral : 5.170 36.830 5130 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 2.37 % Allowed : 10.04 % Favored : 87.60 % 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: 2.12 (0.20), residues: 648 sheet: -0.01 (0.15), residues: 1128 loop : -0.70 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.034 0.001 TYR B 351 PHE 0.025 0.002 PHE B 497 TRP 0.021 0.002 TRP C 36 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00324 (31611) covalent geometry : angle 0.58534 (43014) SS BOND : bond 0.00412 ( 48) SS BOND : angle 1.35483 ( 96) hydrogen bonds : bond 0.04624 ( 1226) hydrogen bonds : angle 5.77480 ( 3354) link_BETA1-4 : bond 0.00447 ( 12) link_BETA1-4 : angle 1.99387 ( 36) link_NAG-ASN : bond 0.00340 ( 33) link_NAG-ASN : angle 2.18760 ( 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 429 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 349 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7613 (mp) REVERT: A 335 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7312 (tt) REVERT: A 634 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8198 (mtm180) REVERT: A 979 ASP cc_start: 0.8203 (t0) cc_final: 0.7868 (t0) REVERT: A 984 LEU cc_start: 0.7842 (tp) cc_final: 0.7363 (tp) REVERT: H 32 TYR cc_start: 0.7471 (m-80) cc_final: 0.7146 (m-80) REVERT: H 36 TRP cc_start: 0.7958 (m100) cc_final: 0.7143 (m100) REVERT: H 61 GLN cc_start: 0.8318 (tp40) cc_final: 0.7620 (pp30) REVERT: H 80 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.4915 (ttp) REVERT: L 32 TYR cc_start: 0.7000 (m-80) cc_final: 0.6758 (m-80) REVERT: L 48 ILE cc_start: 0.6280 (mt) cc_final: 0.6037 (mp) REVERT: B 140 PHE cc_start: 0.9189 (p90) cc_final: 0.8363 (p90) REVERT: B 449 TYR cc_start: 0.8326 (m-80) cc_final: 0.8046 (m-80) REVERT: B 977 LEU cc_start: 0.8201 (mp) cc_final: 0.7941 (mt) REVERT: B 984 LEU cc_start: 0.8132 (tp) cc_final: 0.7759 (tp) REVERT: B 1138 TYR cc_start: 0.8549 (t80) cc_final: 0.8269 (t80) REVERT: C 36 TRP cc_start: 0.7638 (m100) cc_final: 0.6131 (m100) REVERT: C 61 GLN cc_start: 0.8467 (tp40) cc_final: 0.7725 (pp30) REVERT: C 91 TYR cc_start: 0.6872 (p90) cc_final: 0.6583 (p90) REVERT: C 100 PHE cc_start: 0.7028 (m-80) cc_final: 0.6549 (m-10) REVERT: E 131 CYS cc_start: 0.4431 (OUTLIER) cc_final: 0.4066 (m) REVERT: E 449 TYR cc_start: 0.8310 (m-80) cc_final: 0.7856 (m-80) REVERT: E 565 PHE cc_start: 0.7051 (t80) cc_final: 0.6597 (t80) REVERT: E 646 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8388 (tpp-160) REVERT: E 904 TYR cc_start: 0.8653 (m-10) cc_final: 0.8436 (m-10) REVERT: E 957 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7934 (tm-30) REVERT: E 973 ILE cc_start: 0.8880 (pt) cc_final: 0.8527 (pt) REVERT: E 977 LEU cc_start: 0.7855 (mp) cc_final: 0.7623 (mt) REVERT: E 979 ASP cc_start: 0.8370 (t0) cc_final: 0.8161 (t0) REVERT: E 984 LEU cc_start: 0.8172 (tp) cc_final: 0.7805 (tp) REVERT: F 61 GLN cc_start: 0.8173 (tp40) cc_final: 0.7559 (pm20) REVERT: F 80 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5050 (tpp) REVERT: F 90 TYR cc_start: 0.8347 (p90) cc_final: 0.7718 (p90) REVERT: G 4 MET cc_start: 0.3966 (tmm) cc_final: 0.3618 (tmm) REVERT: G 14 SER cc_start: 0.7881 (m) cc_final: 0.7413 (p) REVERT: G 32 TYR cc_start: 0.6971 (m-80) cc_final: 0.6576 (m-10) REVERT: G 37 GLN cc_start: 0.6585 (pp30) cc_final: 0.6299 (tm-30) outliers start: 80 outliers final: 59 residues processed: 397 average time/residue: 0.1787 time to fit residues: 115.4197 Evaluate side-chains 386 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 322 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain A residue 233 ILE 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 723 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 1094 VAL 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 233 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 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 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 80 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 