Starting phenix.real_space_refine on Sun Jul 5 07:02:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tgy_25889/07_2026/7tgy_25889.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tgy_25889/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tgy_25889/07_2026/7tgy_25889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tgy_25889/07_2026/7tgy_25889.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tgy_25889/07_2026/7tgy_25889.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tgy_25889/07_2026/7tgy_25889.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tgy_25889/07_2026/7tgy_25889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tgy_25889/07_2026/7tgy_25889.cif" } 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-6108/lib/python3.11/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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 5.99, per 1000 atoms: 0.23 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: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.71 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: 5.19 Time building geometry restraints manager: 2.93 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 - 17.83: 14363 17.83 - 35.67: 935 35.67 - 53.50: 140 53.50 - 71.34: 47 71.34 - 89.17: 19 Dihedral angle restraints: 15504 sinusoidal: 6039 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 15501 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: 0.000 Normalize map: mean=0, sd=1: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.880 Find NCS groups from input model: 0.760 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:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 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 : 12.587 89.172 9290 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/Z covalent geometry : bond 0.01047 / 0.44 (26586) covalent geometry : angle 0.86882 / 0.49 (36177) SS BOND : bond 0.00654 / 0.41 ( 42) SS BOND : angle 2.73375 / 2.01 ( 84) hydrogen bonds : bond 0.15018 / 10.25 ( 1001) hydrogen bonds : angle 7.04507 / 4.93 ( 2739) link_BETA1-4 : bond 0.00821 / 0.58 ( 9) link_BETA1-4 : angle 2.87968 / 1.62 ( 27) link_NAG-ASN : bond 0.00651 / 0.39 ( 31) link_NAG-ASN : angle 4.58171 / 3.11 ( 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 : 0.935 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: 0.6459 time to fit residues: 111.7160 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 : 0.836 ------------------------------------------------------------------------------- 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... 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 = 0.3861 r_free = 0.3861 target = 0.111526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066348 restraints weight = 59999.249| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.86 r_work: 0.2838 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26668 Z= 0.144 Angle : 0.694 17.704 36381 Z= 0.350 Chirality : 0.050 0.712 4217 Planarity : 0.005 0.062 4634 Dihedral : 5.358 52.445 3487 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.71 % Allowed : 4.16 % Favored : 95.13 % 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: 0.75 (0.20), residues: 681 sheet: -0.17 (0.19), residues: 667 loop : -2.36 (0.12), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 408 TYR 0.020 0.001 TYR A 473 PHE 0.032 0.001 PHE B 157 TRP 0.017 0.001 TRP C 152 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (26586) covalent geometry : angle 0.65955 / 0.34 (36177) SS BOND : bond 0.00362 / 0.27 ( 42) SS BOND : angle 1.56974 / 1.09 ( 84) hydrogen bonds : bond 0.07435 / 5.03 ( 1001) hydrogen bonds : angle 5.69922 / 3.97 ( 2739) link_BETA1-4 : bond 0.00854 / 0.46 ( 9) link_BETA1-4 : angle 1.66961 / 0.96 ( 27) link_NAG-ASN : bond 0.00526 / 0.35 ( 31) link_NAG-ASN : angle 4.02791 / 2.61 ( 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: 20 poor density : 128 