Starting phenix.real_space_refine on Thu Mar 5 23:47:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tgy_25889/03_2026/7tgy_25889.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tgy_25889/03_2026/7tgy_25889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tgy_25889/03_2026/7tgy_25889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tgy_25889/03_2026/7tgy_25889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tgy_25889/03_2026/7tgy_25889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tgy_25889/03_2026/7tgy_25889.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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 117 5.16 5 C 16556 2.51 5 N 4279 2.21 5 O 5047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25999 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8454 Classifications: {'peptide': 1083} Link IDs: {'PTRANS': 53, 'TRANS': 1029} Chain breaks: 5 Chain: "B" Number of atoms: 8468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8468 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 53, 'TRANS': 1030} Chain breaks: 5 Chain: "C" Number of atoms: 8489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8489 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 54, 'TRANS': 1032} Chain breaks: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "X" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.76, per 1000 atoms: 0.22 Number of scatterers: 25999 At special positions: 0 Unit cell: (158.42, 148.63, 178, 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 117 16.00 O 5047 8.00 N 4279 7.00 C 16556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 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 K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 165 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C1098 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG X 1 " - " ASN B1098 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 933.7 milliseconds 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6088 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 46 sheets defined 24.9% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.254A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.300A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.520A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.720A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.544A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.655A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.727A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.741A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.789A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.881A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.598A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.625A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.089A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.643A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.118A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.876A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.842A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.697A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.631A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.865A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.879A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.641A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.280A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.234A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.001A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 3.951A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.631A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.710A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.719A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.700A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.678A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.998A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.885A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.559A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.546A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.024A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.051A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.303A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.625A pdb=" N GLY C 566 