Starting phenix.real_space_refine on Tue Jun 24 07:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co6_45771/06_2025/9co6_45771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co6_45771/06_2025/9co6_45771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9co6_45771/06_2025/9co6_45771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co6_45771/06_2025/9co6_45771.map" model { file = "/net/cci-nas-00/data/ceres_data/9co6_45771/06_2025/9co6_45771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co6_45771/06_2025/9co6_45771.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.016 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 129 5.16 5 C 17883 2.51 5 N 4662 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28149 Number of models: 1 Model: "" Number of chains: 17 Chain: "B" Number of atoms: 8237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8237 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 56, 'TRANS': 996} Chain breaks: 5 Chain: "C" Number of atoms: 8237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8237 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 56, 'TRANS': 996} Chain breaks: 5 Chain: "A" Number of atoms: 8237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8237 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 56, 'TRANS': 996} Chain breaks: 5 Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "F" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "D" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "C" 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 17.40, per 1000 atoms: 0.62 Number of scatterers: 28149 At special positions: 0 Unit cell: (140.768, 151.392, 236.384, 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 129 16.00 O 5475 8.00 N 4662 7.00 C 17883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 356 " distance=2.02 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS B 666 " distance=2.03 Simple disulfide: pdb=" SG CYS B 733 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B1027 " - pdb=" SG CYS B1038 " distance=2.03 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 161 " distance=2.04 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 533 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 161 " distance=2.04 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS A 733 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1038 " distance=2.03 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 50 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 50 " - pdb=" SG CYS D 104 " 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 H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1300 " - " ASN A 58 " " NAG A1301 " - " ASN A 277 " " NAG A1302 " - " ASN A 611 " " NAG A1303 " - " ASN A 704 " " NAG A1304 " - " ASN A1069 " " NAG A1305 " - " ASN A 326 " " NAG B1300 " - " ASN B 58 " " NAG B1301 " - " ASN B 277 " " NAG B1302 " - " ASN B 796 " " NAG B1303 " - " ASN B 712 " " NAG B1304 " - " ASN B 704 " " NAG B1305 " - " ASN B 326 " " NAG B1306 " - " ASN B 611 " " NAG C1300 " - " ASN C 277 " " NAG C1301 " - " ASN C 611 " " NAG C1302 " - " ASN C 652 " " NAG C1303 " - " ASN C1069 " " NAG C1304 " - " ASN C 704 " " NAG C1305 " - " ASN C1093 " " NAG C1306 " - " ASN C 326 " " NAG H 1 " - " ASN B1093 " " NAG J 1 " - " ASN C 712 " " NAG K 1 " - " ASN C 796 " " NAG L 1 " - " ASN C1129 " " NAG M 1 " - " ASN A 712 " " NAG N 1 " - " ASN A 796 " " NAG O 1 " - " ASN A1093 " " NAG P 1 " - " ASN A1129 " Time building additional restraints: 6.91 Conformation dependent library (CDL) restraints added in 3.3 seconds 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 53 sheets defined 20.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.106A pdb=" N ASN B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 361 through 367' Processing helix chain 'B' and resid 398 through 405 removed outlier: 3.983A pdb=" N VAL B 402 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 403 " --> pdb=" O ASN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 732 through 738 removed outlier: 4.058A pdb=" N TYR B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 737 " --> pdb=" O CYS B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.699A pdb=" N GLN B 750 " --> pdb=" O ASN B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 777 removed outlier: 3.618A pdb=" N GLN B 757 " --> pdb=" O SER B 753 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 773 " --> pdb=" O GLN B 769 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 774 " --> pdb=" O ASP B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 861 through 879 Processing helix chain 'B' and resid 881 through 885 Processing helix chain 'B' and resid 892 through 903 Processing helix chain 'B' and resid 908 through 913 removed outlier: 3.556A pdb=" N TYR B 912 " --> pdb=" O GLN B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 removed outlier: 3.959A pdb=" N ASP B 931 " --> pdb=" O GLY B 927 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER B 934 " --> pdb=" O GLN B 930 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 961 removed outlier: 3.789A pdb=" N GLN B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 979 Processing helix chain 'B' and resid 980 through 1028 removed outlier: 5.057A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG B 990 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B1028 " --> pdb=" O MET B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1144 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.953A pdb=" N ASN C 338 " --> pdb=" O ASP C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 removed outlier: 3.514A pdb=" N TYR C 364 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 366 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 382 removed outlier: 3.838A pdb=" N LEU C 382 " --> pdb=" O PRO C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 402 No H-bonds generated for 'chain 'C' and resid 400 through 402' Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.675A pdb=" N TYR C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 738 removed outlier: 4.061A pdb=" N TYR C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 737 " --> pdb=" O CYS C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 752 removed outlier: 3.802A pdb=" N SER C 745 " --> pdb=" O SER C 741 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 778 removed