131 CYS 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 427 ASP Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR 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 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 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: 0.9980 chunk 157 optimal weight: 0.9990 chunk 369 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 200 optimal weight: 0.0980 chunk 359 optimal weight: 0.0470 chunk 3 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 = 0.4129 r_free = 0.4129 target = 0.154882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096608 restraints weight = 52390.945| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.55 r_work: 0.3055 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31704 Z= 0.138 Angle : 0.596 8.459 43245 Z= 0.307 Chirality : 0.045 0.286 4983 Planarity : 0.004 0.056 5499 Dihedral : 5.040 36.065 5130 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 2.66 % Allowed : 10.39 % Favored : 86.94 % 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: -0.02 (0.14), residues: 3837 helix: 2.18 (0.20), residues: 666 sheet: -0.05 (0.15), residues: 1119 loop : -0.71 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 38 TYR 0.046 0.001 TYR B 351 PHE 0.024 0.002 PHE C 29 TRP 0.017 0.002 TRP C 36 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00315 (31611) covalent geometry : angle 0.58295 (43014) SS BOND : bond 0.00283 ( 48) SS BOND : angle 1.27877 ( 96) hydrogen bonds : bond 0.04429 ( 1226) hydrogen bonds : angle 5.65135 ( 3354) link_BETA1-4 : bond 0.00414 ( 12) link_BETA1-4 : angle 1.88713 ( 36) link_NAG-ASN : bond 0.00282 ( 33) link_NAG-ASN : angle 2.10625 ( 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 422 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 332 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7722 (mp) REVERT: A 335 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7298 (tt) REVERT: A 571 ASP cc_start: 0.7701 (m-30) cc_final: 0.6731 (t0) REVERT: A 982 SER cc_start: 0.8446 (m) cc_final: 0.8133 (p) REVERT: H 32 TYR cc_start: 0.7473 (m-80) cc_final: 0.7182 (m-80) REVERT: H 36 TRP cc_start: 0.7969 (m100) cc_final: 0.7143 (m100) REVERT: H 61 GLN cc_start: 0.8302 (tp40) cc_final: 0.7643 (pp30) REVERT: H 80 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.4911 (ttp) REVERT: H 100 GLN cc_start: 0.6097 (mp10) cc_final: 0.5511 (pm20) REVERT: L 32 TYR cc_start: 0.7056 (m-80) cc_final: 0.6758 (m-80) REVERT: L 38 GLN cc_start: 0.3922 (OUTLIER) cc_final: 0.3630 (mp10) REVERT: L 48 ILE cc_start: 0.6482 (mt) cc_final: 0.6101 (mp) REVERT: B 140 PHE cc_start: 0.9247 (p90) cc_final: 0.8384 (p90) REVERT: B 241 LEU cc_start: 0.7927 (mt) cc_final: 0.7675 (mp) REVERT: B 312 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8894 (tt) REVERT: B 449 TYR cc_start: 0.8478 (m-80) cc_final: 0.8270 (m-80) REVERT: B 634 ARG cc_start: 0.8397 (mtm180) cc_final: 0.7926 (mtm-85) REVERT: B 755 GLN cc_start: 0.8948 (tt0) cc_final: 0.8496 (tm-30) REVERT: B 977 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7950 (mt) REVERT: B 984 LEU cc_start: 0.7512 (tp) cc_final: 0.7132 (tp) REVERT: C 36 TRP cc_start: 0.7468 (m100) cc_final: 0.5981 (m100) REVERT: C 61 GLN cc_start: 0.8458 (tp40) cc_final: 0.7765 (pp30) REVERT: C 66 ARG cc_start: 0.7298 (mtm110) cc_final: 0.6991 (mtm110) REVERT: C 91 TYR cc_start: 0.6980 (p90) cc_final: 0.6652 (p90) REVERT: C 100 GLN cc_start: 0.5809 (mp10) cc_final: 0.5493 (pm20) REVERT: C 100 PHE cc_start: 0.6866 (m-80) cc_final: 0.6489 (m-10) REVERT: E 449 TYR cc_start: 0.8399 (m-80) cc_final: 0.7925 (m-80) REVERT: E 634 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8536 (mtm-85) REVERT: E 646 ARG cc_start: 0.8934 (tpp80) cc_final: 0.8565 (tpp-160) REVERT: E 755 GLN cc_start: 0.8860 (tt0) cc_final: 0.8506 (tm-30) REVERT: E 904 TYR cc_start: 0.8791 (m-10) cc_final: 0.8521 (m-10) REVERT: E 957 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8232 (tm-30) REVERT: E 973 ILE cc_start: 0.8889 (pt) cc_final: 0.8535 (pt) REVERT: E 977 LEU cc_start: 0.7813 (mp) cc_final: 0.7544 (mt) REVERT: E 984 LEU cc_start: 0.8197 (tp) cc_final: 0.7796 (tp) REVERT: F 36 TRP cc_start: 0.7933 (m100) cc_final: 0.5935 (m100) REVERT: F 61 GLN cc_start: 0.8172 (tp40) cc_final: 0.7576 (pp30) REVERT: F 80 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.4967 (tpp) REVERT: G 4 MET cc_start: 0.3896 (tmm) cc_final: 0.3579 (tmm) REVERT: G 14 SER cc_start: 0.7842 (m) cc_final: 0.7439 (p) REVERT: G 32 TYR cc_start: 0.6881 (m-80) cc_final: 0.6477 (m-10) outliers start: 90 outliers final: 61 residues processed: 387 average time/residue: 0.1782 time to fit residues: 112.6222 Evaluate side-chains 388 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 320 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS 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 723 THR Chi-restraints excluded: chain A residue 915 VAL 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 1094 VAL 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 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE 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 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 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 1001 LEU 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 53 ILE 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 38 GLN 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 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 617 CYS Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 966 LEU 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 109 VAL 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: 10.0000 chunk 104 optimal weight: 0.6980 chunk 381 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 360 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 243 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** 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 = 0.4138 r_free = 0.4138 target = 0.155423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105239 restraints weight = 52595.247| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.14 r_work: 0.3148 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 31704 Z= 0.141 Angle : 0.597 11.764 43245 Z= 0.307 Chirality : 0.045 0.284 4983 Planarity : 0.004 0.057 5499 Dihedral : 4.980 35.571 5130 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 2.40 % Allowed : 10.63 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3837 helix: 2.21 (0.20), residues: 666 sheet: -0.02 (0.15), residues: 1116 loop : -0.74 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.046 0.001 TYR B 351 PHE 0.029 0.002 PHE H 29 TRP 0.018 0.002 TRP H 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00326 (31611) covalent geometry : angle 0.58241 (43014) SS BOND : bond 0.00252 ( 48) SS BOND : angle 1.73947 ( 96) hydrogen bonds : bond 0.04428 ( 1226) hydrogen bonds : angle 5.57966 ( 3354) link_BETA1-4 : bond 0.00440 ( 12) link_BETA1-4 : angle 1.84195 ( 36) link_NAG-ASN : bond 0.00273 ( 33) link_NAG-ASN : angle 2.05745 ( 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 414 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 333 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 335 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7341 (tt) REVERT: A 571 ASP cc_start: 0.7603 (m-30) cc_final: 0.6779 (t0) REVERT: A 982 SER cc_start: 0.8434 (m) cc_final: 0.8119 (p) REVERT: A 984 LEU cc_start: 0.7563 (tp) cc_final: 0.7143 (tp) REVERT: A 1029 MET cc_start: 0.8919 (tpp) cc_final: 0.8678 (ttm) REVERT: H 36 TRP cc_start: 0.7896 (m100) cc_final: 0.7180 (m100) REVERT: H 66 ARG cc_start: 0.7343 (mtm110) cc_final: 0.6985 (mtm110) REVERT: H 80 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.5041 (ttp) REVERT: H 100 GLN cc_start: 0.6142 (mp10) cc_final: 0.5516 (pm20) REVERT: L 4 MET cc_start: 0.4063 (tmm) cc_final: 0.3226 (tmm) REVERT: L 32 TYR cc_start: 0.7010 (m-80) cc_final: 0.6757 (m-80) REVERT: L 38 GLN cc_start: 0.3905 (OUTLIER) cc_final: 0.3549 (mp10) REVERT: L 48 ILE cc_start: 0.6152 (mt) cc_final: 0.5897 (mp) REVERT: B 140 PHE cc_start: 0.9225 (p90) cc_final: 0.8307 (p90) REVERT: B 241 LEU cc_start: 0.7811 (mt) cc_final: 0.7601 (mp) REVERT: B 312 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8820 (tt) REVERT: B 634 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7835 (mtm-85) REVERT: B 755 GLN cc_start: 0.8789 (tt0) cc_final: 0.8404 (tm-30) REVERT: B 977 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7980 (mt) REVERT: B 984 LEU cc_start: 0.7492 (tp) cc_final: 0.7053 (tp) REVERT: C 36 TRP cc_start: 0.7475 (m100) cc_final: 0.6077 (m100) REVERT: C 61 GLN cc_start: 0.8423 (tp40) cc_final: 0.7755 (pp30) REVERT: C 66 ARG cc_start: 0.7337 (mtm110) cc_final: 0.7104 (mtm110) REVERT: C 91 TYR cc_start: 0.6801 (p90) cc_final: 0.6531 (p90) REVERT: C 100 GLN cc_start: 0.5829 (mp10) cc_final: 0.5541 (pm20) REVERT: C 100 PHE cc_start: 0.6903 (m-80) cc_final: 0.6582 (m-10) REVERT: D 4 MET cc_start: 0.3895 (tmm) cc_final: 0.3625 (tmm) REVERT: E 131 CYS cc_start: 0.4438 (OUTLIER) cc_final: 0.4026 (m) REVERT: E 133 PHE cc_start: 0.8068 (m-80) cc_final: 0.7810 (m-80) REVERT: E 449 TYR cc_start: 0.8326 (m-80) cc_final: 0.7851 (m-80) REVERT: E 646 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8512 (tpt170) REVERT: E 755 GLN cc_start: 0.8798 (tt0) cc_final: 0.8479 (tm-30) REVERT: E 904 TYR cc_start: 0.8712 (m-10) cc_final: 0.8458 (m-10) REVERT: E 957 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8225 (tm-30) REVERT: E 977 LEU cc_start: 0.7811 (mp) cc_final: 0.7579 (mt) REVERT: E 984 LEU cc_start: 0.7526 (tp) cc_final: 0.7221 (tp) REVERT: E 1029 MET cc_start: 0.9116 (tpp) cc_final: 0.8840 (ttm) REVERT: F 36 TRP cc_start: 0.7951 (m100) cc_final: 0.7258 (m100) REVERT: F 61 GLN cc_start: 0.8082 (tp40) cc_final: 0.7516 (pp30) REVERT: F 80 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.4926 (tpp) REVERT: G 4 MET cc_start: 0.3859 (tmm) cc_final: 0.3585 (tmm) REVERT: G 14 SER cc_start: 0.7852 (m) cc_final: 0.7396 (p) REVERT: G 32 TYR cc_start: 0.6795 (m-80) cc_final: 0.6415 (m-10) outliers start: 81 outliers final: 65 residues processed: 382 average time/residue: 0.1833 time to fit residues: 113.8203 Evaluate side-chains 392 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 319 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 312 ILE 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 915 VAL 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 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 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 312 ILE 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 427 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS 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 914 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 1001 LEU 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 C residue 80 MET 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 40 ASP 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 312 ILE 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 366 optimal weight: 7.9990 chunk 278 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN ** E 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 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 = 0.4124 r_free = 0.4124 target = 0.154227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.104176 restraints weight = 52446.485| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.23 r_work: 0.3116 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31704 Z= 0.178 Angle : 0.621 12.495 43245 Z= 0.318 Chirality : 0.046 0.317 4983 Planarity : 0.004 0.053 5499 Dihedral : 5.045 36.434 5130 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 2.52 % Allowed : 11.04 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3837 helix: 1.89 (0.20), residues: 702 sheet: -0.02 (0.15), residues: 1131 loop : -0.82 