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.054A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.718A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.549A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.620A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.930A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.552A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.678A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.549A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.620A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.952A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.763A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.531A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.931A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.728A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.006A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.724A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.104A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.192A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.916A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.364A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.586A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.618A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.693A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.869A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.060A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 566 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.686A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.589A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.939A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.003A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.120A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.232A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.601A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.919A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 11.944A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 13.337A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.489A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.786A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.231A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.332A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.564A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 714 removed outlier: 4.021A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.020A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 1013 hydrogen bonds defined for protein. 2739 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: 5.25 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8241 1.34 - 1.46: 6567 1.46 - 1.59: 11631 1.59 - 1.71: 0 1.71 - 1.84: 147 Bond restraints: 26586 Sorted by residual: bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.324 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C VAL C 382 " pdb=" N SER C 383 " ideal model delta sigma weight residual 1.335 1.249 0.085 3.04e-02 1.08e+03 7.84e+00 bond pdb=" C1 NAG X 1 " pdb=" C2 NAG X 1 " ideal model delta sigma weight residual 1.532 1.477 0.055 2.00e-02 2.50e+03 7.55e+00 ... (remaining 26581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 34258 1.81 - 3.62: 1701 3.62 - 5.43: 198 5.43 - 7.24: 15 7.24 - 9.05: 5 Bond angle restraints: 36177 Sorted by residual: angle pdb=" C PHE A1121 " pdb=" CA PHE A1121 " pdb=" CB PHE A1121 " ideal model delta sigma weight residual 112.07 103.02 9.05 1.48e+00 4.57e-01 3.74e+01 angle pdb=" CA PHE A1121 " pdb=" C PHE A1121 " pdb=" N VAL A1122 " ideal model delta sigma weight residual 114.59 121.46 -6.87 1.48e+00 4.57e-01 2.16e+01 angle pdb=" N PHE A1121 " pdb=" CA PHE A1121 " pdb=" C PHE A1121 " ideal model delta sigma weight residual 109.71 116.09 -6.38 1.41e+00 5.03e-01 2.05e+01 angle pdb=" N PHE B 906 " pdb=" CA PHE B 906 " pdb=" CB PHE B 906 " ideal model delta sigma weight residual 110.07 115.96 -5.89 1.45e+00 4.76e-01 1.65e+01 angle pdb=" CA CYS A 738 " pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 114.40 122.92 -8.52 2.30e+00 1.89e-01 1.37e+01 ... (remaining 36172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 15566 24.48 - 48.96: 645 48.96 - 73.44: 110 73.44 - 97.92: 36 97.92 - 122.39: 29 Dihedral angle restraints: 16386 sinusoidal: 6921 harmonic: 9465 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 179.29 -86.29 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -4.45 -81.55 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.31 -80.31 1 1.00e+01 1.00e-02 7.98e+01 ... (remaining 16383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 4211 0.285 - 0.569: 4 0.569 - 0.854: 1 0.854 - 1.139: 0 1.139 - 1.423: 1 