outlier: 3.701A pdb=" N GLN C 757 " --> pdb=" O SER C 753 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 774 " --> pdb=" O ASP C 770 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 776 " --> pdb=" O ASN C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 845 through 849 removed outlier: 3.737A pdb=" N LYS C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 845 through 849' Processing helix chain 'C' and resid 861 through 879 Processing helix chain 'C' and resid 892 through 903 Processing helix chain 'C' and resid 908 through 913 removed outlier: 3.509A pdb=" N TYR C 912 " --> pdb=" O GLN C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 removed outlier: 4.031A pdb=" N ASP C 931 " --> pdb=" O GLY C 927 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C 934 " --> pdb=" O GLN C 930 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR C 936 " --> pdb=" O SER C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 961 removed outlier: 3.747A pdb=" N GLN C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 977 removed outlier: 3.610A pdb=" N ILE C 975 " --> pdb=" O VAL C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 1028 removed outlier: 4.479A pdb=" N VAL C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1144 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.677A pdb=" N ASN A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.804A pdb=" N TYR A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 738 removed outlier: 4.059A pdb=" N TYR A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 737 " --> pdb=" O CYS A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 removed outlier: 3.796A pdb=" N GLN A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 778 removed outlier: 3.759A pdb=" N GLN A 757 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 776 " --> pdb=" O ASN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 821 Processing helix chain 'A' and resid 861 through 879 Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 892 through 903 Processing helix chain 'A' and resid 908 through 913 removed outlier: 3.562A pdb=" N TYR A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 removed outlier: 3.632A pdb=" N ASP A 931 " --> pdb=" O GLY A 927 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 961 removed outlier: 3.868A pdb=" N GLN A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 977 Processing helix chain 'A' and resid 980 through 1028 removed outlier: 5.090A pdb=" N VAL A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1143 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.186A pdb=" N THR E 91 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.084A pdb=" N THR D 91 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.536A pdb=" N SER B 57 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN B 58 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TYR B 264 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 262 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 85 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE B 198 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 222 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER B 200 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N HIS B 202 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 9.728A pdb=" N LEU B 218 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL B 33 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 40 removed outlier: 5.964A pdb=" N PHE B 40 " --> pdb=" O ARG C 562 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY C 561 " --> pdb=" O ASP C 569 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASP C 569 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 548 " --> pdb=" O ASP C 581 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY C 543 " --> pdb=" O PHE C 536 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 52 removed outlier: 3.868A pdb=" N ASP B 282 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167 removed outlier: 4.233A pdb=" N SER B 167 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL B 121 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 113 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP B 99 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 306 through 314 removed outlier: 5.413A pdb=" N ILE B 307 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR B 594 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN B 309 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 592 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 311 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 589 " --> pdb=" O GLN B 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 319 through 323 removed outlier: 4.438A pdb=" N GLU B 319 " --> pdb=" O CYS B 533 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP B 569 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY B 561 " --> pdb=" O ASP B 569 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE B 560 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 349 through 352 removed outlier: 4.002A pdb=" N ASN B 349 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 394 " --> pdb=" O ASN B 349 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 389 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 428 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 373 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 357 removed outlier: 6.501A pdb=" N CYS B 356 " --> pdb=" O CYS B 520 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 469 removed outlier: 3.689A pdb=" N TYR B 484 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 649 through 655 removed outlier: 3.523A pdb=" N GLU B 649 " --> pdb=" O ILE B 687 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR B 691 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN B 653 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 667 " --> pdb=" O PRO B 660 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 696 through 697 removed outlier: 6.596A pdb=" N ALA B 696 " --> pdb=" O ILE A 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 706 through 710 removed outlier: 3.539A pdb=" N THR B1071 " --> pdb=" O SER B1092 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B1073 " --> pdb=" O PHE B1090 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE B1090 " --> pdb=" O ALA B1073 