Starting phenix.real_space_refine on Sun Jun 22 19:15:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tgy_25889/06_2025/7tgy_25889.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tgy_25889/06_2025/7tgy_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_25889/06_2025/7tgy_25889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tgy_25889/06_2025/7tgy_25889.map" model { file = "/net/cci-nas-00/data/ceres_data/7tgy_25889/06_2025/7tgy_25889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tgy_25889/06_2025/7tgy_25889.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25999 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8454 Classifications: {'peptide': 1083} Link IDs: {'PTRANS': 53, 'TRANS': 1029} Chain breaks: 5 Chain: "B" Number of atoms: 8468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8468 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 53, 'TRANS': 1030} Chain breaks: 5 Chain: "C" Number of atoms: 8489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8489 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 54, 'TRANS': 1032} Chain breaks: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.15, per 1000 atoms: 0.66 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: 6.89 Conformation dependent library (CDL) restraints added in 3.7 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: 4.38 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: 12.19 Time building geometry restraints manager: 8.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8241 1.34 - 1.46: 6567 1.46 - 1.59: 11631 1.59 - 1.71: 0 1.71 - 1.84: 147 Bond restraints: 26586 Sorted by residual: bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.324 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C VAL C 382 " pdb=" N SER C 383 " ideal model delta sigma weight residual 1.335 1.249 0.085 3.04e-02 1.08e+03 7.84e+00 bond pdb=" C1 NAG X 1 " pdb=" C2 NAG X 1 " ideal model delta sigma weight residual 1.532 1.477 0.055 2.00e-02 2.50e+03 7.55e+00 ... (remaining 26581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 34258 1.81 - 3.62: 1701 3.62 - 5.43: 198 5.43 - 7.24: 15 7.24 - 9.05: 5 Bond angle restraints: 36177 Sorted by residual: angle pdb=" C PHE A1121 " pdb=" CA PHE A1121 " pdb=" CB PHE A1121 " ideal model delta sigma weight residual 112.07 103.02 9.05 1.48e+00 4.57e-01 3.74e+01 angle pdb=" CA PHE A1121 " pdb=" C PHE A1121 " pdb=" N VAL A1122 " ideal model delta sigma weight residual 114.59 121.46 -6.87 1.48e+00 4.57e-01 2.16e+01 angle pdb=" N PHE A1121 " pdb=" CA PHE A1121 " pdb=" C PHE A1121 " ideal model delta sigma weight residual 109.71 116.09 -6.38 1.41e+00 5.03e-01 2.05e+01 angle pdb=" N PHE B 906 " pdb=" CA PHE B 906 " pdb=" CB PHE B 906 " ideal model delta sigma weight residual 110.07 115.96 -5.89 1.45e+00 4.76e-01 1.65e+01 angle pdb=" CA CYS A 738 " pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 114.40 122.92 -8.52 2.30e+00 1.89e-01 1.37e+01 ... (remaining 36172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 15566 24.48 - 48.96: 645 48.96 - 73.44: 110 73.44 - 97.92: 36 97.92 - 122.39: 29 Dihedral angle restraints: 16386 sinusoidal: 6921 harmonic: 9465 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 179.29 -86.29 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -4.45 -81.55 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.31 -80.31 1 1.00e+01 1.00e-02 7.98e+01 ... (remaining 16383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 4211 0.285 - 0.569: 4 0.569 - 0.854: 1 0.854 - 1.139: 0 1.139 - 1.423: 1 Chirality restraints: 4217 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.98 -1.42 2.00e-01 2.50e+01 5.06e+01 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.99e+01 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 ... (remaining 4214 not shown) Planarity restraints: 4665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " 0.051 2.00e-02 2.50e+03 4.58e-02 3.68e+01 pdb=" CG PHE B 906 " -0.105 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " -0.045 2.00e-02 2.50e+03 3.86e-02 2.61e+01 pdb=" CG PHE C 906 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.043 2.00e-02 2.50e+03 3.64e-02 2.32e+01 pdb=" CG PHE A 906 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " 0.012 2.00e-02 2.50e+03 ... (remaining 4662 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 160 2.49 - 3.09: 19254 3.09 - 3.69: 34460 3.69 - 4.30: 51509 4.30 - 4.90: 89055 Nonbonded interactions: 194438 Sorted by model distance: nonbonded pdb=" O3 NAG C1307 " pdb=" O7 NAG C1307 " model vdw 1.886 3.040 nonbonded pdb=" O3 NAG A1305 " pdb=" O7 NAG A1305 " model vdw 1.951 3.040 nonbonded pdb=" OG SER B 172 " pdb=" OE1 GLN B 173 " model vdw 2.013 3.040 nonbonded pdb=" O3 NAG e 1 " pdb=" O5 NAG e 2 " model vdw 2.081 3.040 nonbonded pdb=" OG SER A 383 " pdb=" OD2 ASP B 985 " model vdw 2.085 3.040 ... (remaining 194433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 623 or resid 634 through 1146 or resid 1301 thr \ ough 1306)) selection = (chain 'C' and (resid 14 through 623 or resid 634 through 1146 or resid 1301 thr \ ough 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: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 65.360 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.150 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:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.085 26668 Z= 0.444 Angle : 0.910 17.548 36381 Z= 0.501 Chirality : 0.062 1.423 4217 Planarity : 0.006 0.073 4634 Dihedral : 14.874 122.395 10172 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 0.18 % Allowed : 0.25 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.038 0.004 TRP C 152 HIS 0.010 0.002 HIS B1064 PHE 0.105 0.003 PHE B 906 TYR 0.034 0.003 TYR B 266 ARG 0.013 0.001 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 31) link_NAG-ASN : angle 4.58171 ( 93) link_BETA1-4 : bond 0.00821 ( 9) link_BETA1-4 : angle 2.87968 ( 27) hydrogen bonds : bond 0.15018 ( 1001) hydrogen bonds : angle 7.04507 ( 2739) SS BOND : bond 0.00654 ( 42) SS BOND : angle 2.73375 ( 84) covalent geometry : bond 0.01047 (26586) covalent geometry : angle 0.86882 (36177) *********************** 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 : 2.785 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: B 414 GLN cc_start: 0.8287 (mt0) cc_final: 0.8031 (mt0) 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: 1.5392 time to fit residues: 266.4936 Evaluate side-chains 86 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 273 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 388 ASN B 188 ASN B 196 ASN B 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 = 0.3840 r_free = 0.3840 target = 0.110007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.064600 restraints weight = 59922.228| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.84 r_work: 0.2800 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1271 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= 0.172 Angle : 0.724 17.990 36381 Z= 0.363 Chirality : 0.052 0.872 4217 Planarity : 0.005 0.062 4634 Dihedral : 11.140 116.528 4369 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.74 % Allowed : 4.02 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3218 helix: 0.68 (0.20), residues: 681 sheet: -0.22 (0.20), residues: 652 loop : -2.41 (0.12), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 152 HIS 0.003 0.001 HIS C 69 PHE 0.032 0.002 PHE B 157 TYR 0.020 0.001 TYR A 473 ARG 0.012 0.001 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 31) link_NAG-ASN : angle 4.27864 ( 93) link_BETA1-4 : bond 0.00627 ( 9) link_BETA1-4 : angle 1.94871 ( 27) hydrogen bonds : bond 0.08121 ( 1001) hydrogen bonds : angle 5.78227 ( 2739) SS BOND : bond 0.00400 ( 42) SS BOND : angle 1.75090 ( 84) covalent geometry : bond 0.00389 (26586) covalent geometry : angle 0.68593 (36177) *********************** 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 133 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5872 (pmm) cc_final: 0.5548 (pmm) REVERT: A 177 MET cc_start: 0.2136 (ptp) cc_final: 0.0106 (mtt) REVERT: A 414 GLN cc_start: 0.4571 (pp30) cc_final: 0.4258 (pp30) REVERT: A 441 LEU cc_start: 0.9230 (tm) cc_final: 0.8992 (tm) REVERT: A 515 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.7831 (p90) REVERT: A 636 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6658 (t80) REVERT: A 855 PHE cc_start: 0.8565 (m-80) cc_final: 0.8232 (m-80) REVERT: B 153 MET cc_start: 0.6750 (pmm) cc_final: 0.6275 (pmm) REVERT: B 200 TYR cc_start: 0.8169 (m-80) cc_final: 0.7889 (t80) REVERT: B 258 TRP cc_start: 0.3085 (p90) cc_final: 0.2766 (m100) REVERT: B 414 GLN cc_start: 0.8500 (mt0) cc_final: 0.8236 (pp30) REVERT: B 740 MET cc_start: 0.9408 (mmm) cc_final: 0.9206 (tpt) REVERT: B 855 PHE cc_start: 0.8660 (m-10) cc_final: 0.8315 (m-80) REVERT: C 153 MET cc_start: 0.7642 (pmm) cc_final: 0.7247 (ppp) REVERT: C 258 TRP cc_start: 0.5873 (p-90) cc_final: 0.2554 (m100) REVERT: C 408 ARG cc_start: 0.8494 (tmm-80) cc_final: 0.8256 (tmm160) outliers start: 21 outliers final: 5 residues processed: 127 average time/residue: 1.4107 time to fit residues: 212.9779 Evaluate side-chains 97 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 2.808 ------------------------------------------------------------------------------- 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 517 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 279 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.108440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062798 restraints weight = 59648.741| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.84 r_work: 0.2765 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26668 Z= 0.221 Angle : 0.708 17.421 36381 Z= 0.352 Chirality : 0.051 0.811 4217 Planarity : 0.004 0.054 4634 Dihedral : 9.296 113.762 4369 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.85 % Allowed : 5.82 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3218 helix: 1.17 (0.21), residues: 679 sheet: -0.03 (0.20), residues: 646 loop : -2.25 (0.12), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.005 0.001 HIS B1064 PHE 0.021 0.002 PHE C 906 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 31) link_NAG-ASN : angle 4.18074 ( 93) link_BETA1-4 : bond 0.00668 ( 9) link_BETA1-4 : angle 1.98898 ( 27) hydrogen bonds : bond 0.08247 ( 1001) hydrogen bonds : angle 5.57505 ( 2739) SS BOND : bond 0.00463 ( 42) SS BOND : angle 1.76527 ( 84) covalent geometry : bond 0.00529 (26586) covalent geometry : angle 0.67051 (36177) *********************** 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 124 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5944 (pmm) cc_final: 0.5673 (pmm) REVERT: A 177 MET cc_start: 0.2014 (ptp) cc_final: 0.0118 (mtt) REVERT: A 515 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.7997 (p90) REVERT: A 855 PHE cc_start: 0.8488 (m-80) cc_final: 0.8109 (m-80) REVERT: B 101 ILE cc_start: 0.8594 (mm) cc_final: 0.8360 (tp) REVERT: B 258 TRP cc_start: 0.3047 (p90) cc_final: 0.2424 (m100) REVERT: B 414 GLN cc_start: 0.8419 (mt0) cc_final: 0.8210 (pp30) REVERT: B 515 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8166 (p90) REVERT: B 855 PHE cc_start: 0.8648 (m-10) cc_final: 0.8248 (m-80) REVERT: C 153 MET cc_start: 0.7736 (pmm) cc_final: 0.7384 (ppp) REVERT: C 177 MET cc_start: 0.4035 (ptt) cc_final: 0.0553 (mtt) REVERT: C 258 TRP cc_start: 0.5687 (p-90) cc_final: 0.2570 (m100) REVERT: C 855 PHE cc_start: 0.8487 (m-10) cc_final: 0.8196 (m-10) outliers start: 24 outliers final: 9 residues processed: 120 average time/residue: 1.3073 time to fit residues: 186.3361 Evaluate side-chains 98 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 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 76 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 260 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 59 optimal weight: 0.0050 chunk 115 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.109309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.064142 restraints weight = 59954.322| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.91 r_work: 0.2748 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26668 Z= 0.141 Angle : 0.638 16.273 36381 Z= 0.315 Chirality : 0.048 0.740 4217 Planarity : 0.004 0.048 4634 Dihedral : 8.333 112.605 4369 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.13 % Allowed : 6.49 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3218 helix: 1.57 (0.21), residues: 676 sheet: 0.18 (0.19), residues: 643 loop : -2.09 (0.12), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS A1088 PHE 0.014 0.001 PHE C 79 TYR 0.018 0.001 TYR C 473 ARG 0.010 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 31) link_NAG-ASN : angle 3.86178 ( 93) link_BETA1-4 : bond 0.00801 ( 