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5653 (pmm) cc_final: 0.5313 (pmm) REVERT: A 177 MET cc_start: 0.2125 (ptp) cc_final: 0.0179 (mtt) REVERT: A 515 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7767 (p90) REVERT: A 636 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6586 (t80) REVERT: A 855 PHE cc_start: 0.8552 (m-80) cc_final: 0.8214 (m-80) REVERT: B 153 MET cc_start: 0.6688 (pmm) cc_final: 0.6218 (pmm) REVERT: B 855 PHE cc_start: 0.8702 (m-10) cc_final: 0.8365 (m-80) REVERT: C 153 MET cc_start: 0.7596 (pmm) cc_final: 0.7182 (ppp) REVERT: C 258 TRP cc_start: 0.5804 (p-90) cc_final: 0.2573 (m100) REVERT: C 408 ARG cc_start: 0.8470 (tmm-80) cc_final: 0.8236 (tmm-80) REVERT: C 1138 TYR cc_start: 0.8841 (t80) cc_final: 0.8503 (t80) outliers start: 20 outliers final: 5 residues processed: 142 average time/residue: 0.5953 time to fit residues: 100.2343 Evaluate side-chains 94 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 A residue 1098 ASN 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: 3.9990 chunk 68 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 323 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 914 ASN B 196 ASN B 414 GLN B 907 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.109624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064166 restraints weight = 60427.844| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.86 r_work: 0.2796 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26668 Z= 0.181 Angle : 0.663 16.483 36381 Z= 0.333 Chirality : 0.049 0.637 4217 Planarity : 0.004 0.053 4634 Dihedral : 5.049 53.630 3487 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.09 % Allowed : 5.65 % Favored : 93.26 % 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: -1.34 (0.14), residues: 3218 helix: 1.29 (0.21), residues: 679 sheet: 0.07 (0.19), residues: 652 loop : -2.21 (0.12), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.019 0.001 TYR B1067 PHE 0.020 0.002 PHE A 906 TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (26586) covalent geometry : angle 0.63088 / 0.32 (36177) SS BOND : bond 0.00563 / 0.33 ( 42) SS BOND : angle 1.62826 / 1.15 ( 84) hydrogen bonds : bond 0.07644 / 5.20 ( 1001) hydrogen bonds : angle 5.46325 / 3.80 ( 2739) link_BETA1-4 : bond 0.00567 / 0.29 ( 9) link_BETA1-4 : angle 1.56140 / 0.91 ( 27) link_NAG-ASN : bond 0.00418 / 0.29 ( 31) link_NAG-ASN : angle 3.77412 / 2.41 ( 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 130 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5825 (pmm) cc_final: 0.5545 (pmm) REVERT: A 177 MET cc_start: 0.1997 (ptp) cc_final: 0.0112 (mtt) REVERT: A 242 LEU cc_start: 0.9296 (tp) cc_final: 0.9039 (tm) REVERT: A 455 LEU cc_start: 0.8881 (mt) cc_final: 0.8651 (mp) REVERT: A 515 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8010 (p90) REVERT: A 855 PHE cc_start: 0.8468 (m-80) cc_final: 0.8107 (m-80) REVERT: B 200 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7865 (t80) REVERT: B 515 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8072 (p90) REVERT: B 855 PHE cc_start: 0.8608 (m-10) cc_final: 0.8223 (m-80) REVERT: C 153 MET cc_start: 0.7647 (pmm) cc_final: 0.7293 (ppp) REVERT: C 177 MET cc_start: 0.3869 (ptt) cc_final: 0.0435 (mtt) REVERT: C 190 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7499 (mmt180) REVERT: C 200 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8066 (t80) REVERT: C 258 TRP cc_start: 0.5628 (p-90) cc_final: 0.2568 (m100) REVERT: C 855 PHE cc_start: 0.8439 (m-10) cc_final: 0.8176 (m-10) outliers start: 31 outliers final: 9 residues processed: 126 average time/residue: 0.5892 time to fit residues: 88.1775 Evaluate side-chains 98 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE 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 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 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: 0.8980 chunk 121 optimal weight: 7.9990 chunk 297 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 22 optimal weight: 0.0770 chunk 166 optimal weight: 2.