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 713 through 723 removed outlier: 7.013A pdb=" N GLY B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER B1050 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B1056 " --> pdb=" O PRO B1048 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B1058 " --> pdb=" O SER B1046 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B1046 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B1060 " --> pdb=" O LEU B1044 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 728 through 731 removed outlier: 4.361A pdb=" N LYS B 728 " --> pdb=" O LEU B 856 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 782 through 785 removed outlier: 5.884A pdb=" N ILE B 783 " --> pdb=" O ASN C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 1115 through 1120 removed outlier: 4.618A pdb=" N ALA B1082 " --> pdb=" O SER B1118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 24 through 28 removed outlier: 4.061A pdb=" N SER C 24 " --> pdb=" O TRP C 61 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 57 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 44 through 52 removed outlier: 3.822A pdb=" N ASP C 50 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR C 269 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASP C 285 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU C 271 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA C 283 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS C 273 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 219 through 225 removed outlier: 7.340A pdb=" N ILE C 198 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP C 223 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE C 196 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 88 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 165 removed outlier: 5.861A pdb=" N ASN C 116 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ARG C 97 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY C 98 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 306 through 314 removed outlier: 5.162A pdb=" N ILE C 307 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR C 594 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN C 309 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 592 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 311 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY C 589 " --> pdb=" O GLN C 608 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 351 through 353 removed outlier: 3.616A pdb=" N LYS C 373 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AC7, first strand: chain 'C' and resid 468 through 469 removed outlier: 3.526A pdb=" N TYR C 468 " --> pdb=" O TYR C 484 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR C 484 " --> pdb=" O TYR C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 649 through 650 removed outlier: 6.123A pdb=" N GLU C 649 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR C 691 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 706 through 710 Processing sheet with id=AD1, first strand: chain 'C' and resid 713 through 723 removed outlier: 7.017A pdb=" N GLY C1054 " --> pdb=" O SER C1050 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER C1050 " --> pdb=" O GLY C1054 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C1056 " --> pdb=" O PRO C1048 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU C1058 " --> pdb=" O SER C1046 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C1046 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C1060 " --> pdb=" O LEU C1044 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 728 through 731 removed outlier: 4.320A pdb=" N LYS C 728 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 782 through 785 removed outlier: 5.835A pdb=" N ILE C 783 " --> pdb=" O ASN A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 1115 through 1117 Processing sheet with id=AD5, first strand: chain 'C' and resid 1089 through 1092 Processing sheet with id=AD6, first strand: chain 'A' and resid 24 through 28 removed outlier: 4.194A pdb=" N SER A 24 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A 57 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN A 58 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 264 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 60 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 203 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 190 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 197 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 192 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N PHE A 196 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP A 223 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE A 198 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 221 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS A 202 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N ALA A 217 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL A 33 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 45 through 52 removed outlier: 3.700A pdb=" N ASP A 50 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 282 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AD9, first strand: chain 'A' and resid 111 through 113 removed outlier: 3.786A pdb=" N VAL A 121 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 167 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 306 through 312 removed outlier: 5.397A pdb=" N ILE A 307 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR A 594 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN A 309 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 592 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 311 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 589 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 320 through 323 removed outlier: 3.685A pdb=" N LEU A 541 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP A 569 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY A 561 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 351 through 353 removed outlier: 3.675A pdb=" N ILE A 353 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 390 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 389 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 511 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 373 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 