9) link_BETA1-4 : angle 1.93945 ( 27) hydrogen bonds : bond 0.06859 ( 1001) hydrogen bonds : angle 5.28666 ( 2739) SS BOND : bond 0.00390 ( 42) SS BOND : angle 1.37143 ( 84) covalent geometry : bond 0.00315 (26586) covalent geometry : angle 0.60346 (36177) *********************** 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 132 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6101 (pmm) cc_final: 0.5817 (pmm) REVERT: A 177 MET cc_start: 0.2113 (ptp) cc_final: 0.0226 (mtt) REVERT: A 515 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.7827 (p90) REVERT: A 855 PHE cc_start: 0.8504 (m-10) cc_final: 0.8160 (m-80) REVERT: B 153 MET cc_start: 0.6594 (pmm) cc_final: 0.6276 (pmm) REVERT: B 224 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7725 (pp20) REVERT: B 258 TRP cc_start: 0.2868 (p90) cc_final: 0.2073 (m100) REVERT: B 414 GLN cc_start: 0.8445 (mt0) cc_final: 0.8197 (pp30) REVERT: B 515 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8043 (p90) REVERT: B 855 PHE cc_start: 0.8643 (m-10) cc_final: 0.8253 (m-80) REVERT: C 177 MET cc_start: 0.4166 (ptt) cc_final: 0.0759 (mtt) REVERT: C 258 TRP cc_start: 0.5504 (p-90) cc_final: 0.2574 (m100) REVERT: C 855 PHE cc_start: 0.8453 (m-10) cc_final: 0.8136 (m-10) outliers start: 32 outliers final: 9 residues processed: 124 average time/residue: 1.1425 time to fit residues: 172.2489 Evaluate side-chains 101 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 2.744 ------------------------------------------------------------------------------- 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 878 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 738 CYS 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 211 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 247 optimal weight: 0.0770 chunk 219 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 181 optimal weight: 0.0470 chunk 225 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** 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 = 0.3901 r_free = 0.3901 target = 0.110997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.067891 restraints weight = 58809.825| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.81 r_work: 0.2822 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26668 Z= 0.108 Angle : 0.599 15.149 36381 Z= 0.292 Chirality : 0.047 0.669 4217 Planarity : 0.004 0.044 4634 Dihedral : 7.603 110.151 4369 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.38 % Allowed : 7.02 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3218 helix: 1.94 (0.21), residues: 680 sheet: 0.34 (0.19), residues: 653 loop : -1.92 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 633 HIS 0.003 0.001 HIS A1101 PHE 0.014 0.001 PHE C 79 TYR 0.019 0.001 TYR C 473 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 31) link_NAG-ASN : angle 3.53887 ( 93) link_BETA1-4 : bond 0.00795 ( 9) link_BETA1-4 : angle 1.92724 ( 27) hydrogen bonds : bond 0.05445 ( 1001) hydrogen bonds : angle 4.99160 ( 2739) SS BOND : bond 0.00320 ( 42) SS BOND : angle 1.09759 ( 84) covalent geometry : bond 0.00220 (26586) covalent geometry : angle 0.56808 (36177) *********************** 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 146 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6208 (pmm) cc_final: 0.5893 (pmm) REVERT: A 177 MET cc_start: 0.2131 (ptp) cc_final: 0.0274 (mtt) REVERT: A 515 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7648 (p90) REVERT: A 745 ASP cc_start: 0.8083 (t0) cc_final: 0.7759 (t0) REVERT: A 855 PHE cc_start: 0.8458 (m-10) cc_final: 0.8186 (m-80) REVERT: B 153 MET cc_start: 0.6492 (pmm) cc_final: 0.6169 (pmm) REVERT: B 224 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7856 (pp20) REVERT: B 258 TRP cc_start: 0.2803 (p90) cc_final: 0.0689 (m100) REVERT: B 414 GLN cc_start: 0.8466 (mt0) cc_final: 0.8240 (pp30) REVERT: B 855 PHE cc_start: 0.8618 (m-10) cc_final: 0.8273 (m-80) REVERT: C 153 MET cc_start: 0.7707 (ppp) cc_final: 0.7377 (pmm) REVERT: C 177 MET cc_start: 0.4159 (ptt) cc_final: 0.0810 (mtt) REVERT: C 258 TRP cc_start: 0.5383 (p-90) cc_final: 0.2632 (m100) REVERT: C 855 PHE cc_start: 0.8431 (m-10) cc_final: 0.8072 (m-10) REVERT: C 1138 TYR cc_start: 0.8847 (t80) cc_final: 0.8176 (t80) outliers start: 39 outliers