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 218 GLN A1101 HIS B 196 ASN B 965 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.109099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063790 restraints weight = 59529.830| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.90 r_work: 0.2740 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26668 Z= 0.162 Angle : 0.634 15.719 36381 Z= 0.317 Chirality : 0.048 0.593 4217 Planarity : 0.004 0.047 4634 Dihedral : 4.866 53.300 3487 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.16 % Allowed : 6.35 % Favored : 92.48 % 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: -1.13 (0.14), residues: 3218 helix: 1.55 (0.21), residues: 678 sheet: 0.14 (0.19), residues: 652 loop : -2.09 (0.12), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.017 0.001 TYR A 473 PHE 0.015 0.001 PHE C 79 TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (26586) covalent geometry : angle 0.60408 / 0.31 (36177) SS BOND : bond 0.00397 / 0.26 ( 42) SS BOND : angle 1.43687 / 1.00 ( 84) hydrogen bonds : bond 0.07195 / 4.89 ( 1001) hydrogen bonds : angle 5.30420 / 3.69 ( 2739) link_BETA1-4 : bond 0.00559 / 0.29 ( 9) link_BETA1-4 : angle 1.48774 / 0.88 ( 27) link_NAG-ASN : bond 0.00419 / 0.30 ( 31) link_NAG-ASN : angle 3.57363 / 2.27 ( 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: 33 poor density : 96 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5917 (pmm) cc_final: 0.5629 (pmm) REVERT: A 177 MET cc_start: 0.2080 (ptp) cc_final: 0.0214 (mtt) REVERT: A 242 LEU cc_start: 0.9320 (tp) cc_final: 0.9079 (tm) REVERT: A 455 LEU cc_start: 0.8838 (mt) cc_final: 0.8633 (mp) REVERT: A 515 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7941 (p90) REVERT: A 855 PHE cc_start: 0.8518 (m-10) cc_final: 0.8159 (m-80) REVERT: B 153 MET cc_start: 0.6572 (pmm) cc_final: 0.6254 (pmm) REVERT: B 200 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7860 (t80) REVERT: B 224 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7689 (pp20) REVERT: B 515 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8076 (p90) REVERT: B 855 PHE cc_start: 0.8653 (m-10) cc_final: 0.8251 (m-80) REVERT: C 153 MET cc_start: 0.7707 (pmm) cc_final: 0.7240 (ppp) REVERT: C 177 MET cc_start: 0.4136 (ptt) cc_final: 0.0721 (mtt) REVERT: C 200 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.8035 (t80) REVERT: C 258 TRP cc_start: 0.5515 (p-90) cc_final: 0.2571 (m100) REVERT: C 855 PHE cc_start: 0.8456 (m-10) cc_final: 0.8128 (m-10) REVERT: C 1138 TYR cc_start: 0.8830 (t80) cc_final: 0.8224 (t80) outliers start: 33 outliers final: 10 residues processed: 122 average time/residue: 0.6167 time to fit residues: 88.9981 Evaluate side-chains 103 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 1098 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 200 TYR 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 1098 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 231 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 168 optimal weight: 0.0470 chunk 292 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 414 GLN B 196 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** 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 = 0.3832 r_free = 0.3832 target = 0.109660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064654 restraints weight = 59595.073| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.89 r_work: 0.2761 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26668 Z= 0.140 Angle : 0.602 14.866 36381 Z= 0.300 Chirality : 0.047 0.536 4217 Planarity : 0.004 0.043 4634 Dihedral : 4.633 52.980 3487 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.48 % Allowed : 6.88 % Favored : 91.64 % 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: -0.91 (0.14), residues: 3218 helix: 1.83 (0.21), residues: 677 sheet: 0.25 (0.19), residues: 653 loop : -1.97 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.016 0.001 TYR C 473 PHE 0.013 0.001 PHE C 79 TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (26586) covalent geometry : angle 0.57412 / 0.29 (36177) SS BOND : bond 0.00359 / 0.24 ( 42) SS BOND : angle 1.32416 / 0.92 ( 84) hydrogen bonds : bond 0.06559 / 4.45 ( 1001) hydrogen bonds : angle 5.11545 / 3.56 ( 2739) link_BETA1-4 : bond 0.00569 / 0.31 ( 9) link_BETA1-4 : angle 1.43014 / 0.84 ( 27) link_NAG-ASN : bond 0.00419 / 0.30 ( 31) link_NAG-ASN : angle 3.34055 / 2.11 ( 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 141 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6234 (pmm) cc_final: 0.5935 (pmm) REVERT: A 177 MET cc_start: 0.2108 (ptp) cc_final: 0.0230 (mtt) REVERT: A 515 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.7930 (p90) REVERT: A 855 PHE cc_start: 0.8447 (m-10) cc_final: 0.8122 (m-80) REVERT: A 988 GLU cc_start: 0.8720 (mp0) cc_final: 0.8341 (mp0) REVERT: B 153 MET cc_start: 0.6585 (pmm) cc_final: 0.6171 (pmm) REVERT: B 200 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7911 (t80) REVERT: B 224 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7772 (pp20) REVERT: B 661 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: B 855 PHE cc_start: 0.8637 (m-10) cc_final: 0.8235 (m-80) REVERT: C 153 MET cc_start: 0.7690 (pmm) cc_final: 0.7356 (ppp) REVERT: C 177 MET cc_start: 0.4273 (ptt) cc_final: 0.0865 (mtt) REVERT: C 190 ARG cc_start: 0.7615 (mmt180) cc_final: 0.7248 (mmt180) REVERT: C 200 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.8044 (t80) REVERT: C 258 TRP cc_start: 0.5452 (p-90) cc_final: 0.2545 (m100) REVERT: C 855 PHE cc_start: 0.8462 (m-10) cc_final: 0.8101 (m-80) REVERT: C 1138 TYR cc_start: 0.8844 (t80) cc_final: 0.8198 (t80) outliers start: 42 outliers final: 16 residues processed: 133 average time/residue: 0.5132 time to fit residues: 82.7221 Evaluate side-chains 111 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 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 1098 ASN 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 661 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET 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 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: 0.8980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 110 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 58 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 196 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.109481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065938 restraints weight = 58825.445| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.81 r_work: 0.2778 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26668 Z= 0.126 Angle : 0.604 14.424 36381 Z= 0.299 Chirality : 0.047 0.512 4217 Planarity : 0.004 0.041 4634 Dihedral : 4.528 52.952 3487 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.38 % Allowed : 7.13 % Favored : 91.50 % 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: -0.76 (0.14), residues: 3218 helix: 1.97 (0.21), residues: 678 sheet: 0.35 (0.19), residues: 654 loop : -1.88 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.017 0.001 TYR C 473 PHE 0.014 0.001 PHE C 79 TRP 0.009 0.001 TRP C 886 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (26586) covalent geometry : angle 0.57807 / 0.29 (36177) SS BOND : bond 0.00427 / 0.26 ( 42) SS BOND : angle 1.44641 / 0.96 ( 84) hydrogen bonds : bond 0.06224 / 4.22 ( 1001) hydrogen bonds : angle 5.03471 / 3.51 ( 2739) link_BETA1-4 : bond 0.00599 / 0.32 ( 9) link_BETA1-4 : angle 1.38728 / 0.80 ( 27) link_NAG-ASN : bond 0.00433 / 0.31 ( 31) link_NAG-ASN : angle 3.21549 / 2.03 ( 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 138 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6387 (pmm) cc_final: 0.6083 (pmm) REVERT: A 177 MET cc_start: 0.2175 (ptp) cc_final: 0.0295 (mtt) REVERT: A 242 LEU