Starting phenix.real_space_refine on Sat Aug 8 03:18:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12jt_76493/08_2026/12jt_76493.cif Found real_map, /net/cci-nas-00/data/ceres_data/12jt_76493/08_2026/12jt_76493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12jt_76493/08_2026/12jt_76493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12jt_76493/08_2026/12jt_76493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12jt_76493/08_2026/12jt_76493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12jt_76493/08_2026/12jt_76493.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 108 5.16 5 C 15775 2.51 5 N 4003 2.21 5 O 4725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24611 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8039 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 55, 'TRANS': 966} Chain breaks: 9 Chain: "B" Number of atoms: 7999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7999 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 962} Chain breaks: 11 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7957 Classifications: {'peptide': 1013} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 56, 'TRANS': 956} Chain breaks: 11 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" 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 Time building chain proxies: 5.66, per 1000 atoms: 0.23 Number of scatterers: 24611 At special positions: 0 Unit cell: (133.952, 126.464, 168.896, 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 108 16.00 O 4725 8.00 N 4003 7.00 C 15775 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 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 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 165 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 801 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C1134 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 902.3 milliseconds 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 43 sheets defined 27.1% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.749A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.049A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.644A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.724A pdb=" N CYS A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.516A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.213A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.280A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.093A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.735A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.663A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.481A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 630 through 636 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.963A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.664A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.283A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.893A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.290A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.237A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.997A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.612A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.414A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.606A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 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: 3.648A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.805A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 841 " --> pdb=" O TYR C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.572A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.345A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.629A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.435A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 202 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP A 228 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A 204 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N HIS A 208 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N ALA A 222 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.617A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.960A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.839A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.765A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.361A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS A 537 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 