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 765 TYR 0.042 0.002 TYR B 351 PHE 0.020 0.002 PHE B 497 TRP 0.012 0.002 TRP C 36 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00422 (31611) covalent geometry : angle 0.60829 (43014) SS BOND : bond 0.00282 ( 48) SS BOND : angle 1.55145 ( 96) hydrogen bonds : bond 0.04659 ( 1226) hydrogen bonds : angle 5.58990 ( 3354) link_BETA1-4 : bond 0.00306 ( 12) link_BETA1-4 : angle 1.82222 ( 36) link_NAG-ASN : bond 0.00238 ( 33) link_NAG-ASN : angle 2.04046 ( 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 410 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 325 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7620 (mp) REVERT: A 335 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7319 (tt) REVERT: A 449 TYR cc_start: 0.8500 (m-80) cc_final: 0.8117 (m-80) REVERT: A 571 ASP cc_start: 0.7522 (m-30) cc_final: 0.6882 (t0) REVERT: A 984 LEU cc_start: 0.7575 (tp) cc_final: 0.7128 (tp) REVERT: A 1029 MET cc_start: 0.8984 (tpp) cc_final: 0.8723 (ttm) REVERT: H 36 TRP cc_start: 0.7916 (m100) cc_final: 0.7159 (m100) REVERT: H 63 PHE cc_start: 0.7686 (m-10) cc_final: 0.7473 (m-10) REVERT: H 66 ARG cc_start: 0.7389 (mtm110) cc_final: 0.7068 (mtm110) REVERT: H 80 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.4896 (ttp) REVERT: H 100 GLN cc_start: 0.6030 (mp10) cc_final: 0.5313 (pm20) REVERT: L 32 TYR cc_start: 0.7005 (m-80) cc_final: 0.6738 (m-80) REVERT: L 38 GLN cc_start: 0.3913 (OUTLIER) cc_final: 0.3361 (mp10) REVERT: L 48 ILE cc_start: 0.6195 (mt) cc_final: 0.5936 (mp) REVERT: B 241 LEU cc_start: 0.7825 (mt) cc_final: 0.7585 (mp) REVERT: B 312 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8819 (tt) REVERT: B 346 ARG cc_start: 0.7863 (mmp80) cc_final: 0.7649 (tpt170) REVERT: B 571 ASP cc_start: 0.7512 (m-30) cc_final: 0.6818 (t0) REVERT: B 755 GLN cc_start: 0.8869 (tt0) cc_final: 0.8525 (tm-30) REVERT: B 977 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8105 (mt) REVERT: B 984 LEU cc_start: 0.7513 (tp) cc_final: 0.7072 (tp) REVERT: C 36 TRP cc_start: 0.7636 (m100) cc_final: 0.6150 (m100) REVERT: C 61 GLN cc_start: 0.8421 (tp40) cc_final: 0.7755 (pp30) REVERT: C 66 ARG cc_start: 0.7373 (mtm110) cc_final: 0.7154 (mtm110) REVERT: C 91 TYR cc_start: 0.6858 (p90) cc_final: 0.6575 (p90) REVERT: C 100 GLN cc_start: 0.5856 (mp10) cc_final: 0.5537 (pm20) REVERT: C 100 PHE cc_start: 0.6811 (m-80) cc_final: 0.6538 (m-10) REVERT: D 4 MET cc_start: 0.4044 (tmm) cc_final: 0.3827 (tmm) REVERT: E 131 CYS cc_start: 0.4766 (OUTLIER) cc_final: 0.4282 (m) REVERT: E 133 PHE cc_start: 0.8111 (m-80) cc_final: 0.7819 (m-80) REVERT: E 177 MET cc_start: 0.5853 (mtt) cc_final: 0.5083 (mtp) REVERT: E 449 TYR cc_start: 0.8366 (m-80) cc_final: 0.7911 (m-80) REVERT: E 646 ARG cc_start: 0.8812 (tpp80) cc_final: 0.8529 (tpt170) REVERT: E 755 GLN cc_start: 0.8844 (tt0) cc_final: 0.8602 (tm-30) REVERT: E 957 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8383 (tm-30) REVERT: E 973 ILE cc_start: 0.8864 (pt) cc_final: 0.8631 (pt) REVERT: E 977 LEU cc_start: 0.7913 (mp) cc_final: 0.7678 (mt) REVERT: E 984 LEU cc_start: 0.7647 (tp) cc_final: 0.7314 (tp) REVERT: E 1029 MET cc_start: 0.9112 (tpp) cc_final: 0.8898 (ttm) REVERT: F 36 TRP cc_start: 0.7965 (m100) cc_final: 0.7290 (m100) REVERT: F 61 GLN cc_start: 0.8101 (tp40) cc_final: 0.7564 (pp30) REVERT: F 80 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5010 (tpp) REVERT: G 4 MET cc_start: 0.3834 (tmm) cc_final: 0.3572 (tmm) REVERT: G 14 SER cc_start: 0.7741 (m) cc_final: 0.7290 (p) REVERT: G 32 TYR cc_start: 0.6725 (m-80) cc_final: 0.6339 (m-10) outliers start: 85 outliers final: 69 residues processed: 376 average time/residue: 0.1781 time to fit residues: 109.4371 Evaluate side-chains 380 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 303 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE 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 915 VAL 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 