cc_start: 0.9259 (tp) cc_final: 0.9001 (tm) REVERT: A 515 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.7986 (p90) REVERT: A 745 ASP cc_start: 0.8208 (t0) cc_final: 0.7840 (t0) REVERT: A 855 PHE cc_start: 0.8435 (m-10) cc_final: 0.8145 (m-80) REVERT: A 988 GLU cc_start: 0.8732 (mp0) cc_final: 0.8324 (mp0) REVERT: B 153 MET cc_start: 0.6623 (pmm) cc_final: 0.6315 (pmm) REVERT: B 200 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7898 (t80) REVERT: B 224 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7753 (pp20) REVERT: B 515 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8027 (p90) REVERT: B 855 PHE cc_start: 0.8647 (m-10) cc_final: 0.8282 (m-80) REVERT: C 153 MET cc_start: 0.7685 (pmm) cc_final: 0.7417 (ppp) REVERT: C 177 MET cc_start: 0.4107 (ptt) cc_final: 0.0863 (mtt) REVERT: C 258 TRP cc_start: 0.5446 (p-90) cc_final: 0.2585 (m100) REVERT: C 855 PHE cc_start: 0.8476 (m-10) cc_final: 0.8083 (m-80) REVERT: C 1138 TYR cc_start: 0.8843 (t80) cc_final: 0.8191 (t80) outliers start: 39 outliers final: 19 residues processed: 130 average time/residue: 0.5594 time to fit residues: 87.2598 Evaluate side-chains 116 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 878 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 200 TYR 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 878 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 410 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 116 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 310 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 242 optimal weight: 0.8980 chunk 259 optimal weight: 0.0070 chunk 106 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 196 ASN B 519 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** 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 = 0.3892 r_free = 0.3892 target = 0.110274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066959 restraints weight = 58521.955| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.79 r_work: 0.2802 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2548 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= 0.112 Angle : 0.585 13.805 36381 Z= 0.289 Chirality : 0.046 0.485 4217 Planarity : 0.004 0.039 4634 Dihedral : 4.382 52.419 3487 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.24 % Allowed : 7.45 % Favored : 91.32 % 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: 2.05 (0.21), residues: 685 sheet: 0.46 (0.19), residues: 650 loop : -1.79 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.017 0.001 TYR C 473 PHE 0.022 0.001 PHE C 456 TRP 0.008 0.001 TRP C 633 HIS 0.002 0.000 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (26586) covalent geometry : angle 0.56184 / 0.28 (36177) SS BOND : bond 0.00384 / 0.23 ( 42) SS BOND : angle 1.15928 / 0.79 ( 84) hydrogen bonds : bond 0.05715 / 3.88 ( 1001) hydrogen bonds : angle 4.91030 / 3.41 ( 2739) link_BETA1-4 : bond 0.00572 / 0.31 ( 9) link_BETA1-4 : angle 1.34439 / 0.78 ( 27) link_NAG-ASN : bond 0.00452 / 0.32 ( 31) link_NAG-ASN : angle 3.06614 / 1.93 ( 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 141 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6392 (pmm) cc_final: 0.6083 (pmm) REVERT: A 177 MET cc_start: 0.2227 (ptp) cc_final: 0.0407 (mtt) REVERT: A 242 LEU cc_start: 0.9177 (tp) cc_final: 0.8947 (tm) REVERT: A 515 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7889 (p90) REVERT: A 745 ASP cc_start: 0.8166 (t0) cc_final: 0.7812 (t0) REVERT: A 855 PHE cc_start: 0.8383 (m-10) cc_final: 0.8100 (m-80) REVERT: A 988 GLU cc_start: 0.8754 (mp0) cc_final: 0.8304 (mp0) REVERT: B 153 MET cc_start: 0.6610 (pmm) cc_final: 0.6268 (pmm) REVERT: B 224 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7709 (pp20) REVERT: B 242 LEU cc_start: 0.9107 (mm) cc_final: 0.8742 (mp) REVERT: B 855 PHE cc_start: 0.8608 (m-10) cc_final: 0.8271 (m-80) REVERT: C 18 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5159 (mm) REVERT: C 153 MET cc_start: 0.7676 (pmm) cc_final: 0.7398 (ppp) REVERT: C 177 MET cc_start: 0.4108 (ptt) cc_final: 0.0826 (mtt) REVERT: C 258 TRP cc_start: 0.5377 (p-90) cc_final: 0.2843 (m100) REVERT: C 855 PHE cc_start: 0.8513 (m-10) cc_final: 0.8136 (m-80) REVERT: C 1138 TYR cc_start: 0.8852 (t80) cc_final: 0.8181 (t80) outliers start: 35 outliers final: 14 residues processed: 135 average time/residue: 0.4928 time to fit residues: 80.9133 Evaluate side-chains 115 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 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 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 1098 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 50 optimal weight: 8.9990 chunk 289 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 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: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 914 ASN B 196 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.108979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063892 restraints weight = 59885.680| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.88 r_work: 0.2784 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26668 Z= 0.157 Angle : 0.616 14.200 36381 Z= 0.307 Chirality : 0.047 0.483 4217 Planarity : 0.004 0.040 4634 Dihedral : 4.443 51.922 3487 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.20 % Allowed : 8.05 % Favored : 90.76 % 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: -0.63 (0.14), residues: 3218 helix: 1.99 (0.21), residues: 687 sheet: 0.46 (0.19), residues: 643 loop : -1.78 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.018 0.001 TYR B1067 PHE 0.015 0.001 PHE B1121 TRP 0.013 0.001 TRP A 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (26586) covalent geometry : angle 0.59258 / 0.30 (36177) SS BOND : bond 0.00377 / 0.24 ( 42) SS BOND : angle 1.36759 / 0.94 ( 84) hydrogen bonds : bond 0.06784 / 4.61 ( 1001) hydrogen bonds : angle 4.99807 / 3.47 ( 2739) link_BETA1-4 : bond 0.00571 / 0.34 ( 9) link_BETA1-4 : angle 1.39904 / 0.82 ( 27) link_NAG-ASN : bond 0.00391 / 0.28 ( 31) link_NAG-ASN : angle 3.11620 / 1.96 ( 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 132 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6471 (pmm) cc_final: 0.6146 (pmm) REVERT: A 177 MET cc_start: 0.2217 (ptp) cc_final: 0.0382 (mtt) REVERT: A 515 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8049 (p90) REVERT: A 745 ASP cc_start: 0.8299 (t0) cc_final: 0.7982 (t0) REVERT: A 855 PHE cc_start: 0.8411 (m-10) cc_final: 0.8152 (m-80) REVERT: A 988 GLU cc_start: 0.8807 (mp0) cc_final: 0.8333 (mp0) REVERT: B 153 MET cc_start: 0.6646 (pmm) cc_final: 0.6288 (pmm) REVERT: B 224 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7737 (pp20) REVERT: B 242 LEU cc_start: 0.9176 (mm) cc_final: 0.8837 (mp) REVERT: B 408 ARG cc_start: 0.8914 (ppt170) cc_final: 0.8632 (ppt90) REVERT: B 515 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8148 (p90) REVERT: B 661 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: B 855 PHE cc_start: 0.8625 (m-10) cc_final: 0.8276 (m-80) REVERT: C 153 MET cc_start: 0.7742 (pmm) cc_final: 0.7468 (ppp) REVERT: C 177 MET cc_start: 0.4132 (ptt) cc_final: 0.0846 (mtt) REVERT: C 200 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: C 408 ARG cc_start: 0.8343 (tmm-80) cc_final: 0.8125 (ppt90) REVERT: C 414 GLN cc_start: 0.7808 (tp40) cc_final: 0.7544 (tp40) REVERT: C 855 PHE cc_start: 0.8539 (m-10) cc_final: 0.8173 (m-80) REVERT: C 1138 TYR cc_start: 0.8873 (t80) cc_final: 0.8219 (t80) outliers start: 34 outliers final: 20 residues processed: 126 average time/residue: 0.5851 time to fit residues: 88.0940 Evaluate side-chains 120 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 B residue 196 ASN Chi-restraints excluded: chain B residue 200 TYR 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 661 GLU 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: 