final: 15 residues processed: 138 average time/residue: 1.0809 time to fit residues: 181.9966 Evaluate side-chains 114 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 2.698 ------------------------------------------------------------------------------- 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 1098 ASN Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 455 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 C residue 414 GLN 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 10 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 314 optimal weight: 0.1980 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** 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 = 0.3796 r_free = 0.3796 target = 0.107292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061677 restraints weight = 59759.871| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.89 r_work: 0.2727 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 26668 Z= 0.245 Angle : 0.698 16.527 36381 Z= 0.347 Chirality : 0.050 0.751 4217 Planarity : 0.004 0.041 4634 Dihedral : 7.548 109.970 4369 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.48 % Allowed : 7.34 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3218 helix: 1.71 (0.21), residues: 685 sheet: 0.24 (0.19), residues: 650 loop : -1.95 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.005 0.001 HIS B1064 PHE 0.020 0.002 PHE B1121 TYR 0.021 0.001 TYR B1067 ARG 0.008 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 31) link_NAG-ASN : angle 3.88946 ( 93) link_BETA1-4 : bond 0.00453 ( 9) link_BETA1-4 : angle 1.70703 ( 27) hydrogen bonds : bond 0.08271 ( 1001) hydrogen bonds : angle 5.32437 ( 2739) SS BOND : bond 0.00702 ( 42) SS BOND : angle 1.78324 ( 84) covalent geometry : bond 0.00594 (26586) covalent geometry : angle 0.66423 (36177) *********************** 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 137 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6441 (pmm) cc_final: 0.6132 (pmm) REVERT: A 177 MET cc_start: 0.2255 (ptp) cc_final: 0.0320 (mtt) REVERT: A 515 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7984 (p90) REVERT: A 855 PHE cc_start: 0.8482 (m-10) cc_final: 0.8144 (m-80) REVERT: A 988 GLU cc_start: 0.8798 (mp0) cc_final: 0.8405 (mp0) REVERT: B 153 MET cc_start: 0.6665 (pmm) cc_final: 0.6359 (pmm) REVERT: B 224 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7859 (pp20) REVERT: B 309 GLU cc_start: 0.7965 (mp0) cc_final: 0.7646 (pm20) REVERT: B 414 GLN cc_start: 0.8444 (mt0) cc_final: 0.8208 (pp30) REVERT: B 515 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8235 (p90) REVERT: B 855 PHE cc_start: 0.8689 (m-10) cc_final: 0.8313 (m-80) REVERT: C 177 MET cc_start: 0.4213 (ptt) cc_final: 0.1003 (mtt) REVERT: C 414 GLN cc_start: 0.5346 (OUTLIER) cc_final: 0.4683 (pp30) REVERT: C 855 PHE cc_start: 0.8531 (m-10) cc_final: 0.8127 (m-10) outliers start: 42 outliers final: 20 residues processed: 129 average time/residue: 1.1980 time to fit residues: 186.0498 Evaluate side-chains 108 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 2.949 ------------------------------------------------------------------------------- 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 A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 414 GLN 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 754 LEU 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 92 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 232 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 302 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** 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 = 0.3819 r_free = 0.3819 target = 0.108680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063452 restraints weight = 59650.095| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.89 r_work: 0.2773 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26668 Z= 0.138 Angle : 0.635 15.848 36381 Z= 0.311 Chirality : 0.048 0.716 4217 Planarity : 0.004 0.047 4634 Dihedral : 7.277 109.631 4369 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.24 % Allowed : 8.05 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3218 helix: 1.93 (0.21), residues: 680 sheet: 0.36 (0.19), residues: 656 loop : -1.84 