447 through 449 Processing sheet with id=AE5, first strand: chain 'A' and resid 468 through 469 removed outlier: 3.792A pdb=" N TYR A 484 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 649 through 655 removed outlier: 5.951A pdb=" N GLU A 649 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N THR A 691 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL A 651 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 706 through 710 removed outlier: 3.601A pdb=" N ILE A 707 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A1068 " --> pdb=" O ILE A 709 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 713 through 723 removed outlier: 5.921A pdb=" N TYR A1062 " --> pdb=" O HIS A1043 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A1043 " --> pdb=" O TYR A1062 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 730 through 731 Processing sheet with id=AF1, first strand: chain 'A' and resid 1115 through 1120 removed outlier: 4.482A pdb=" N ALA A1082 " --> pdb=" O SER A1118 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id=AF3, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.244A pdb=" N GLY E 10 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS E 50 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 12 removed outlier: 5.903A pdb=" N GLY F 10 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR F 34 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS F 50 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.938A pdb=" N GLY D 10 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR D 34 " --> pdb=" O CYS D 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N CYS D 50 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) 957 hydrogen bonds defined for protein. 2637 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: 13.70 Time building geometry restraints manager: 8.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8824 1.34 - 1.46: 6384 1.46 - 1.58: 13415 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 28785 Sorted by residual: bond pdb=" C VAL A 615 " pdb=" N PRO A 616 " ideal model delta sigma weight residual 1.341 1.373 -0.032 1.60e-02 3.91e+03 3.96e+00 bond pdb=" C VAL B 615 " pdb=" N PRO B 616 " ideal model delta sigma weight residual 1.341 1.370 -0.029 1.60e-02 3.91e+03 3.38e+00 bond pdb=" C PRO B 981 " pdb=" N PRO B 982 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.19e-02 7.06e+03 3.21e+00 bond pdb=" CB ASP C 740 " pdb=" CG ASP C 740 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.16e+00 bond pdb=" CA ASP C 193 " pdb=" CB ASP C 193 " ideal model delta sigma weight residual 1.530 1.557 -0.026 1.69e-02 3.50e+03 2.46e+00 ... (remaining 28780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 38415 2.64 - 5.28: 609 5.28 - 7.92: 83 7.92 - 10.57: 27 10.57 - 13.21: 4 Bond angle restraints: 39138 Sorted by residual: angle pdb=" C HIS A 514 " pdb=" N ALA A 515 " pdb=" CA ALA A 515 " ideal model delta sigma weight residual 121.80 135.01 -13.21 2.44e+00 1.68e-01 2.93e+01 angle pdb=" C SER B 438 " pdb=" N LYS B 439 " pdb=" CA LYS B 439 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C THR A 526 " pdb=" N ASN A 527 " pdb=" CA ASN A 527 " ideal model delta sigma weight residual 122.78 130.15 -7.37 1.52e+00 4.33e-01 2.35e+01 angle pdb=" C ASP C 137 " pdb=" N VAL C 138 " pdb=" CA VAL C 138 " ideal model delta sigma weight residual 121.70 130.37 -8.67 1.80e+00 3.09e-01 2.32e+01 angle pdb=" C ASN A 82 " pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.23e+01 ... (remaining 39133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 16216 17.97 - 35.94: 1122 35.94 - 53.91: 200 53.91 - 71.88: 57 71.88 - 89.85: 21 Dihedral angle restraints: 17616 sinusoidal: 7335 harmonic: 10281 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 161 " pdb=" CB CYS C 161 " ideal model delta sinusoidal sigma weight residual -86.00 -6.06 -79.94 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS C1077 " pdb=" SG CYS C1077 " pdb=" SG CYS C1121 " pdb=" CB CYS C1121 " ideal model delta sinusoidal sigma weight residual -86.00 -153.98 67.98 1 1.00e+01 1.00e-02 6.00e+01 dihedral pdb=" CB CYS A1077 " pdb=" SG CYS A1077 " pdb=" SG CYS A1121 " pdb=" CB CYS A1121 " ideal model delta sinusoidal sigma weight residual -86.00 -151.43 65.43 1 1.00e+01 1.00e-02 5.61e+01 ... (remaining 17613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 4423 0.146 - 0.291: 64 0.291 - 0.437: 5 0.437 - 0.583: 3 0.583 - 0.728: 2 Chirality restraints: 4497 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 326 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG A1300 " pdb=" ND2 ASN A 58 " pdb=" C2 NAG A1300 " pdb=" O5 NAG A1300 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.05e+00 chirality pdb=" CB ILE B 96 " pdb=" CA ILE B 96 " pdb=" CG1 ILE B 96 " pdb=" CG2 ILE B 96 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 4494 not shown) Planarity restraints: 5074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 326 " -0.057 2.00e-02 2.50e+03 5.19e-02 3.37e+01 pdb=" CG ASN C 326 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN C 326 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 326 " 0.059 2.00e-02 2.50e+03 pdb=" C1 NAG C1306 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 326 " -0.005 2.00e-02 2.50e+03 3.23e-02 1.30e+01 pdb=" CG ASN B 326 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 326 " -0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN B 326 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 58 " -0.003 2.00e-02 2.50e+03 3.13e-02 1.23e+01 pdb=" CG ASN A 58 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 58 " -0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN A 58 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A1300 " -0.031 2.00e-02 2.50e+03 ... (remaining 5071 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 109 2.55 - 3.14: 20626 3.14 - 3.72: 40575 3.72 - 4.31: 56357 4.31 - 4.90: 95659 Nonbonded interactions: 213326 Sorted by model distance: nonbonded pdb=" CD1 LEU C 450 " pdb=" OE1 GLN C 488 " model vdw 1.961 3.460 nonbonded pdb=" OG1 THR A 318 " pdb=" OE1 GLU A 319 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 318 " pdb=" OE1 GLU B 319 " model vdw 2.246 3.040 nonbonded pdb=" OG SER E 7 " pdb=" OG SER E 21 " model vdw 2.263 3.040 nonbonded pdb=" OG SER F 7 " pdb=" OG SER F 21 " model vdw 2.278 3.040 ... (remaining 