1.9990 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 296 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 0.0030 chunk 224 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.109318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.066058 restraints weight = 58371.699| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.76 r_work: 0.2780 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2663 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= 0.121 Angle : 0.591 13.599 36381 Z= 0.294 Chirality : 0.046 0.471 4217 Planarity : 0.004 0.069 4634 Dihedral : 4.349 51.883 3487 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.95 % Allowed : 8.43 % 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: -0.51 (0.14), residues: 3218 helix: 2.09 (0.21), residues: 686 sheet: 0.54 (0.19), residues: 642 loop : -1.70 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 408 TYR 0.017 0.001 TYR C 473 PHE 0.026 0.001 PHE C 456 TRP 0.010 0.001 TRP C 886 HIS 0.002 0.000 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (26586) covalent geometry : angle 0.56899 / 0.29 (36177) SS BOND : bond 0.00345 / 0.22 ( 42) SS BOND : angle 1.20008 / 0.82 ( 84) hydrogen bonds : bond 0.06125 / 4.16 ( 1001) hydrogen bonds : angle 4.89319 / 3.39 ( 2739) link_BETA1-4 : bond 0.00543 / 0.29 ( 9) link_BETA1-4 : angle 1.32967 / 0.78 ( 27) link_NAG-ASN : bond 0.00449 / 0.31 ( 31) link_NAG-ASN : angle 2.99924 / 1.88 ( 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 126 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6495 (pmm) cc_final: 0.6143 (pmm) REVERT: A 177 MET cc_start: 0.2237 (ptp) cc_final: 0.0437 (mtt) REVERT: A 515 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8007 (p90) REVERT: A 619 GLU cc_start: 0.8389 (mp0) cc_final: 0.7881 (mp0) REVERT: A 745 ASP cc_start: 0.8301 (t0) cc_final: 0.7983 (t0) REVERT: A 855 PHE cc_start: 0.8422 (m-10) cc_final: 0.8143 (m-80) REVERT: A 988 GLU cc_start: 0.8759 (mp0) cc_final: 0.8266 (mp0) REVERT: B 224 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7693 (pp20) REVERT: B 242 LEU cc_start: 0.9192 (mm) cc_final: 0.8870 (mp) REVERT: B 408 ARG cc_start: 0.8911 (ppt170) cc_final: 0.8626 (ppt90) REVERT: B 661 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: B 855 PHE cc_start: 0.8631 (m-10) cc_final: 0.8301 (m-80) REVERT: C 153 MET cc_start: 0.7731 (pmm) cc_final: 0.7386 (ppp) REVERT: C 177 MET cc_start: 0.4161 (ptt) cc_final: 0.0890 (mtt) REVERT: C 200 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: C 309 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7578 (tm-30) REVERT: C 414 GLN cc_start: 0.7855 (tp40) cc_final: 0.7650 (tp40) REVERT: C 780 GLU cc_start: 0.8673 (tt0) cc_final: 0.8424 (tt0) REVERT: C 855 PHE cc_start: 0.8558 (m-10) cc_final: 0.8211 (m-80) REVERT: C 1138 TYR cc_start: 0.8860 (t80) cc_final: 0.8190 (t80) outliers start: 27 outliers final: 19 residues processed: 120 average time/residue: 0.6237 time to fit residues: 88.9807 Evaluate side-chains 121 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 515 PHE Chi-restraints excluded: chain A residue 517 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 878 LEU 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 661 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 187 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 196 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.108378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063165 restraints weight = 59898.989| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.87 r_work: 0.2774 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26668 Z= 0.171 Angle : 0.622 13.996 36381 Z= 0.310 Chirality : 0.047 0.472 4217 Planarity : 0.004 0.041 4634 Dihedral : 4.419 51.258 3487 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.92 % Allowed : 8.75 % Favored : 90.33 % 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: -0.57 (0.14), residues: 3218 helix: 1.99 (0.21), residues: 685 sheet: 0.50 (0.19), residues: 645 loop : -1.72 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 408 TYR 0.018 0.001 TYR B1067 PHE 0.015 0.001 PHE C1121 TRP 0.015 0.001 TRP C 886 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (26586) covalent geometry : angle 0.59913 / 0.30 (36177) SS BOND : bond 0.00377 / 0.24 ( 42) SS BOND : angle 1.38490 / 0.96 ( 84) hydrogen bonds : bond 0.07085 / 4.82 ( 1001) hydrogen bonds : angle 5.00624 / 3.47 ( 2739) link_BETA1-4 : bond 0.00425 / 0.26 ( 9) link_BETA1-4 : angle 1.40297 / 0.84 ( 27) link_NAG-ASN : bond 0.00381 / 0.27 ( 31) link_NAG-ASN : angle 3.09858 / 1.94 ( 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 127 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6579 (pmm) cc_final: 0.6159 (pmm) REVERT: A 177 MET cc_start: 0.2269 (ptp) cc_final: 0.0469 (mtt) REVERT: A 515 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8096 (p90) REVERT: A 619 GLU cc_start: 0.8517 (mp0) cc_final: 0.8014 (mp0) REVERT: A 745 ASP cc_start: 0.8444 (t0) cc_final: 0.8179 (t0) REVERT: A 855 PHE cc_start: 0.8446 (m-10) cc_final: 0.8186 (m-80) REVERT: A 988 GLU cc_start: 0.8824 (mp0) cc_final: 0.8329 (mp0) REVERT: B 153 MET cc_start: 0.6748 (pmm) cc_final: 0.6386 (pmm) REVERT: B 224 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7789 (pp20) REVERT: B 242 LEU cc_start: 0.9198 (mm) cc_final: 0.8876 (mp) REVERT: B 408 ARG cc_start: 0.8939 (ppt170) cc_final: 0.8734 (ppt170) REVERT: B 661 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: B 855 PHE cc_start: 0.8612 (m-10) cc_final: 0.8273 (m-80) REVERT: C 153 MET cc_start: 0.7824 (pmm) cc_final: 0.7477 (ppp) REVERT: C 177 MET cc_start: 0.4198 (ptt) cc_final: 0.0902 (mtt) REVERT: C 200 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: C 414 GLN cc_start: 0.7871 (tp40) cc_final: 0.7472 (tp40) REVERT: C 855 PHE cc_start: 0.8554 (m-10) cc_final: 0.8191 (m-80) REVERT: C 1138 TYR cc_start: 0.8913 (t80) cc_final: 0.8288 (t80) outliers start: 26 outliers final: 20 residues processed: 121 average time/residue: 0.5948 time to fit residues: 85.5631 Evaluate side-chains 118 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 878 LEU Chi-restraints excluded: chain B residue 196 ASN 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 661 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 0.1980 chunk 319 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 231 optimal weight: 0.3980 chunk 240 optimal weight: 1.9990 chunk 192 optimal weight: 0.0570 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.108803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063594 restraints weight = 59593.261| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.87 r_work: 0.2785 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 26668 Z= 0.155 Angle : 0.766 59.189 36381 Z= 0.409 Chirality : 0.048 0.714 4217 Planarity : 0.005 0.157 4634 Dihedral : 4.473 51.582 3487 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.25 % Rotamer: Outliers : 0.92 % Allowed : 8.75 % Favored : 90.33 % Cbeta Deviations : 0.03 % 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: -0.56 (0.14), residues: 3218 helix: 2.00 (0.21), residues: 685 sheet: 0.48 (0.19), residues: 645 loop : -1.70 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG C 408 TYR 0.018 0.001 TYR B1067 PHE 0.014 0.001 PHE C 79 TRP 0.012 0.001 TRP C 886 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (26586) covalent geometry : angle 0.74828 / 0.41 (36177) SS BOND : bond 0.00382 / 0.25 ( 42) SS BOND : angle 1.33217 / 0.91 ( 84) hydrogen bonds : bond 0.06982 / 4.70 ( 1001) hydrogen bonds : angle 4.99788 / 3.46 ( 2739) link_BETA1-4 : bond 0.00408 / 0.24 ( 9) link_BETA1-4 : angle 1.38673 / 0.81 ( 27) link_NAG-ASN : bond 0.00418 / 0.30 ( 31) link_NAG-ASN : angle 3.08023 / 1.93 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7483.34 seconds wall clock time: 128 minutes 32.30 seconds (7712.30 seconds total)