Chirality restraints: 4217 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.98 -1.42 2.00e-01 2.50e+01 5.06e+01 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.99e+01 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 ... (remaining 4214 not shown) Planarity restraints: 4665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " 0.051 2.00e-02 2.50e+03 4.58e-02 3.68e+01 pdb=" CG PHE B 906 " -0.105 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " -0.045 2.00e-02 2.50e+03 3.86e-02 2.61e+01 pdb=" CG PHE C 906 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.043 2.00e-02 2.50e+03 3.64e-02 2.32e+01 pdb=" CG PHE A 906 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " 0.012 2.00e-02 2.50e+03 ... (remaining 4662 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 160 2.49 - 3.09: 19254 3.09 - 3.69: 34460 3.69 - 4.30: 51509 4.30 - 4.90: 89055 Nonbonded interactions: 194438 Sorted by model distance: nonbonded pdb=" O3 NAG C1307 " pdb=" O7 NAG C1307 " model vdw 1.886 3.040 nonbonded pdb=" O3 NAG A1305 " pdb=" O7 NAG A1305 " model vdw 1.951 3.040 nonbonded pdb=" OG SER B 172 " pdb=" OE1 GLN B 173 " model vdw 2.013 3.040 nonbonded pdb=" O3 NAG e 1 " pdb=" O5 NAG e 2 " model vdw 2.081 3.040 nonbonded pdb=" OG SER A 383 " pdb=" OD2 ASP B 985 " model vdw 2.085 3.040 ... (remaining 194433 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 14 through 623 or resid 634 through 1306)) selection = (chain 'C' and (resid 14 through 623 or resid 634 through 1306)) } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } 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: 0.010 Normalize map: mean=0, sd=1: 3.750 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.830 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.010 0.085 26668 Z= 0.444 Angle : 0.910 17.548 36381 Z= 0.501 Chirality : 0.062 1.423 4217 Planarity : 0.006 0.073 4634 Dihedral : 14.874 122.395 10172 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 0.18 % Allowed : 0.25 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.13), residues: 3218 helix: -0.34 (0.19), residues: 662 sheet: -0.42 (0.20), residues: 643 loop : -2.76 (0.11), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 765 TYR 0.034 0.003 TYR B 266 PHE 0.105 0.003 PHE B 906 TRP 0.038 0.004 TRP C 152 HIS 0.010 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.01047 (26586) covalent geometry : angle 0.86882 (36177) SS BOND : bond 0.00654 ( 42) SS BOND : angle 2.73375 ( 84) hydrogen bonds : bond 0.15018 ( 1001) hydrogen bonds : angle 7.04507 ( 2739) link_BETA1-4 : bond 0.00821 ( 9) link_BETA1-4 : angle 2.87968 ( 27) link_NAG-ASN : bond 0.00651 ( 31) link_NAG-ASN : angle 4.58171 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1554 (ptp) cc_final: -0.0205 (mtt) REVERT: C 190 ARG cc_start: 0.7873 (mmt180) cc_final: 0.7661 (mmt180) outliers start: 5 outliers final: 1 residues processed: 150 average time/residue: 0.7525 time to fit residues: 128.9033 Evaluate side-chains 89 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 388 ASN B 188 ASN B 196 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 919 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.110594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.067399 restraints weight = 58445.204| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.75 r_work: 0.2847 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26668 Z= 0.144 Angle : 0.710 17.467 36381 Z= 0.354 Chirality : 0.051 0.850 4217 Planarity : 0.005 0.063 4634 Dihedral : 10.964 116.030 4369 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.67 % Allowed : 4.16 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.14), residues: 3218 helix: 0.73 (0.20), residues: 681 sheet: -0.16 (0.19), residues: 660 loop : -2.36 (0.12), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 408 TYR 0.021 0.001 TYR A 473 PHE 0.032 0.002 PHE B 157 TRP 0.018 0.001 TRP C 152 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00297 (26586) covalent geometry : angle 0.67274 (36177) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.57556 ( 84) hydrogen bonds : bond 0.07456 ( 1001) hydrogen bonds : angle 5.69753 ( 2739) link_BETA1-4 : bond 0.00911 ( 9) link_BETA1-4 : angle 1.95162 ( 27) link_NAG-ASN : bond 0.00523 ( 31) link_NAG-ASN : angle 4.19245 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5598 (pmm) cc_final: 0.5256 (pmm) REVERT: A 177 MET cc_start: 0.1945 (ptp) cc_final: 0.0111 (mtt) REVERT: A 414 GLN cc_start: 0.4615 (pp30) cc_final: 0.4290 (pp30) REVERT: A 515 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.7750 (p90) REVERT: A 636 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6585 (t80) REVERT: A 855 PHE cc_start: 0.8545 (m-80) cc_final: 0.8200 (m-80) REVERT: B 153 MET cc_start: 0.6642 (pmm) cc_final: 0.6171 (pmm) REVERT: B 855 PHE cc_start: 0.8698 (m-10) cc_final: 0.8366 (m-80) REVERT: C 153 MET cc_start: 0.7572 (pmm) cc_final: 0.7150 (ppp) REVERT: C 258 TRP cc_start: 0.5790 (p-90) cc_final: 0.2571 (m100) REVERT: C 408 ARG cc_start: 0.8464 (tmm-80) cc_final: 0.8226 (tmm-80) REVERT: C 1138 TYR cc_start: 0.8824 (t80) cc_final: 0.8483 (t80) outliers start: 19 outliers final: 4 residues processed: 143 average time/residue: 0.5819 time to fit residues: 98.2297 Evaluate side-chains 93 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 134 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 250 optimal weight: 0.5980 chunk 323 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 914 ASN B 196 ASN B 414 GLN B 519 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 907 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.113815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.069166 restraints weight = 61081.992| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.80 r_work: 0.2863 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26668 Z= 0.130 Angle : 0.650 16.393 36381 Z= 0.318 Chirality : 0.049 0.747 4217 Planarity : 0.004 0.054 4634 Dihedral : 9.228 112.723 4369 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.02 % Allowed : 5.68 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3218 helix: 1.39 (0.21), residues: 678 sheet: 0.13 (0.20), residues: 648 loop : -2.16 (0.12), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.020 0.001 TYR A 473 PHE 0.017 0.001 PHE B 157 TRP 0.010 0.001 TRP C 633 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00277 (26586) covalent geometry : angle 0.61428 (36177) SS BOND : bond 0.00397 ( 42) SS BOND : angle 1.37148 ( 84) hydrogen bonds : bond 0.06538 ( 1001) hydrogen bonds : angle 5.35522 ( 2739) link_BETA1-4 : bond 0.00887 ( 9) link_BETA1-4 : angle 1.99354 ( 27) link_NAG-ASN : bond 0.00468 ( 31) link_NAG-ASN : angle 3.92273 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5603 (pmm) cc_final: 0.5312 (pmm) REVERT: A 177 MET cc_start: 0.1952 (ptp) cc_final: 0.0137 (mtt) REVERT: A 242 LEU cc_start: 0.9292 (tp) cc_final: 0.9041 (tm) REVERT: A 455 LEU cc_start: 0.8879 (mt) cc_final: 0.8651 (mp) REVERT: A 855 PHE cc_start: 0.8460 (m-80) cc_final: 0.8077 (m-80) REVERT: B 200 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7865 (t80) REVERT: B 224 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7704 (pp20) REVERT: B 855 PHE cc_start: 0.8579 (m-10) cc_final: 0.8198 (m-80) REVERT: C 153 MET cc_start: 0.7579 (pmm) cc_final: 0.7081 (ppp) REVERT: C 177 MET cc_start: 0.3811 (ptt) cc_final: 0.0377 (mtt) REVERT: C 190 ARG cc_start: 0.7677 (mmt180) cc_final: 0.7463 (mmt180) REVERT: C 200 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.8055 (t80) REVERT: C 258 TRP cc_start: 0.5553 (p-90) cc_final: 0.2603 (m100) REVERT: C 1138 TYR cc_start: 0.8816 (t80) cc_final: 0.8321 (t80) outliers start: 29 outliers final: 10 residues processed: 129 average time/residue: 0.6033 time to fit residues: 91.9220 Evaluate side-chains 98 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 907 ASN C 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.107403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.061676 restraints weight = 60242.208| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.84 r_work: 0.2747 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 26668 Z= 0.295 Angle : 0.743 17.523 36381 Z= 0.371 Chirality : 0.052 0.819 4217 Planarity : 0.005 0.048 4634 Dihedral : 8.538 112.056 4369 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.38 % Allowed : 6.42 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3218 helix: 1.33 (0.21), residues: 680 sheet: 0.07 (0.19), residues: 642 loop : -2.17 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 905 TYR 0.023 0.002 TYR C 265 PHE 0.027 0.002 PHE B 906 TRP 0.016 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00725 (26586) covalent geometry : angle 0.70680 (36177) SS BOND : bond 0.00503 ( 42) SS BOND : angle 1.84835 ( 84) hydrogen bonds : bond 0.08979 ( 1001) hydrogen bonds : angle 5.57207 ( 2739) link_BETA1-4 : bond 0.00560 ( 9) link_BETA1-4 : angle 1.98083 ( 27) link_NAG-ASN : bond 0.00423 ( 31) link_NAG-ASN : angle 4.16152 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6052 (pmm) cc_final: 0.5775 (pmm) REVERT: A 177 MET cc_start: 