552 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.616A pdb=" N THR A 376 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.093A pdb=" N LYS A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N THR A 696 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.804A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.804A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.551A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.122A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.645A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.002A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.715A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.105A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.282A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.040A pdb=" N LYS B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR B 696 " --> pdb=" O LYS B 654 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.820A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.820A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.615A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 6.119A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.283A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE C 202 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP C 228 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE C 204 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N HIS C 208 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ALA C 222 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.825A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.772A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.206A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.547A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.537A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.066A pdb=" N LYS C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR C 696 " --> pdb=" O LYS C 654 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.888A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.888A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.598A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 1028 hydrogen bonds defined for protein. 2820 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: 6.04 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6633 1.33 - 1.45: 4925 1.45 - 1.58: 13490 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25180 Sorted by residual: bond pdb=" N VAL C 401 " pdb=" CA VAL C 401 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.47e+00 bond pdb=" N VAL C 510 " pdb=" CA VAL C 510 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.18e-02 7.18e+03 9.18e+00 bond pdb=" N VAL A 401 " pdb=" CA VAL A 401 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 9.05e+00 bond pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.78e+00 bond pdb=" N VAL C 289 " pdb=" CA VAL C 289 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.54e+00 ... (remaining 25175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 33745 1.98 - 3.96: 477 3.96 - 5.94: 29 5.94 - 7.91: 1 7.91 - 9.89: 2 Bond angle restraints: 34254 Sorted by residual: angle pdb=" CA SER C 496 " pdb=" C SER C 496 " pdb=" O SER C 496 " ideal model delta sigma weight residual 122.13 118.23 3.90 1.13e+00 7.83e-01 1.19e+01 angle pdb=" CA SER C 443 " pdb=" C SER C 443 " pdb=" O SER C 443 " ideal model delta sigma weight residual 121.89 117.98 3.91 1.17e+00 7.31e-01 1.12e+01 angle pdb=" C2 NAG G 1 " pdb=" N2 NAG G 1 " pdb=" C7 NAG G 1 " ideal model delta sigma weight residual 124.56 134.45 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA THR C 500 " pdb=" C THR C 500 " pdb=" O THR C 500 " ideal model delta sigma weight residual 121.84 118.02 3.82 1.16e+00 7.43e-01 1.09e+01 angle pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" O VAL A 350 " ideal model delta sigma weight residual 120.95 117.53 3.42 1.04e+00 9.25e-01 1.08e+01 ... (remaining 34249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 14068 17.54 - 35.07: 1079 35.07 - 52.61: 247 52.61 - 70.15: 131 70.15 - 87.68: 14 Dihedral angle restraints: 15539 sinusoidal: 6647 harmonic: 8892 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 6.78 86.22 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -1.09 -84.91 1 1.00e+01 1.00e-02 8.75e+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 -12.67 -73.33 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 15536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3611 