213321 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 22 through 1145 or resid 1300 through 1305)) selection = (chain 'C' and (resid 22 through 1145 or resid 1300 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.220 Set scattering table: 0.310 Process input model: 66.790 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.180 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.004 0.053 28863 Z= 0.176 Angle : 0.869 16.297 39330 Z= 0.438 Chirality : 0.058 0.728 4497 Planarity : 0.007 0.083 5046 Dihedral : 12.946 89.855 10902 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.39 % Favored : 94.43 % Rotamer: Outliers : 0.03 % Allowed : 0.10 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3504 helix: 0.66 (0.20), residues: 626 sheet: 0.01 (0.18), residues: 820 loop : -1.76 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 348 HIS 0.007 0.001 HIS A 240 PHE 0.029 0.002 PHE B 152 TYR 0.021 0.001 TYR B 490 ARG 0.011 0.001 ARG A 241 Details of bonding type rmsd link_NAG-ASN : bond 0.00945 ( 28) link_NAG-ASN : angle 5.36014 ( 84) link_BETA1-4 : bond 0.00697 ( 8) link_BETA1-4 : angle 1.85729 ( 24) hydrogen bonds : bond 0.13557 ( 957) hydrogen bonds : angle 6.44067 ( 2637) SS BOND : bond 0.00255 ( 42) SS BOND : angle 1.13931 ( 84) covalent geometry : bond 0.00368 (28785) covalent geometry : angle 0.83220 (39138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8605 (tm-30) REVERT: B 116 ASN cc_start: 0.7403 (m-40) cc_final: 0.5873 (t0) REVERT: B 334 ASP cc_start: 0.8766 (p0) cc_final: 0.8309 (t0) REVERT: B 450 LEU cc_start: 0.9052 (tt) cc_final: 0.8671 (pt) REVERT: B 490 TYR cc_start: 0.7797 (p90) cc_final: 0.7551 (p90) REVERT: B 997 GLN cc_start: 0.8757 (tt0) cc_final: 0.8490 (tp40) REVERT: B 1137 GLN cc_start: 0.8485 (mm110) cc_final: 0.8189 (tp40) REVERT: C 172 MET cc_start: 0.8522 (ppp) cc_final: 0.7803 (mmm) REVERT: C 560 PHE cc_start: 0.6833 (m-80) cc_final: 0.6617 (m-10) REVERT: C 897 MET cc_start: 0.9359 (mmt) cc_final: 0.9154 (mmt) REVERT: A 148 MET cc_start: 0.5410 (tpt) cc_final: 0.4660 (tpt) REVERT: A 1137 GLN cc_start: 0.8437 (pp30) cc_final: 0.8151 (pp30) REVERT: E 37 PHE cc_start: 0.7728 (m-80) cc_final: 0.7363 (m-80) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.3803 time to fit residues: 142.2764 Evaluate side-chains 144 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 147 optimal weight: 40.0000 chunk 90 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 275 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS ** B 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 GLN ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS A1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.147931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079187 restraints weight = 54901.011| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.36 r_work: 0.2822 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 28863 Z= 0.208 Angle : 0.677 13.466 39330 Z= 0.337 Chirality : 0.048 0.422 4497 Planarity : 0.005 0.063 5046 Dihedral : 6.650 73.827 4575 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.35 % Rotamer: Outliers : 0.39 % Allowed : 5.04 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3504 helix: 1.66 (0.22), residues: 636 sheet: -0.05 (0.18), residues: 844 loop : -1.63 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 99 HIS 0.007 0.001 HIS C1083 PHE 0.033 0.002 PHE B 901 TYR 0.025 0.002 TYR A 165 ARG 0.016 0.001 ARG B 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 28) link_NAG-ASN : angle 4.22469 ( 84) link_BETA1-4 : bond 0.00158 ( 8) link_BETA1-4 : angle 1.27506 ( 24) hydrogen bonds : bond 0.05293 ( 957) hydrogen bonds : angle 5.28622 ( 2637) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.28829 ( 84) covalent geometry : bond 0.00502 (28785) covalent geometry : angle 0.64672 (39138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 2.903 Fit side-chains revert: symmetry clash REVERT: B 334 ASP cc_start: 0.8851 (p0) cc_final: 0.8323 (t70) REVERT: B 391 TYR cc_start: 0.8246 (m-80) cc_final: 0.7491 (m-80) REVERT: B 850 PHE cc_start: 0.7118 (m-10) cc_final: 0.6656 (m-10) REVERT: B 1137 GLN cc_start: 0.8456 (mm110) cc_final: 0.8137 (mm110) REVERT: C 170 PHE cc_start: 0.7556 (m-10) cc_final: 0.7247 (m-10) REVERT: C 172 MET cc_start: 0.8661 (ppp) cc_final: 0.7841 (mmm) REVERT: A 128 PHE cc_start: 0.7023 (m-80) cc_final: 0.6550 (m-80) REVERT: A 148 MET cc_start: 0.5763 (tpt) cc_final: 0.5329 (tpt) REVERT: A 172 MET cc_start: 0.8148 (mmm) cc_final: 0.7862 (mmp) REVERT: A 1137 GLN cc_start: 0.8280 (pp30) cc_final: 0.8000 (pp30) outliers start: 12 outliers final: 10 residues processed: 149 average time/residue: 0.3794 time to fit residues: 94.7858 Evaluate side-chains 136 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain E residue 104 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 252 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 290 optimal weight: 0.6980 chunk 171 optimal weight: 0.0270 chunk 259 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 GLN ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A1000 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.148308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078564 restraints weight = 54686.933| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.27 r_work: 0.2851 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28863 Z= 0.115 Angle : 0.588 11.642 39330 Z= 0.290 Chirality : 0.045 0.372 4497 Planarity : 0.004 0.062 5046 Dihedral : 6.182 62.622 4575 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.34 % Favored : 95.49 % Rotamer: Outliers : 0.85 % Allowed : 6.28 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3504 helix: 2.13 (0.22), residues: 630 sheet: 0.02 (0.18), residues: 837 loop : -1.53 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 99 HIS 0.004 0.001 HIS B1083 PHE 0.017 0.001 PHE A 587 TYR 0.022 0.001 TYR A 165 ARG 0.005 0.000 ARG B 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 28) link_NAG-ASN : angle 3.69953 ( 84) link_BETA1-4 : bond 0.00286 ( 8) link_BETA1-4 : angle 1.14430 ( 24) hydrogen bonds : bond 0.04281 ( 957) hydrogen bonds : angle 4.99304 ( 2637) SS BOND : bond 0.00200 ( 42) SS BOND : angle 1.00941 ( 84) covalent geometry : bond 0.00259 (28785) covalent geometry : angle 0.56160 (39138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 3.121 Fit