0.2087 (ptp) cc_final: 0.0160 (mtt) REVERT: A 197 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8195 (pp) REVERT: A 242 LEU cc_start: 0.9297 (tp) cc_final: 0.9058 (tm) REVERT: A 455 LEU cc_start: 0.8867 (mt) cc_final: 0.8661 (mp) REVERT: A 490 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7891 (t80) REVERT: A 515 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8165 (p90) REVERT: A 855 PHE cc_start: 0.8497 (m-10) cc_final: 0.8128 (m-80) REVERT: A 988 GLU cc_start: 0.8792 (mp0) cc_final: 0.8469 (mp0) REVERT: B 153 MET cc_start: 0.6581 (pmm) cc_final: 0.6165 (pmm) REVERT: B 200 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7841 (t80) REVERT: B 408 ARG cc_start: 0.8806 (ppt170) cc_final: 0.8461 (ppt90) REVERT: B 414 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.5834 (pp30) REVERT: B 515 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8326 (p90) REVERT: B 855 PHE cc_start: 0.8651 (m-10) cc_final: 0.8258 (m-80) REVERT: C 153 MET cc_start: 0.7718 (pmm) cc_final: 0.7273 (ppp) REVERT: C 177 MET cc_start: 0.4039 (ptt) cc_final: 0.0646 (mtt) REVERT: C 200 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.8062 (t80) REVERT: C 258 TRP cc_start: 0.5689 (p-90) cc_final: 0.2586 (m100) REVERT: C 855 PHE cc_start: 0.8423 (m-80) cc_final: 0.8117 (m-80) outliers start: 39 outliers final: 16 residues processed: 122 average time/residue: 0.5733 time to fit residues: 82.9061 Evaluate side-chains 108 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 231 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN A1101 HIS B 196 ASN B 965 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.108523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.063230 restraints weight = 59452.714| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.89 r_work: 0.2766 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26668 Z= 0.162 Angle : 0.653 16.473 36381 Z= 0.323 Chirality : 0.049 0.752 4217 Planarity : 0.004 0.044 4634 Dihedral : 8.002 111.958 4369 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.48 % Allowed : 6.95 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3218 helix: 1.66 (0.21), residues: 675 sheet: 0.18 (0.19), residues: 645 loop : -2.05 (0.12), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.018 0.001 TYR C 473 PHE 0.014 0.001 PHE C 906 TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00374 (26586) covalent geometry : angle 0.61772 (36177) SS BOND : bond 0.00494 ( 42) SS BOND : angle 1.57848 ( 84) hydrogen bonds : bond 0.07250 ( 1001) hydrogen bonds : angle 5.29767 ( 2739) link_BETA1-4 : bond 0.00705 ( 9) link_BETA1-4 : angle 1.88194 ( 27) link_NAG-ASN : bond 0.00431 ( 31) link_NAG-ASN : angle 3.85332 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6231 (pmm) cc_final: 0.5951 (pmm) REVERT: A 177 MET cc_start: 0.2102 (ptp) cc_final: 0.0173 (mtt) REVERT: A 515 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8000 (p90) REVERT: A 855 PHE cc_start: 0.8474 (m-10) cc_final: 0.8150 (m-80) REVERT: A 988 GLU cc_start: 0.8782 (mp0) cc_final: 0.8143 (mp0) REVERT: B 153 MET cc_start: 0.6651 (pmm) cc_final: 0.6239 (pmm) REVERT: B 200 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7957 (t80) REVERT: B 224 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7801 (pp20) REVERT: B 515 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8095 (p90) REVERT: B 855 PHE cc_start: 0.8659 (m-10) cc_final: 0.8258 (m-80) REVERT: C 153 MET cc_start: 0.7736 (pmm) cc_final: 0.7267 (ppp) REVERT: C 177 MET cc_start: 0.4239 (ptt) cc_final: 0.0863 (mtt) REVERT: C 200 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.8058 (t80) REVERT: C 258 TRP cc_start: 0.5540 (p-90) cc_final: 0.2553 (m100) REVERT: C 855 PHE cc_start: 0.8379 (m-80) cc_final: 0.8014 (m-80) REVERT: C 1138 TYR cc_start: 0.8852 (t80) cc_final: 0.8239 (t80) outliers start: 42 outliers final: 15 residues processed: 129 average time/residue: 0.5240 time to fit residues: 81.2080 Evaluate side-chains 110 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 125 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 0.0030 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 153 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 58 optimal weight: 0.8980 chunk 218 optimal weight: 0.0670 chunk 296 optimal weight: 1.9990 overall best weight: 0.5730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.110969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066316 restraints weight = 60002.654| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.90 r_work: 0.2799 