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 258 HIS 0.004 0.001 HIS C 519 PHE 0.024 0.001 PHE C 456 TYR 0.019 0.001 TYR C 473 ARG 0.011 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 31) link_NAG-ASN : angle 3.70739 ( 93) link_BETA1-4 : bond 0.00580 ( 9) link_BETA1-4 : angle 1.71447 ( 27) hydrogen bonds : bond 0.06871 ( 1001) hydrogen bonds : angle 5.12682 ( 2739) SS BOND : bond 0.00462 ( 42) SS BOND : angle 1.39208 ( 84) covalent geometry : bond 0.00305 (26586) covalent geometry : angle 0.60311 (36177) *********************** 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 130 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6480 (pmm) cc_final: 0.6170 (pmm) REVERT: A 177 MET cc_start: 0.2282 (ptp) cc_final: 0.0375 (mtt) REVERT: A 515 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.7851 (p90) REVERT: A 745 ASP cc_start: 0.8277 (t0) cc_final: 0.7970 (t0) REVERT: A 855 PHE cc_start: 0.8441 (m-10) cc_final: 0.8176 (m-80) REVERT: A 988 GLU cc_start: 0.8779 (mp0) cc_final: 0.8346 (mp0) REVERT: B 153 MET cc_start: 0.6681 (pmm) cc_final: 0.6357 (pmm) REVERT: B 224 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7895 (pp20) REVERT: B 309 GLU cc_start: 0.7975 (mp0) cc_final: 0.7664 (pm20) REVERT: B 414 GLN cc_start: 0.8413 (mt0) cc_final: 0.8195 (pp30) REVERT: B 855 PHE cc_start: 0.8635 (m-10) cc_final: 0.8293 (m-80) REVERT: C 153 MET cc_start: 0.7938 (ppp) cc_final: 0.7151 (pmm) REVERT: C 177 MET cc_start: 0.4229 (ptt) cc_final: 0.0981 (mtt) REVERT: C 414 GLN cc_start: 0.5180 (OUTLIER) cc_final: 0.4591 (pp30) REVERT: C 855 PHE cc_start: 0.8521 (m-10) cc_final: 0.8189 (m-80) outliers start: 35 outliers final: 18 residues processed: 122 average time/residue: 1.1754 time to fit residues: 173.7810 Evaluate side-chains 114 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 878 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 455 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 878 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 414 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 250 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 261 optimal weight: 0.0570 chunk 106 optimal weight: 0.0670 chunk 185 optimal weight: 0.9980 chunk 320 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 168 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN B 519 HIS C 388 ASN C 519 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.110434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065377 restraints weight = 59001.677| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.90 r_work: 0.2808 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26668 Z= 0.109 Angle : 0.597 14.751 36381 Z= 0.291 Chirality : 0.046 0.651 4217 Planarity : 0.004 0.038 4634 Dihedral : 6.818 106.912 4369 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.06 % Allowed : 8.29 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3218 helix: 2.11 (0.21), residues: 686 sheet: 0.53 (0.19), residues: 652 loop : -1.71 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.000 HIS C 519 PHE 0.015 0.001 PHE C 79 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 31) link_NAG-ASN : angle 3.39881 ( 93) link_BETA1-4 : bond 0.00594 ( 9) link_BETA1-4 : angle 1.60621 ( 27) hydrogen bonds : bond 0.05357 ( 1001) hydrogen bonds : angle 4.84616 ( 2739) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.06162 ( 84) covalent geometry : bond 0.00224 (26586) covalent geometry : angle 0.56962 (36177) *********************** 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 138 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6511 (pmm) cc_final: 0.6167 (pmm) REVERT: A 177 MET cc_start: 0.2292 (ptp) cc_final: 0.0481 (mtt) REVERT: A 515 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7706 (p90) REVERT: A 619 GLU cc_start: 0.8364 (mp0) cc_final: 0.8148 (mp0) REVERT: A 745 ASP cc_start: 0.8304 (t0) cc_final: 0.7982 (t0) REVERT: A 855 PHE cc_start: 0.8427 (m-10) cc_final: 0.8173 (m-80) REVERT: A 988 GLU cc_start: 0.8730 (mp0) cc_final: 0.8204 (mp0) REVERT: B 224 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7848 (pp20) REVERT: B 242 LEU cc_start: 0.9124 (mm) cc_final: 0.8842 (mp) REVERT: B 309 GLU cc_start: 0.7901 (mp0) cc_final: 0.7590 (pm20) REVERT: B 414 GLN cc_start: 