H residue 32 TYR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 90 TYR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 38 GLN 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 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE 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 427 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 636 TYR 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 914 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 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL 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 80 MET 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 D residue 48 ILE Chi-restraints excluded: chain E residue 40 ASP 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 208 THR 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 427 ASP Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 966 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 161 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 344 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.154651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.097183 restraints weight = 52074.728| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.55 r_work: 0.3041 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31704 Z= 0.155 Angle : 0.611 12.932 43245 Z= 0.312 Chirality : 0.046 0.283 4983 Planarity : 0.004 0.054 5499 Dihedral : 5.001 36.337 5130 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 2.37 % Allowed : 11.37 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3837 helix: 1.95 (0.20), residues: 702 sheet: -0.01 (0.15), residues: 1128 loop : -0.84 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.027 0.002 TYR B 351 PHE 0.026 0.002 PHE E 855 TRP 0.026 0.002 TRP H 47 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00362 (31611) covalent geometry : angle 0.59949 (43014) SS BOND : bond 0.00252 ( 48) SS BOND : angle 1.37812 ( 96) hydrogen bonds : bond 0.04489 ( 1226) hydrogen bonds : angle 5.55023 ( 3354) link_BETA1-4 : bond 0.00354 ( 12) link_BETA1-4 : angle 1.79039 ( 36) link_NAG-ASN : bond 0.00248 ( 33) link_NAG-ASN : angle 2.01506 ( 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 388 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 308 time to evaluate : 0.837 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: 0.8225 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 335 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7379 (tt) REVERT: A 449 TYR cc_start: 0.8543 (m-80) cc_final: 0.8127 (m-80) REVERT: A 571 ASP cc_start: 0.7696 (m-30) cc_final: 0.7046 (t0) REVERT: A 634 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8490 (mtm-85) REVERT: A 984 LEU cc_start: 0.7485 (tp) cc_final: 0.7005 (tp) REVERT: A 1029 MET cc_start: 0.9055 (tpp) cc_final: 0.8810 (ttm) REVERT: H 36 TRP cc_start: 0.7931 (m100) cc_final: 0.7130 (m100) REVERT: H 66 ARG cc_start: 0.7421 (mtm110) cc_final: 0.7044 (mtm110) REVERT: H 80 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.5125 (ttp) REVERT: L 32 TYR cc_start: 0.7017 (m-80) cc_final: 0.6776 (m-80) REVERT: L 38 GLN cc_start: 0.3592 (OUTLIER) cc_final: 0.3147 (mp10) REVERT: L 48 ILE cc_start: 0.6260 (mt) cc_final: 0.6019 (mp) REVERT: B 140 PHE cc_start: 0.9028 (p90) cc_final: 0.8301 (p90) REVERT: B 312 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8859 (tt) REVERT: B 346 ARG cc_start: 0.7884 (mmp80) cc_final: 0.7597 (tpt170) REVERT: B 464 PHE cc_start: 0.9068 (m-80) cc_final: 0.8610 (m-80) REVERT: B 571 ASP cc_start: 0.7799 (m-30) cc_final: 0.7019 (t0) REVERT: B 755 GLN cc_start: 0.9002 (tt0) cc_final: 0.8601 (tm-30) REVERT: B 977 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8054 (mt) REVERT: B 984 LEU cc_start: 0.7480 (tp) cc_final: 0.6974 (tp) REVERT: C 36 TRP cc_start: 0.7568 (m100) cc_final: 0.6070 (m100) REVERT: C 61 GLN cc_start: 0.8441 (tp40) cc_final: 0.7788 (pp30) REVERT: C 83 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7413 (ptt90) REVERT: C 91 TYR cc_start: 0.6955 (p90) cc_final: 0.6652 (p90) REVERT: C 100 GLN cc_start: 0.5840 (mp10) cc_final: 0.5511 (pm20) REVERT: C 100 PHE cc_start: 0.6787 (m-80) cc_final: 0.6475 (m-10) REVERT: D 4 MET cc_start: 0.4166 (tmm) cc_final: 0.3928 (tmm) REVERT: E 449 TYR cc_start: 0.8422 (m-80) cc_final: 0.7979 (m-80) REVERT: E 464 PHE cc_start: 0.9100 (m-80) cc_final: 0.8708 (m-80) REVERT: E 646 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8633 (tpt170) REVERT: E 755 GLN cc_start: 0.8928 (tt0) cc_final: 0.8632 (tm-30) REVERT: E 957 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8483 (tm-30) REVERT: E 973 ILE cc_start: 0.8904 (pt) cc_final: 0.8671 (pt) REVERT: E 977 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7657 (mt) REVERT: E 984 LEU cc_start: 0.7591 (tp) cc_final: 0.7262 (tp) REVERT: E 1029 MET cc_start: 0.9249 (tpp) cc_final: 0.8925 (ttm) REVERT: F 36 TRP cc_start: 0.7940 (m100) cc_final: 0.7189 (m100) REVERT: F 61 GLN cc_start: 0.8099 (tp40) cc_final: 0.7543 (pp30) REVERT: F 80 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.4892 (tpp) REVERT: G 4 MET cc_start: 0.3837 (tmm) cc_final: 0.3555 (tmm) REVERT: G 14 SER cc_start: 0.7747 (m) cc_final: 0.7347 (p) REVERT: G 32 TYR cc_start: 0.6780 (m-80) cc_final: 0.6360 (m-10) outliers start: 80 outliers final: 65 residues processed: 361 average time/residue: 0.1788 time to fit residues: 104.7508 Evaluate side-chains 371 residues out of total 3378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 298 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE 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 915 VAL 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 H residue 32 TYR 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 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE 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 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 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 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 C residue 80 MET 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 D residue 48 ILE 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 312 ILE 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 546 LEU Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 966 LEU Chi-restraints excluded: chain E residue 977 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 319 optimal weight: 1.9990 chunk 279 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 207 optimal weight: 0.0060 chunk 320 optimal weight: 0.1980 chunk 352 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN C 6 GLN E 856 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 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 = 0.4129 r_free = 0.4129 target = 0.154621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104508 restraints weight = 52415.549| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.20 r_work: 0.3130 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31704 Z= 0.151 Angle : 0.613 11.945 43245 Z= 0.312 Chirality : 0.046 0.282 4983 Planarity : 0.004 0.082 5499 Dihedral : 4.983 36.706 5130 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 2.34 % Allowed : 11.46 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3837 helix: 1.99 (0.20), residues: 702 sheet: 0.01 (0.15), residues: 1128 loop : -0.86 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.023 0.002 TYR B 351 PHE 0.020 0.002 PHE B 497 TRP 0.012 0.001 TRP F 36 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00351 (31611) covalent geometry : angle 0.60184 (43014) SS BOND : bond 0.00246 ( 48) SS BOND : angle 1.32655 ( 96) hydrogen bonds : bond 0.04445 ( 1226) hydrogen bonds : angle 5.51249 ( 3354) link_BETA1-4 : bond 0.00363 ( 12) link_BETA1-4 : angle 1.75689 ( 36) link_NAG-ASN : bond 0.00238 ( 33) link_NAG-ASN : angle 1.99621 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9662.54 seconds wall clock time: 165 minutes 30.24 seconds (9930.24 seconds total)