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26668 Z= 0.113 Angle : 0.611 15.148 36381 Z= 0.297 Chirality : 0.047 0.677 4217 Planarity : 0.004 0.041 4634 Dihedral : 7.391 109.438 4369 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.34 % Allowed : 7.52 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3218 helix: 1.98 (0.21), residues: 679 sheet: 0.37 (0.19), residues: 654 loop : -1.89 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.017 0.001 TYR C 473 PHE 0.021 0.001 PHE C 456 TRP 0.009 0.001 TRP C 633 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00235 (26586) covalent geometry : angle 0.58080 (36177) SS BOND : bond 0.00380 ( 42) SS BOND : angle 1.15920 ( 84) hydrogen bonds : bond 0.05643 ( 1001) hydrogen bonds : angle 4.99401 ( 2739) link_BETA1-4 : bond 0.00671 ( 9) link_BETA1-4 : angle 1.80528 ( 27) link_NAG-ASN : bond 0.00487 ( 31) link_NAG-ASN : angle 3.54174 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6404 (pmm) cc_final: 0.6113 (pmm) REVERT: A 177 MET cc_start: 0.2171 (ptp) cc_final: 0.0312 (mtt) REVERT: A 242 LEU cc_start: 0.9254 (tp) cc_final: 0.9026 (tm) REVERT: A 745 ASP cc_start: 0.8227 (t0) cc_final: 0.7894 (t0) REVERT: A 855 PHE cc_start: 0.8422 (m-10) cc_final: 0.8133 (m-80) REVERT: A 988 GLU cc_start: 0.8720 (mp0) cc_final: 0.8316 (mp0) REVERT: B 153 MET cc_start: 0.6636 (pmm) cc_final: 0.6314 (pmm) REVERT: B 224 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7730 (pp20) REVERT: B 242 LEU cc_start: 0.9093 (mm) cc_final: 0.8874 (mm) REVERT: B 855 PHE cc_start: 0.8610 (m-10) cc_final: 0.8272 (m-80) REVERT: C 153 MET cc_start: 0.7711 (pmm) cc_final: 0.7387 (ppp) REVERT: C 177 MET cc_start: 0.4127 (ptt) cc_final: 0.0877 (mtt) REVERT: C 200 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7974 (t80) REVERT: C 258 TRP cc_start: 0.5422 (p-90) cc_final: 0.2584 (m100) REVERT: C 1138 TYR cc_start: 0.8854 (t80) cc_final: 0.8224 (t80) outliers start: 38 outliers final: 16 residues processed: 135 average time/residue: 0.5073 time to fit residues: 82.8935 Evaluate side-chains 114 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 116 optimal weight: 8.9990 chunk 262 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 310 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 259 optimal weight: 0.0070 chunk 106 optimal weight: 3.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.110026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066661 restraints weight = 58523.600| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.78 r_work: 0.2794 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26668 Z= 0.120 Angle : 0.611 15.086 36381 Z= 0.296 Chirality : 0.047 0.671 4217 Planarity : 0.004 0.043 4634 Dihedral : 7.114 108.050 4369 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.24 % Allowed : 7.94 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3218 helix: 2.05 (0.21), residues: 685 sheet: 0.45 (0.19), residues: 652 loop : -1.80 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 408 TYR 0.017 0.001 TYR C 473 PHE 0.014 0.001 PHE C 79 TRP 0.008 0.001 TRP C 633 HIS 0.002 0.000 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00261 (26586) covalent geometry : angle 0.58057 (36177) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.15373 ( 84) hydrogen bonds : bond 0.05794 ( 1001) hydrogen bonds : angle 4.94124 ( 2739) link_BETA1-4 : bond 0.00584 ( 9) link_BETA1-4 : angle 1.67185 ( 27) link_NAG-ASN : bond 0.00493 ( 31) link_NAG-ASN : angle 3.57940 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6401 (pmm) cc_final: 0.6088 (pmm) REVERT: A 177 MET cc_start: 0.2222 (ptp) cc_final: 0.0376 (mtt) REVERT: A 242 LEU cc_start: 0.9202 (tp) cc_final: 0.8990 (tm) REVERT: A 619 GLU cc_start: 0.8342 (mp0) cc_final: 0.8068 (mp0) REVERT: A 745 ASP cc_start: 0.8228 (t0) cc_final: 0.7876 (t0) REVERT: A 855 PHE cc_start: 0.8408 (m-10) cc_final: 0.8122 (m-80) REVERT: A 988 GLU cc_start: 0.8754 (mp0) cc_final: 0.8306 (mp0) REVERT: B 224 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7730 (pp20) REVERT: B 855 PHE cc_start: 0.8604 (m-10) cc_final: 0.8271 (m-80) REVERT: C 18 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5104 (mm) REVERT: C 153 MET cc_start: 0.7718 (pmm) cc_final: 0.7462 (ppp) REVERT: C 177 MET cc_start: 0.4186 (ptt) cc_final: 0.0854 (mtt) REVERT: C 200 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7977 (t80) REVERT: C 258 TRP cc_start: 0.5408 (p-90) cc_final: 0.2848 (m100) REVERT: C 1138 TYR cc_start: 0.8859 (t80) cc_final: 0.8201 (t80) outliers start: 35 outliers final: 19 residues processed: 128 