side-chains revert: symmetry clash REVERT: B 49 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8442 (tm-30) REVERT: B 334 ASP cc_start: 0.8863 (p0) cc_final: 0.8334 (t70) REVERT: B 391 TYR cc_start: 0.8183 (m-80) cc_final: 0.7420 (m-80) REVERT: B 1137 GLN cc_start: 0.8448 (mm110) cc_final: 0.8124 (mm110) REVERT: C 172 MET cc_start: 0.8645 (ppp) cc_final: 0.7794 (mmm) REVERT: A 148 MET cc_start: 0.5823 (tpt) cc_final: 0.5442 (tpt) REVERT: A 542 THR cc_start: 0.8801 (p) cc_final: 0.8546 (m) REVERT: A 1137 GLN cc_start: 0.8312 (pp30) cc_final: 0.8067 (pp30) outliers start: 26 outliers final: 11 residues processed: 158 average time/residue: 0.3514 time to fit residues: 95.5216 Evaluate side-chains 136 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain E residue 104 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 8 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 241 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 278 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.147140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078295 restraints weight = 55626.813| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.32 r_work: 0.2818 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28863 Z= 0.154 Angle : 0.605 11.475 39330 Z= 0.300 Chirality : 0.045 0.366 4497 Planarity : 0.004 0.056 5046 Dihedral : 6.045 55.531 4575 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.65 % Favored : 95.18 % Rotamer: Outliers : 1.20 % Allowed : 7.74 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3504 helix: 2.24 (0.22), residues: 633 sheet: -0.02 (0.18), residues: 849 loop : -1.47 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 61 HIS 0.004 0.001 HIS E 32 PHE 0.019 0.001 PHE B 901 TYR 0.018 0.001 TYR C 260 ARG 0.004 0.000 ARG B 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 28) link_NAG-ASN : angle 3.51048 ( 84) link_BETA1-4 : bond 0.00178 ( 8) link_BETA1-4 : angle 1.16107 ( 24) hydrogen bonds : bond 0.04652 ( 957) hydrogen bonds : angle 4.86848 ( 2637) SS BOND : bond 0.00476 ( 42) SS BOND : angle 1.62225 ( 84) covalent geometry : bond 0.00367 (28785) covalent geometry : angle 0.57880 (39138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 2.943 Fit side-chains revert: symmetry clash REVERT: B 334 ASP cc_start: 0.8893 (p0) cc_final: 0.8339 (t70) REVERT: B 391 TYR cc_start: 0.8229 (m-80) cc_final: 0.7403 (m-80) REVERT: B 1137 GLN cc_start: 0.8487 (mm110) cc_final: 0.8276 (mm-40) REVERT: C 172 MET cc_start: 0.8584 (ppp) cc_final: 0.7931 (mmt) REVERT: C 850 PHE cc_start: 0.6220 (m-10) cc_final: 0.5984 (m-10) REVERT: A 148 MET cc_start: 0.5869 (tpt) cc_final: 0.5393 (tpt) REVERT: A 232 ARG cc_start: 0.6585 (mtm180) cc_final: 0.6352 (mtm110) REVERT: A 234 GLN cc_start: 0.6788 (tm-30) cc_final: 0.6540 (tm-30) REVERT: A 542 THR cc_start: 0.8882 (p) cc_final: 0.8596 (m) outliers start: 37 outliers final: 20 residues processed: 159 average time/residue: 0.3583 time to fit residues: 97.0247 Evaluate side-chains 139 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 TRP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 268 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 229 optimal weight: 0.4980 chunk 219 optimal weight: 0.0170 chunk 51 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.147469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.078918 restraints weight = 54892.135| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.31 r_work: 0.2824 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 28863 Z= 0.129 Angle : 0.592 11.478 39330 Z= 0.292 Chirality : 0.044 0.345 4497 Planarity : 0.004 0.055 5046 Dihedral : 5.847 59.014 4575 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 1.14 % Allowed : 8.29 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3504 helix: 2.39 (0.22), residues: 626 sheet: 0.03 (0.18), residues: 846 loop : -1.43 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 881 HIS 0.003 0.001 HIS C1083 PHE 0.018 0.001 PHE A 587 TYR 0.020 0.001 TYR A 165 ARG 0.006 0.000 ARG B 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 28) link_NAG-ASN : angle 3.40818 ( 84) link_BETA1-4 : bond 0.00277 ( 8) link_BETA1-4 : angle 1.10480 ( 24) hydrogen bonds : bond 0.04172 ( 957) hydrogen bonds : angle 4.76641 ( 2637) SS BOND : bond 0.00301 ( 42) SS BOND : angle 2.27698 ( 84) covalent geometry : bond 0.00308 (28785) covalent geometry : angle 0.56200 (39138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8446 (tm-30) REVERT: B 234 GLN cc_start: 0.7401 (tm-30) cc_final: 0.6930 (tp40) REVERT: B 319 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7767 (pm20) REVERT: B 334 ASP cc_start: 0.8906 (p0) cc_final: 0.8351 (t0) REVERT: B 391 TYR cc_start: 0.8187 (m-80) cc_final: 0.7336 (m-80) REVERT: B 1137 GLN cc_start: 0.8468 (mm110) cc_final: 0.8265 (mm-40) REVERT: C 172 MET cc_start: 0.8594 (ppp) cc_final: 0.7895 (mmm) REVERT: C 850 PHE cc_start: 0.6357 (m-10) cc_final: 0.6065 (m-10) REVERT: A 148 MET cc_start: 0.6051 (tpt) cc_final: 0.5399 (tpp) outliers start: 35 outliers final: 20 residues processed: 157 average time/residue: 0.3484 time to fit residues: 94.2401 Evaluate side-chains 146 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 TRP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 104 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 228 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 333 optimal weight: 50.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 GLN ** E 32 HIS ** 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 = 0.4157 r_free = 0.4157 target = 0.146724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078074 restraints weight = 55177.770| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.30 r_work: 0.2802 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28863 Z= 0.138 Angle : 0.587 11.260 39330 Z= 0.288 Chirality : 0.044 0.345 4497 Planarity : 0.004 0.054 5046 Dihedral : 5.726 59.989 4575 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.54 % Favored : 95.32 % Rotamer: Outliers : 1.01 % Allowed : 9.14 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3504 helix: 2.39 (0.22), residues: 626 sheet: 0.05 (0.18), residues: 847 loop : -1.37 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 881 HIS 0.004 0.001 HIS E 30 PHE 0.018 0.001 PHE A 587 TYR 0.025 0.001 TYR A 165 ARG 0.008 0.000 ARG B 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 