0.8544 (mt0) cc_final: 0.8321 (pp30) REVERT: B 661 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8391 (pm20) REVERT: B 855 PHE cc_start: 0.8639 (m-10) cc_final: 0.8311 (m-80) REVERT: C 153 MET cc_start: 0.7896 (ppp) cc_final: 0.7419 (pmm) REVERT: C 177 MET cc_start: 0.4287 (ptt) cc_final: 0.0937 (mtt) REVERT: C 309 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7497 (tm-30) REVERT: C 780 GLU cc_start: 0.8541 (tt0) cc_final: 0.8307 (tt0) REVERT: C 855 PHE cc_start: 0.8549 (m-10) cc_final: 0.8209 (m-80) REVERT: C 1138 TYR cc_start: 0.8865 (t80) cc_final: 0.8203 (t80) outliers start: 30 outliers final: 18 residues processed: 132 average time/residue: 1.1504 time to fit residues: 184.4313 Evaluate side-chains 121 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 2.880 ------------------------------------------------------------------------------- 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 455 LEU 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 C residue 500 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 161 optimal weight: 0.7980 chunk 229 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN ** C 239 GLN ** 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 = 0.3880 r_free = 0.3880 target = 0.109578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066202 restraints weight = 58764.120| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.78 r_work: 0.2787 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26668 Z= 0.124 Angle : 0.601 15.024 36381 Z= 0.293 Chirality : 0.047 0.661 4217 Planarity : 0.004 0.049 4634 Dihedral : 6.673 105.603 4369 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.99 % Allowed : 8.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3218 helix: 2.18 (0.21), residues: 687 sheet: 0.55 (0.19), residues: 655 loop : -1.68 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.006 0.001 HIS C 519 PHE 0.028 0.001 PHE C 456 TYR 0.017 0.001 TYR B1067 ARG 0.011 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 31) link_NAG-ASN : angle 3.38237 ( 93) link_BETA1-4 : bond 0.00520 ( 9) link_BETA1-4 : angle 1.52055 ( 27) hydrogen bonds : bond 0.05874 ( 1001) hydrogen bonds : angle 4.84860 ( 2739) SS BOND : bond 0.00332 ( 42) SS BOND : angle 1.14169 ( 84) covalent geometry : bond 0.00277 (26586) covalent geometry : angle 0.57368 (36177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6523 (pmm) cc_final: 0.6080 (pmm) REVERT: A 177 MET cc_start: 0.2385 (ptp) cc_final: 0.0583 (mtt) REVERT: A 515 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7822 (p90) REVERT: A 745 ASP cc_start: 0.8326 (t0) cc_final: 0.8012 (t0) REVERT: A 855 PHE cc_start: 0.8430 (m-10) cc_final: 0.8171 (m-80) REVERT: A 988 GLU cc_start: 0.8749 (mp0) cc_final: 0.8250 (mp0) REVERT: B 101 ILE cc_start: 0.8498 (mp) cc_final: 0.8287 (tp) REVERT: B 153 MET cc_start: 0.6515 (pmm) cc_final: 0.6146 (pmm) REVERT: B 224 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7874 (pp20) REVERT: B 242 LEU cc_start: 0.9200 (mm) cc_final: 0.8844 (mp) REVERT: B 309 GLU cc_start: 0.7930 (mp0) cc_final: 0.7622 (pm20) REVERT: B 414 GLN cc_start: 0.8546 (mt0) cc_final: 0.8333 (pp30) REVERT: B 661 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8418 (pm20) REVERT: B 855 PHE cc_start: 0.8621 (m-10) cc_final: 0.8273 (m-80) REVERT: C 153 MET cc_start: 0.7896 (ppp) cc_final: 0.7426 (pmm) REVERT: C 177 MET cc_start: 0.4216 (ptt) cc_final: 0.0872 (mtt) REVERT: C 309 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7611 (tm-30) REVERT: C 780 GLU cc_start: 0.8638 (tt0) cc_final: 0.8416 (tt0) REVERT: C 855 PHE cc_start: 0.8552 (m-10) cc_final: 0.8223 (m-80) REVERT: C 1138 TYR cc_start: 0.8882 (t80) cc_final: 0.8196 (t80) outliers start: 28 outliers final: 19 residues processed: 123 average time/residue: 1.1735 time to fit residues: 173.5171 Evaluate side-chains 116 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 2.628 ------------------------------------------------------------------------------- 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 878 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 455 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 133 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 303 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 91 optimal weight: 0.0470 chunk 184 optimal weight: 0.0170 chunk 171 optimal weight: 6.