average time/residue: 0.5335 time to fit residues: 81.9873 Evaluate side-chains 117 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 50 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 133 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN C 388 ASN C 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.109192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064142 restraints weight = 59876.093| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.87 r_work: 0.2750 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26668 Z= 0.154 Angle : 0.626 15.449 36381 Z= 0.307 Chirality : 0.047 0.689 4217 Planarity : 0.004 0.045 4634 Dihedral : 6.941 107.183 4369 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.27 % Allowed : 8.12 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3218 helix: 2.02 (0.21), residues: 687 sheet: 0.45 (0.19), residues: 653 loop : -1.77 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 408 TYR 0.018 0.001 TYR B1067 PHE 0.033 0.001 PHE B 456 TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00359 (26586) covalent geometry : angle 0.59655 (36177) SS BOND : bond 0.00369 ( 42) SS BOND : angle 1.29171 ( 84) hydrogen bonds : bond 0.06623 ( 1001) hydrogen bonds : angle 5.00585 ( 2739) link_BETA1-4 : bond 0.00458 ( 9) link_BETA1-4 : angle 1.58388 ( 27) link_NAG-ASN : bond 0.00429 ( 31) link_NAG-ASN : angle 3.58151 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6492 (pmm) cc_final: 0.6159 (pmm) REVERT: A 177 MET cc_start: 0.2272 (ptp) cc_final: 0.0420 (mtt) REVERT: A 619 GLU cc_start: 0.8421 (mp0) cc_final: 0.8018 (mp0) REVERT: A 745 ASP cc_start: 0.8357 (t0) cc_final: 0.8031 (t0) REVERT: A 855 PHE cc_start: 0.8444 (m-10) cc_final: 0.8171 (m-80) REVERT: A 988 GLU cc_start: 0.8770 (mp0) cc_final: 0.8293 (mp0) REVERT: B 153 MET cc_start: 0.6527 (pmm) cc_final: 0.6155 (pmm) REVERT: B 224 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7732 (pp20) REVERT: B 242 LEU cc_start: 0.9138 (mm) cc_final: 0.8876 (mp) REVERT: B 855 PHE cc_start: 0.8635 (m-10) cc_final: 0.8289 (m-80) REVERT: C 153 MET cc_start: 0.7776 (pmm) cc_final: 0.7517 (ppp) REVERT: C 177 MET cc_start: 0.4234 (ptt) cc_final: 0.0914 (mtt) REVERT: C 200 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.8008 (t80) REVERT: C 855 PHE cc_start: 0.8378 (m-80) cc_final: 0.7971 (m-80) REVERT: C 1138 TYR cc_start: 0.8857 (t80) cc_final: 0.8190 (t80) outliers start: 36 outliers final: 21 residues processed: 128 average time/residue: 0.5290 time to fit residues: 81.7611 Evaluate side-chains 117 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 296 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 291 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN C 388 ASN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.107425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061872 restraints weight = 59700.505| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.89 r_work: 0.2738 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 26668 Z= 0.204 Angle : 0.668 16.374 36381 Z= 0.331 Chirality : 0.049 0.740 4217 Planarity : 0.004 0.040 4634 Dihedral : 6.947 107.501 4369 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.16 % Allowed : 8.33 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3218 helix: 1.87 (0.21), residues: 684 sheet: 0.45 (0.19), residues: 640 loop : -1.80 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.019 0.001 TYR B 265 PHE 0.017 0.001 PHE C1121 TRP 0.020 0.001 TRP C 886 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00486 (26586) covalent geometry : angle 0.63709 (36177) SS BOND : bond 0.00439 ( 42) SS BOND : angle 1.57434 ( 84) hydrogen bonds : bond 0.07943 ( 1001) hydrogen bonds : angle 5.20140 ( 2739) link_BETA1-4 : bond 0.00480 ( 9) link_BETA1-4 : angle 1.59102 ( 27) link_NAG-ASN : bond 0.00410 ( 31) link_NAG-ASN : angle 3.71928 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6639 (pmm) cc_final: 0.6309 (pmm) REVERT: A 177 MET cc_start: 0.2342 (ptp) cc_final: 0.0468 (mtt) REVERT: A 619 GLU cc_start: 0.8590 (mp0) cc_final: 0.8087 (mp0) REVERT: A 855 PHE cc_start: 0.8491 (m-10) cc_final: 0.8225 (m-80) REVERT: A 988 GLU cc_start: 0.8836 (mp0) cc_final: 0.8355 (mp0) REVERT: B 153 MET cc_start: 0.6736 (pmm) cc_final: 0.6359 (pmm) REVERT: B 224 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7744 (pp20) REVERT: B 242 LEU cc_start: 0.9157 (mm) cc_final: 0.8930 (mp) REVERT: B 855 PHE cc_start: 0.8627 (m-10) cc_final: 0.8284 (m-80) REVERT: C 140 PHE cc_start: 0.9253 (p90) cc_final: 0.8894 (p90) REVERT: C 153 MET cc_start: 