28) link_NAG-ASN : angle 3.30116 ( 84) link_BETA1-4 : bond 0.00241 ( 8) link_BETA1-4 : angle 1.14506 ( 24) hydrogen bonds : bond 0.04340 ( 957) hydrogen bonds : angle 4.69349 ( 2637) SS BOND : bond 0.00267 ( 42) SS BOND : angle 1.73125 ( 84) covalent geometry : bond 0.00330 (28785) covalent geometry : angle 0.56175 (39138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8451 (tm-30) REVERT: B 234 GLN cc_start: 0.7419 (tm-30) cc_final: 0.6572 (tm-30) REVERT: B 334 ASP cc_start: 0.8892 (p0) cc_final: 0.8330 (t0) REVERT: B 391 TYR cc_start: 0.8214 (m-80) cc_final: 0.7313 (m-80) REVERT: B 1137 GLN cc_start: 0.8472 (mm110) cc_final: 0.8272 (mm-40) REVERT: C 172 MET cc_start: 0.8630 (ppp) cc_final: 0.8261 (tmm) REVERT: C 850 PHE cc_start: 0.6418 (m-10) cc_final: 0.6078 (m-10) REVERT: A 148 MET cc_start: 0.6317 (tpt) cc_final: 0.5693 (tpp) REVERT: A 171 LEU cc_start: 0.8977 (mt) cc_final: 0.8754 (mt) REVERT: A 569 ASP cc_start: 0.7662 (t0) cc_final: 0.7449 (t0) outliers start: 31 outliers final: 22 residues processed: 162 average time/residue: 0.3430 time to fit residues: 95.7698 Evaluate side-chains 150 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 TRP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 287 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 55 optimal weight: 0.0470 chunk 232 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 326 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 344 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 241 optimal weight: 0.0970 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 987 GLN ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.146607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078061 restraints weight = 54823.728| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.29 r_work: 0.2808 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28863 Z= 0.129 Angle : 0.572 11.352 39330 Z= 0.281 Chirality : 0.044 0.332 4497 Planarity : 0.004 0.053 5046 Dihedral : 5.597 59.282 4575 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 1.07 % Allowed : 9.46 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3504 helix: 2.43 (0.22), residues: 629 sheet: 0.07 (0.18), residues: 849 loop : -1.33 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 881 HIS 0.004 0.001 HIS E 30 PHE 0.018 0.001 PHE A 587 TYR 0.022 0.001 TYR A 165 ARG 0.008 0.000 ARG B 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 28) link_NAG-ASN : angle 3.21728 ( 84) link_BETA1-4 : bond 0.00261 ( 8) link_BETA1-4 : angle 1.10702 ( 24) hydrogen bonds : bond 0.04179 ( 957) hydrogen bonds : angle 4.65183 ( 2637) SS BOND : bond 0.00220 ( 42) SS BOND : angle 1.40778 ( 84) covalent geometry : bond 0.00306 (28785) covalent geometry : angle 0.54916 (39138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8435 (tm-30) REVERT: B 163 PHE cc_start: 0.7392 (t80) cc_final: 0.6731 (t80) REVERT: B 234 GLN cc_start: 0.7490 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 319 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: B 334 ASP cc_start: 0.8881 (p0) cc_final: 0.8310 (t0) REVERT: B 391 TYR cc_start: 0.8232 (m-80) cc_final: 0.7331 (m-80) REVERT: C 172 MET cc_start: 0.8654 (ppp) cc_final: 0.8306 (tmm) REVERT: C 850 PHE cc_start: 0.6421 (m-10) cc_final: 0.6044 (m-10) REVERT: A 148 MET cc_start: 0.6341 (tpt) cc_final: 0.5721 (tpp) REVERT: A 171 LEU cc_start: 0.8983 (mt) cc_final: 0.8717 (mt) REVERT: A 569 ASP cc_start: 0.7639 (t0) cc_final: 0.7429 (t0) REVERT: A 850 PHE cc_start: 0.6149 (m-10) cc_final: 0.5839 (m-10) outliers start: 33 outliers final: 23 residues processed: 164 average time/residue: 0.3587 time to fit residues: 101.1789 Evaluate side-chains 157 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 TRP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 274 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 326 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 299 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 670 GLN C1083 HIS ** E 77 ASN ** 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 = 0.4102 r_free = 0.4102 target = 0.144223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074210 restraints weight = 54875.192| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.23 r_work: 0.2758 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28863 Z= 0.185 Angle : 0.610 11.374 39330 Z= 0.302 Chirality : 0.046 0.346 4497 Planarity : 0.004 0.053 5046 Dihedral : 5.773 59.822 4575 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.05 % Favored : 94.81 % Rotamer: Outliers : 1.01 % Allowed : 9.85 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3504 helix: 2.28 (0.22), residues: 635 sheet: 0.03 (0.18), residues: 848 loop : -1.36 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 881 HIS 0.005 0.001 HIS B1083 PHE 0.019 0.001 PHE A 587 TYR 0.022 0.001 TYR C 260 ARG 0.011 0.000 ARG B 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 28) link_NAG-ASN : angle 3.27540 ( 84) link_BETA1-4 : bond 0.00163 ( 8) link_BETA1-4 : angle 1.15480 ( 24) hydrogen bonds : bond 0.04968 ( 957) hydrogen bonds : angle 4.78305 ( 2637) SS BOND : bond 0.00299 ( 42) SS BOND : angle 1.76646 ( 84) covalent geometry : bond 0.00448 (28785) covalent geometry : angle 0.58628 (39138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 PHE cc_start: 0.7427 (t80) cc_final: 0.6551 (t80) REVERT: B 234 GLN cc_start: 0.7346 (tm-30) cc_final: 0.6563 (tm-30) REVERT: B 319 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: B 334 ASP cc_start: 0.8891 (p0) cc_final: 0.8172 (t0) REVERT: B 391 TYR cc_start: 0.8069 (m-80) cc_final: 0.7215 (m-80) REVERT: C 172 MET cc_start: 0.8718 (ppp) cc_final: 0.8346 (tmm) REVERT: A 148 MET cc_start: 0.6525 (tpt) cc_final: 0.5959 (tpp) REVERT: A 234 GLN cc_start: 0.6502 (tp40) cc_final: 0.6164 (mm110) REVERT: A 569 ASP cc_start: 0.7717 (t0) cc_final: 0.7493 (t0) REVERT: A 850 PHE cc_start: 0.6431 (m-10) cc_final: 0.6148 (m-10) outliers start: 31 outliers final: 26 residues processed: 161 average time/residue: 0.3552 time to fit residues: 98.6790 Evaluate side-chains 157 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 TRP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 26 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 340 optimal weight: 7.9990 chunk 229 optimal weight: 0.4980 chunk 177 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 