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.110405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065648 restraints weight = 60026.208| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.90 r_work: 0.2790 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26668 Z= 0.116 Angle : 0.591 14.823 36381 Z= 0.290 Chirality : 0.046 0.651 4217 Planarity : 0.004 0.047 4634 Dihedral : 6.495 104.160 4369 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.85 % Allowed : 8.86 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3218 helix: 2.15 (0.21), residues: 692 sheet: 0.55 (0.19), residues: 663 loop : -1.63 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS C 519 PHE 0.013 0.001 PHE C 79 TYR 0.016 0.001 TYR B1067 ARG 0.019 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 31) link_NAG-ASN : angle 3.29716 ( 93) link_BETA1-4 : bond 0.00546 ( 9) link_BETA1-4 : angle 1.49071 ( 27) hydrogen bonds : bond 0.05665 ( 1001) hydrogen bonds : angle 4.79990 ( 2739) SS BOND : bond 0.00323 ( 42) SS BOND : angle 1.08229 ( 84) covalent geometry : bond 0.00253 (26586) covalent geometry : angle 0.56522 (36177) ********************** 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 124 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6597 (pmm) cc_final: 0.6156 (pmm) REVERT: A 177 MET cc_start: 0.2479 (ptp) cc_final: 0.0716 (mtt) REVERT: A 515 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7866 (p90) REVERT: A 586 ASP cc_start: 0.7898 (m-30) cc_final: 0.7623 (m-30) REVERT: A 745 ASP cc_start: 0.8402 (t0) cc_final: 0.8092 (t0) REVERT: A 855 PHE cc_start: 0.8452 (m-10) cc_final: 0.8196 (m-80) REVERT: A 988 GLU cc_start: 0.8782 (mp0) cc_final: 0.8253 (mp0) REVERT: B 153 MET cc_start: 0.6593 (pmm) cc_final: 0.6134 (pmm) REVERT: B 224 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7875 (pp20) REVERT: B 242 LEU cc_start: 0.9221 (mm) cc_final: 0.8951 (mp) REVERT: B 309 GLU cc_start: 0.7911 (mp0) cc_final: 0.7596 (pm20) REVERT: B 661 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: B 855 PHE cc_start: 0.8629 (m-10) cc_final: 0.8288 (m-80) REVERT: C 153 MET cc_start: 0.7908 (ppp) cc_final: 0.7441 (pmm) REVERT: C 177 MET cc_start: 0.4272 (ptt) cc_final: 0.0960 (mtt) REVERT: C 780 GLU cc_start: 0.8641 (tt0) cc_final: 0.8398 (tt0) REVERT: C 855 PHE cc_start: 0.8525 (m-10) cc_final: 0.8178 (m-10) REVERT: C 1138 TYR cc_start: 0.8899 (t80) cc_final: 0.8226 (t80) outliers start: 24 outliers final: 19 residues processed: 119 average time/residue: 1.2275 time to fit residues: 177.1564 Evaluate side-chains 117 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 2.992 ------------------------------------------------------------------------------- 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 878 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 455 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 220 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.107941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062724 restraints weight = 60077.843| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.87 r_work: 0.2761 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26668 Z= 0.192 Angle : 0.639 15.810 36381 Z= 0.317 Chirality : 0.048 0.703 4217 Planarity : 0.004 0.037 4634 Dihedral : 6.554 104.355 4369 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.02 % Allowed : 8.93 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3218 helix: 2.01 (0.21), residues: 689 sheet: 0.46 (0.19), residues: 664 loop : -1.68 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.006 0.001 HIS C 519 PHE 0.024 0.001 PHE C 456 TYR 0.019 0.001 TYR B1067 ARG 0.011 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 31) link_NAG-ASN : angle 3.47913 ( 93) link_BETA1-4 : bond 0.00444 ( 9) link_BETA1-4 : angle 1.46070 ( 27) hydrogen bonds : bond 0.07298 ( 1001) hydrogen bonds : angle 5.01592 ( 2739) SS BOND : bond 0.00395 ( 42) SS BOND : angle 1.40384 ( 84) covalent geometry : bond 0.00462 (26586) covalent geometry : angle 0.61121 (36177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18890.15 seconds wall clock time: 329 minutes 30.33 seconds (19770.33 seconds total)