0.7882 (pmm) cc_final: 0.7556 (ppp) REVERT: C 177 MET cc_start: 0.4285 (ptt) cc_final: 0.1703 (mpt) REVERT: C 200 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.8031 (t80) REVERT: C 258 TRP cc_start: 0.5348 (OUTLIER) cc_final: 0.3617 (p-90) REVERT: C 855 PHE cc_start: 0.8429 (m-80) cc_final: 0.7976 (m-80) outliers start: 33 outliers final: 21 residues processed: 126 average time/residue: 0.5735 time to fit residues: 85.9460 Evaluate side-chains 117 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 187 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 35 optimal weight: 0.0040 chunk 273 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 161 optimal weight: 0.4980 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.107506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061966 restraints weight = 59766.522| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.89 r_work: 0.2741 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 26668 Z= 0.208 Angle : 0.881 59.200 36381 Z= 0.488 Chirality : 0.049 0.740 4217 Planarity : 0.004 0.049 4634 Dihedral : 6.948 107.463 4369 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.06 % Allowed : 8.54 % Favored : 90.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3218 helix: 1.86 (0.21), residues: 684 sheet: 0.43 (0.19), residues: 641 loop : -1.79 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 408 TYR 0.019 0.001 TYR B 265 PHE 0.016 0.001 PHE C1121 TRP 0.017 0.001 TRP C 886 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00477 (26586) covalent geometry : angle 0.85882 (36177) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.55170 ( 84) hydrogen bonds : bond 0.07854 ( 1001) hydrogen bonds : angle 5.19859 ( 2739) link_BETA1-4 : bond 0.00565 ( 9) link_BETA1-4 : angle 1.69817 ( 27) link_NAG-ASN : bond 0.00409 ( 31) link_NAG-ASN : angle 3.71531 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6638 (pmm) cc_final: 0.6305 (pmm) REVERT: A 177 MET cc_start: 0.2338 (ptp) cc_final: 0.0467 (mtt) REVERT: A 515 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8064 (p90) REVERT: A 619 GLU cc_start: 0.8591 (mp0) cc_final: 0.8088 (mp0) REVERT: A 855 PHE cc_start: 0.8487 (m-10) cc_final: 0.8232 (m-80) REVERT: A 988 GLU cc_start: 0.8839 (mp0) cc_final: 0.8358 (mp0) REVERT: B 153 MET cc_start: 0.6727 (pmm) cc_final: 0.6345 (pmm) REVERT: B 224 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7798 (pp20) REVERT: B 242 LEU cc_start: 0.9233 (mm) cc_final: 0.8938 (mp) REVERT: B 855 PHE cc_start: 0.8624 (m-10) cc_final: 0.8282 (m-80) REVERT: C 140 PHE cc_start: 0.9250 (p90) cc_final: 0.8895 (p90) REVERT: C 153 MET cc_start: 0.7880 (pmm) cc_final: 0.7553 (ppp) REVERT: C 177 MET cc_start: 0.4281 (ptt) cc_final: 0.1703 (mpt) REVERT: C 200 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.8030 (t80) REVERT: C 258 TRP cc_start: 0.5318 (OUTLIER) cc_final: 0.3606 (p-90) REVERT: C 855 PHE cc_start: 0.8429 (m-80) cc_final: 0.7971 (m-80) outliers start: 30 outliers final: 23 residues processed: 117 average time/residue: 0.5731 time to fit residues: 79.6198 Evaluate side-chains 118 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 8.9990 chunk 319 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 263 optimal weight: 10.0000 chunk 320 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.107572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.062248 restraints weight = 59861.972| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.87 r_work: 0.2746 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 26668 Z= 0.208 Angle : 0.881 59.200 36381 Z= 0.488 Chirality : 0.049 0.740 4217 Planarity : 0.004 0.049 4634 Dihedral : 6.948 107.463 4369 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.95 % Allowed : 8.65 % Favored : 90.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3218 helix: 1.86 (0.21), residues: 684 sheet: 0.43 (0.19), residues: 641 loop : -1.79 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 408 TYR 0.019 0.001 TYR B 265 PHE 0.016 0.001 PHE C1121 TRP 0.017 0.001 TRP C 886 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00477 (26586) covalent geometry : angle 0.85882 (36177) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.55170 ( 84) hydrogen bonds : bond 0.07854 ( 1001) hydrogen bonds : angle 5.19859 ( 2739) link_BETA1-4 : bond 0.00565 ( 9) link_BETA1-4 : angle 1.69817 ( 27) link_NAG-ASN : bond 0.00409 ( 31) link_NAG-ASN : angle 3.71531 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7669.94 seconds wall clock time: 131 minutes 21.97 seconds (7881.97 seconds total)