284 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.146380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078113 restraints weight = 54946.797| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.28 r_work: 0.2823 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28863 Z= 0.112 Angle : 0.565 11.440 39330 Z= 0.277 Chirality : 0.044 0.326 4497 Planarity : 0.004 0.053 5046 Dihedral : 5.500 59.982 4575 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.25 % Favored : 95.61 % Rotamer: Outliers : 0.94 % Allowed : 10.34 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3504 helix: 2.35 (0.22), residues: 643 sheet: 0.07 (0.18), residues: 840 loop : -1.29 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 881 HIS 0.004 0.000 HIS E 30 PHE 0.019 0.001 PHE A 587 TYR 0.025 0.001 TYR A 165 ARG 0.011 0.000 ARG B 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 28) link_NAG-ASN : angle 3.11850 ( 84) link_BETA1-4 : bond 0.00287 ( 8) link_BETA1-4 : angle 1.07392 ( 24) hydrogen bonds : bond 0.03939 ( 957) hydrogen bonds : angle 4.59937 ( 2637) SS BOND : bond 0.00216 ( 42) SS BOND : angle 1.38895 ( 84) covalent geometry : bond 0.00260 (28785) covalent geometry : angle 0.54341 (39138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 GLN cc_start: 0.7440 (tm-30) cc_final: 0.6592 (tm-30) REVERT: B 319 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: B 334 ASP cc_start: 0.8880 (p0) cc_final: 0.8261 (t0) REVERT: B 391 TYR cc_start: 0.8228 (m-80) cc_final: 0.7427 (m-80) REVERT: C 172 MET cc_start: 0.8677 (ppp) cc_final: 0.8316 (tmm) REVERT: A 148 MET cc_start: 0.6493 (tpt) cc_final: 0.5896 (tpp) REVERT: A 163 PHE cc_start: 0.7643 (t80) cc_final: 0.7209 (t80) REVERT: A 234 GLN cc_start: 0.6788 (tp40) cc_final: 0.6403 (mm110) REVERT: A 850 PHE cc_start: 0.6353 (m-10) cc_final: 0.6005 (m-10) REVERT: E 46 GLU cc_start: 0.9478 (tp30) cc_final: 0.8991 (pm20) outliers start: 29 outliers final: 25 residues processed: 154 average time/residue: 0.3549 time to fit residues: 93.3046 Evaluate side-chains 152 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 TRP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 243 optimal weight: 9.9990 chunk 293 optimal weight: 0.5980 chunk 259 optimal weight: 0.4980 chunk 257 optimal weight: 0.0570 chunk 143 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1000 GLN ** E 32 HIS ** 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 = 0.4160 r_free = 0.4160 target = 0.146873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.078819 restraints weight = 55008.947| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.28 r_work: 0.2839 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28863 Z= 0.104 Angle : 0.557 11.442 39330 Z= 0.273 Chirality : 0.043 0.323 4497 Planarity : 0.004 0.053 5046 Dihedral : 5.283 59.816 4575 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 0.81 % Allowed : 10.63 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3504 helix: 2.46 (0.22), residues: 643 sheet: 0.14 (0.17), residues: 860 loop : -1.24 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 881 HIS 0.004 0.000 HIS E 30 PHE 0.021 0.001 PHE A 101 TYR 0.023 0.001 TYR A 165 ARG 0.013 0.000 ARG B 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 28) link_NAG-ASN : angle 3.04698 ( 84) link_BETA1-4 : bond 0.00253 ( 8) link_BETA1-4 : angle 1.11640 ( 24) hydrogen bonds : bond 0.03669 ( 957) hydrogen bonds : angle 4.48238 ( 2637) SS BOND : bond 0.00184 ( 42) SS BOND : angle 1.16967 ( 84) covalent geometry : bond 0.00236 (28785) covalent geometry : angle 0.53669 (39138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 GLN cc_start: 0.7437 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 319 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: B 334 ASP cc_start: 0.8869 (p0) cc_final: 0.8254 (t0) REVERT: B 391 TYR cc_start: 0.8258 (m-80) cc_final: 0.7429 (m-80) REVERT: C 172 MET cc_start: 0.8675 (ppp) cc_final: 0.8287 (tmm) REVERT: A 148 MET cc_start: 0.6547 (tpt) cc_final: 0.5945 (tpp) REVERT: A 163 PHE cc_start: 0.7774 (t80) cc_final: 0.7268 (t80) REVERT: A 172 MET cc_start: 0.8355 (mmp) cc_final: 0.7761 (ptp) REVERT: A 234 GLN cc_start: 0.6699 (tp40) cc_final: 0.6420 (mm110) REVERT: A 850 PHE cc_start: 0.6354 (m-10) cc_final: 0.6004 (m-10) REVERT: A 1091 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8819 (m) REVERT: E 46 GLU cc_start: 0.9457 (tp30) cc_final: 0.8980 (pm20) outliers start: 25 outliers final: 22 residues processed: 153 average time/residue: 0.3569 time to fit residues: 93.0995 Evaluate side-chains 155 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 TRP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 974 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 139 optimal weight: 5.9990 chunk 318 optimal weight: 20.0000 chunk 337 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 281 optimal weight: 0.0060 chunk 42 optimal weight: 20.0000 chunk 4 optimal weight: 0.4980 chunk 326 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN C 116 ASN ** E 32 HIS ** 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 = 0.4137 r_free = 0.4137 target = 0.145368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076230 restraints weight = 54951.666| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.20 r_work: 0.2829 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28863 Z= 0.134 Angle : 0.572 11.367 39330 Z= 0.282 Chirality : 0.044 0.325 4497 Planarity : 0.004 0.053 5046 Dihedral : 5.328 59.114 4575 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 0.98 % Allowed : 10.70 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3504 helix: 2.28 (0.22), residues: 656 sheet: 0.15 (0.18), residues: 855 loop : -1.24 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 881 HIS 0.004 0.001 HIS E 30 PHE 0.019 0.001 PHE A 587 TYR 0.023 0.001 TYR A 165 ARG 0.010 0.000 ARG B 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 28) link_NAG-ASN : angle 3.09940 ( 84) link_BETA1-4 : bond 0.00224 ( 8) link_BETA1-4 : angle 1.10401 ( 24) hydrogen bonds : bond 0.04197 ( 957) hydrogen bonds : angle 4.55473 ( 2637) SS BOND : bond 0.00233 ( 42) SS BOND : angle 1.16137 ( 84) covalent geometry : bond 0.00319 (28785) covalent geometry : angle 0.55143 (39138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25019.74 seconds wall clock time: 439 minutes 3.36 seconds (26343.36 seconds total)