0.085 - 0.170: 395 0.170 - 0.255: 9 0.255 - 0.339: 0 0.339 - 0.424: 1 Chirality restraints: 4016 Sorted by residual: chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C2 NAG G 1 " pdb=" C1 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" N2 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.27 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 4013 not shown) Planarity restraints: 4371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 440 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.60e+00 pdb=" NE ARG C 440 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 440 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 440 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 440 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 454 " 0.268 9.50e-02 1.11e+02 1.20e-01 8.86e+00 pdb=" NE ARG A 454 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 454 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 454 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 454 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 373 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.026 5.00e-02 4.00e+02 ... (remaining 4368 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 10285 2.92 - 3.42: 21700 3.42 - 3.91: 40336 3.91 - 4.41: 45784 4.41 - 4.90: 77913 Nonbonded interactions: 196018 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.425 3.040 nonbonded pdb=" O ASP A 427 " pdb=" OD1 ASP A 428 " model vdw 2.450 3.040 nonbonded pdb=" OG SER C 349 " pdb=" O TRP C 452 " model vdw 2.500 3.040 nonbonded pdb=" O PRO C 499 " pdb=" OG1 THR C 500 " model vdw 2.508 3.040 nonbonded pdb=" N GLN B 529 " pdb=" OE1 GLN B 529 " model vdw 2.530 3.120 ... (remaining 196013 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' and (resid 28 through 67 or resid 81 through 122 or resid 126 through \ 135 or resid 158 through 172 or resid 188 through 242 or resid 263 through 473 \ or resid 479 through 497 or resid 500 through 517 or resid 520 through 842 or (r \ esid 843 and (name N or name CA or name C or name O )) or resid 849 through 1307 \ )) selection = (chain 'B' and (resid 28 through 67 or resid 81 through 135 or resid 158 through \ 172 or resid 187 through 242 or resid 263 through 473 or resid 479 through 517 \ or resid 520 through 620 or resid 629 through 842 or (resid 843 and (name N or n \ ame CA or name C or name O )) or resid 849 through 1307)) selection = (chain 'C' and (resid 28 through 473 or resid 479 through 497 or resid 500 throu \ gh 620 or resid 629 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 7.020 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.360 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25258 Z= 0.201 Angle : 0.546 9.892 34453 Z= 0.314 Chirality : 0.046 0.424 4016 Planarity : 0.005 0.125 4337 Dihedral : 14.135 87.681 9708 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.56 % Allowed : 11.19 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 2985 helix: 2.02 (0.20), residues: 669 sheet: 0.58 (0.19), residues: 713 loop : -0.88 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.024 0.001 TYR A 170 PHE 0.028 0.001 PHE A 375 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.20 (25180) covalent geometry : angle 0.53523 / 0.31 (34254) SS BOND : bond 0.00232 / 0.17 ( 35) SS BOND : angle 0.79269 / 0.49 ( 70) hydrogen bonds : bond 0.19038 / 12.28 ( 1013) hydrogen bonds : angle 7.88970 / 5.32 ( 2820) link_BETA1-4 : bond 0.00593 / 0.30 ( 9) link_BETA1-4 : angle 2.08946 / 1.46 ( 27) link_NAG-ASN : bond 0.00220 / 0.14 ( 34) link_NAG-ASN : angle 1.74713 / 1.23 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.8411 (m-80) cc_final: 0.8116 (m-80) REVERT: A 214 ARG cc_start: 0.8707 (mtt180) cc_final: 0.8313 (mtt90) REVERT: A 227 VAL cc_start: 0.8699 (t) cc_final: 0.8492 (p) REVERT: A 418 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6769 (mp) REVERT: A 1142 GLN cc_start: 0.8961 (tp40) cc_final: 0.8524 (tm-30) REVERT: B 52 GLN cc_start: 0.8949 (tt0) cc_final: 0.8511 (tm-30) REVERT: B 214 ARG cc_start: 0.7325 (ttt180) cc_final: 0.7035 (ttt180) REVERT: B 314 GLN cc_start: 0.8842 (tt0) cc_final: 0.8341 (tp40) REVERT: B 828 LEU cc_start: 0.8375 (tp) cc_final: 0.8030 (tm) REVERT: C 52 GLN cc_start: 0.8480 (tm-30) cc_final: 0.7920 (tm-30) REVERT: C 198 ILE cc_start: 0.8009 (pt) cc_final: 0.7779 (pp) REVERT: C 265 TYR cc_start: 0.7614 (m-80) cc_final: 0.7266 (m-80) REVERT: C 515 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: C 629 LEU cc_start: 0.7686 (mm) cc_final: 0.7462 (mt) REVERT: C 1038 LYS cc_start: 0.9477 (mttm) cc_final: 0.9127 (mmtt) outliers start: 15 outliers final: 6 residues processed: 131 average time/residue: 0.6269 time to fit residues: 95.8086 Evaluate side-chains 115 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 87 ASN B1005 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.063907 restraints weight = 48439.197| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.66 r_work: 0.2793 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25258 Z= 0.163 Angle : 0.530 9.791 34453 Z= 0.278 Chirality : 0.045 0.227 4016 Planarity : 0.004 0.045 4337 Dihedral : 5.580 58.289 4207 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.97 % Allowed : 10.08 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 2985 helix: 2.45 (0.20), residues: 679 sheet: 0.78 (0.19), residues: 714 loop : -1.00 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.018 0.001 TYR B 170 PHE 0.017 0.001 PHE C 65 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (25180) covalent geometry : angle 0.51873 / 0.28 (34254) SS BOND : bond 0.00294 / 0.20 ( 35) SS BOND : angle 0.97245 / 0.61 ( 70) hydrogen bonds : bond 0.05657 / 3.67 ( 1013) hydrogen bonds : angle 5.83611 / 3.96 ( 2820) link_BETA1-4 : bond 0.00543 / 0.27 ( 9) link_BETA1-4 : angle 2.11467 / 1.48 ( 27) link_NAG-ASN : bond 0.00223 / 0.15 ( 34) link_NAG-ASN : angle 1.68273 / 1.14 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7304 (mp10) REVERT: A 1142 GLN cc_start: 0.8938 (tp40) cc_final: 0.8561 (tm-30) REVERT: B 52 GLN cc_start: 0.8915 (tt0) cc_final: 0.8520 (tm-30) REVERT: B 314 GLN cc_start: 0.8866 (tt0) cc_final: 0.8406 (tp40) REVERT: B 440 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8506 (mtp-110) REVERT: B 471 GLU cc_start: 0.8044 (tt0) cc_final: 0.7364 (pm20) REVERT: B 828 LEU cc_start: 0.8406 (tp) cc_final: 0.8092 (tm) REVERT: C 52 GLN cc_start: 0.8529 (tm-30) cc_final: 0.7981 (tm-30) REVERT: C 198 ILE cc_start: 0.7897 (pt) cc_final: 0.7659 (pp) REVERT: C 265 TYR cc_start: 0.7450 (m-80) cc_final: 0.7131 (m-80) REVERT: C 515 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: C 629 LEU cc_start: 0.7685 (mm) cc_final: 0.7474 (mt) REVERT: C 759 PHE cc_start: 0.8738 (m-80) cc_final: 0.8525 (m-80) REVERT: C 1038 LYS cc_start: 0.9477 (mttm) cc_final: 0.9191 (mmtm) outliers start: 53 outliers final: 27 residues processed: 151 average time/residue: 0.5285 time to fit residues: 95.9066 Evaluate side-chains 137 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 302 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 751 ASN B 66 HIS B 87 ASN B 474 GLN B 949 GLN B1005 GLN C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.061586 restraints weight = 48653.355| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.68 r_work: 0.2741 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 25258 Z= 0.306 Angle : 0.618 10.114 34453 Z= 0.320 Chirality : 0.049 0.229 4016 Planarity : 0.005 0.046 4337 Dihedral : 5.889 58.298 4201 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.45 % Allowed : 10.52 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 2985 helix: 2.06 (0.19), residues: 696 sheet: 0.62 (0.19), residues: 694 loop : -1.12 (0.14), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 319 TYR 0.020 0.002 TYR B 170 PHE 0.021 0.002 PHE B 898 TRP 0.014 0.001 TRP A 436 HIS 0.007 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.31 (25180) covalent geometry : angle 0.60454 / 0.32 (34254) SS BOND : bond 0.00431 / 0.27 ( 35) SS BOND : angle 1.21965 / 0.77 ( 70) hydrogen bonds : bond 0.06682 / 4.33 ( 1013) hydrogen bonds : angle 5.80134 / 3.95 ( 2820) link_BETA1-4 : bond 0.00559 / 0.28 ( 9) link_BETA1-4 : angle 2.30098 / 1.60 ( 27) link_NAG-ASN : bond 0.00353 / 0.24 ( 34) link_NAG-ASN : angle 1.99407 / 1.34 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 110 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7462 (mt0) REVERT: A 675 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: A 1142 GLN cc_start: 0.8947 (tp40) cc_final: 0.8508 (tm-30) REVERT: B 52 GLN cc_start: 0.8929 (tt0) cc_final: 0.8508 (tm-30) REVERT: B 314 GLN cc_start: 0.8890 (tt0) cc_final: 0.8424 (tp40) REVERT: B 440 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8530 (mtp-110) REVERT: C 52 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8033 (tm-30) REVERT: C 198 ILE cc_start: 0.7840 (pt) cc_final: 0.7565 (pp) REVERT: C 265 TYR cc_start: 0.7477 (m-80) cc_final: 0.7231 (m-80) REVERT: C 515 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: C 567 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7931 (mtt-85) REVERT: C 759 PHE cc_start: 0.8790 (m-80) cc_final: 0.8576 (m-80) REVERT: C 1038 LYS cc_start: 0.9497 (mttm) cc_final: 0.9177 (mmtm) outliers start: 66 outliers final: 39 residues processed: 163 average time/residue: 0.5746 time to fit residues: 111.0041 Evaluate side-chains 146 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 22 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 211 optimal weight: 6.9990 chunk 38 optimal weight: 0.0010 chunk 213 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 238 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN B 414 GLN B 949 GLN B1005 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.095038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.063919 restraints weight = 47906.473| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.68 r_work: 0.2792 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25258 Z= 0.112 Angle : 0.501 9.731 34453 Z= 0.259 Chirality : 0.044 0.229 4016 Planarity : 0.004 0.050 4337 Dihedral : 5.582 57.401 4201 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.97 % Allowed : 11.19 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 2985 helix: 2.51 (0.20), residues: 678 sheet: 0.70 (0.19), residues: 712 loop : -1.01 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.011 0.001 TYR C1067 PHE 0.023 0.001 PHE A 375 TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (25180) covalent geometry : angle 0.48873 / 0.26 (34254) SS BOND : bond 0.00236 / 0.15 ( 35) SS BOND : angle 0.92943 / 0.57 ( 70) hydrogen bonds : bond 0.04881 / 3.16 ( 1013) hydrogen bonds : angle 5.35776 / 3.64 ( 2820) link_BETA1-4 : bond 0.00625 / 0.31 ( 9) link_BETA1-4 : angle 2.07106 / 1.46 ( 27) link_NAG-ASN : bond 0.00221 / 0.14 ( 34) link_NAG-ASN : angle 1.69513 / 1.16 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1142 GLN cc_start: 0.8920 (tp40) cc_final: 0.8500 (tm-30) REVERT: B 52 GLN cc_start: 0.8901 (tt0) cc_final: 0.8444 (tm-30) REVERT: B 314 GLN cc_start: 0.8830 (tt0) cc_final: 0.8319 (tp40) REVERT: B 440 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8499 (mtp-110) REVERT: B 471 GLU cc_start: 0.7921 (tt0) cc_final: 0.7257 (pm20) REVERT: B 828 LEU cc_start: 0.8396 (tp) cc_final: 0.8040 (tm) REVERT: C 52 GLN cc_start: 0.8530 (tm-30) cc_final: 0.7988 (tm-30) REVERT: C 198 ILE cc_start: 0.7721 (pt) cc_final: 0.7471 (pp) REVERT: C 265 TYR cc_start: 0.7286 (m-80) cc_final: 0.7029 (m-80) REVERT: C 1038 LYS cc_start: 0.9463 (mttm) cc_final: 0.9117 (mmtm) outliers start: 53 outliers final: 26 residues processed: 153 average time/residue: 0.5525 time to fit residues: 101.0504 Evaluate side-chains 131 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 299 optimal weight: 3.9990 chunk 233 optimal weight: 0.0030 chunk 226 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 277 optimal weight: 0.8980 chunk 239 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B1005 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.095603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064531 restraints weight = 47809.044| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.68 r_work: 0.2807 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25258 Z= 0.105 Angle : 0.488 9.791 34453 Z= 0.252 Chirality : 0.044 0.225 4016 Planarity : 0.004 0.066 4337 Dihedral : 5.411 56.670 4199 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.67 % Allowed : 11.45 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 2985 helix: 2.63 (0.20), residues: 678 sheet: 0.73 (0.19), residues: 726 loop : -0.95 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.022 0.001 TYR B 170 PHE 0.025 0.001 PHE A 375 TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (25180) covalent geometry : angle 0.47647 / 0.25 (34254) SS BOND : bond 0.00215 / 0.14 ( 35) SS BOND : angle 0.83733 / 0.51 ( 70) hydrogen bonds : bond 0.04540 / 2.93 ( 1013) hydrogen bonds : angle 5.16951 / 3.51 ( 2820) link_BETA1-4 : bond 0.00601 / 0.30 ( 9) link_BETA1-4 : angle 2.03964 / 1.43 ( 27) link_NAG-ASN : bond 0.00207 / 0.13 ( 34) link_NAG-ASN : angle 1.62746 / 1.11 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7347 (mt0) REVERT: A 675 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: A 1142 GLN cc_start: 0.8934 (tp40) cc_final: 0.8515 (tm-30) REVERT: B 52 GLN cc_start: 0.8895 (tt0) cc_final: 0.8433 (tm-30) REVERT: B 214 ARG cc_start: 0.7285 (ttt180) cc_final: 0.6977 (ttt180) REVERT: B 314 GLN cc_start: 0.8804 (tt0) cc_final: 0.8319 (tp40) REVERT: B 440 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8468 (mtp-110) REVERT: B 471 GLU cc_start: 0.7973 (tt0) cc_final: 0.7287 (pm20) REVERT: B 828 LEU cc_start: 0.8348 (tp) cc_final: 0.8015 (tm) REVERT: C 52 GLN cc_start: 0.8541 (tm-30) cc_final: 0.7991 (tm-30) REVERT: C 198 ILE cc_start: 0.7700 (pt) cc_final: 0.7442 (pp) REVERT: C 265 TYR cc_start: 0.7222 (m-80) cc_final: 0.6965 (m-80) REVERT: C 629 LEU cc_start: 0.7535 (mm) cc_final: 0.7287 (mt) REVERT: C 1038 LYS cc_start: 0.9464 (mttm) cc_final: 0.9116 (mmtm) outliers start: 45 outliers final: 27 residues processed: 138 average time/residue: 0.5379 time to fit residues: 88.4059 Evaluate side-chains 130 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 227 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1005 GLN C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.063494 restraints weight = 48011.846| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.63 r_work: 0.2754 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25258 Z= 0.181 Angle : 0.528 9.919 34453 Z= 0.272 Chirality : 0.045 0.230 4016 Planarity : 0.004 0.067 4337 Dihedral : 5.542 56.305 4199 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.12 % Allowed : 11.49 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2985 helix: 2.47 (0.20), residues: 688 sheet: 0.71 (0.19), residues: 725 loop : -1.02 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.018 0.001 TYR B 170 PHE 0.025 0.001 PHE A 375 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (25180) covalent geometry : angle 0.51554 / 0.27 (34254) SS BOND : bond 0.00296 / 0.19 ( 35) SS BOND : angle 0.93091 / 0.57 ( 70) hydrogen bonds : bond 0.05264 / 3.42 ( 1013) hydrogen bonds : angle 5.27349 / 3.58 ( 2820) link_BETA1-4 : bond 0.00524 / 0.26 ( 9) link_BETA1-4 : angle 2.11141 / 1.48 ( 27) link_NAG-ASN : bond 0.00237 / 0.16 ( 34) link_NAG-ASN : angle 1.73936 / 1.18 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 102 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8542 (tppt) REVERT: A 529 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7301 (mp10) REVERT: A 675 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: A 1142 GLN cc_start: 0.8934 (tp40) cc_final: 0.8541 (tm-30) REVERT: B 52 GLN cc_start: 0.8935 (tt0) cc_final: 0.8517 (tm-30) REVERT: B 214 ARG cc_start: 0.7350 (ttt180) cc_final: 0.7064 (ttt180) REVERT: B 314 GLN cc_start: 0.8869 (tt0) cc_final: 0.8468 (tp40) REVERT: B 440 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8472 (mtp-110) REVERT: B 471 GLU cc_start: 0.8026 (tt0) cc_final: 0.7374 (pm20) REVERT: B 828 LEU cc_start: 0.8451 (tp) cc_final: 0.8118 (tm) REVERT: B 1038 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9277 (mmtm) REVERT: C 52 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8180 (tm-30) REVERT: C 198 ILE cc_start: 0.7851 (pt) cc_final: 0.7577 (pp) REVERT: C 265 TYR cc_start: 0.7448 (m-80) cc_final: 0.7229 (m-80) REVERT: C 567 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7905 (mtt-85) REVERT: C 629 LEU cc_start: 0.7654 (mm) cc_final: 0.7411 (mt) REVERT: C 1038 LYS cc_start: 0.9478 (mttm) cc_final: 0.9205 (mmtm) outliers start: 57 outliers final: 35 residues processed: 146 average time/residue: 0.5205 time to fit residues: 90.2288 Evaluate side-chains 136 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 271 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 226 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 224 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN B 755 GLN B1005 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065013 restraints weight = 47664.856| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.65 r_work: 0.2819 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25258 Z= 0.104 Angle : 0.486 9.774 34453 Z= 0.250 Chirality : 0.044 0.228 4016 Planarity : 0.004 0.066 4337 Dihedral : 5.390 56.290 4199 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.49 % Allowed : 12.24 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 2985 helix: 2.68 (0.20), residues: 678 sheet: 0.71 (0.19), residues: 738 loop : -0.95 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 319 TYR 0.024 0.001 TYR B 170 PHE 0.031 0.001 PHE A 375 TRP 0.012 0.001 TRP A 436 HIS 0.002 0.000 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (25180) covalent geometry : angle 0.47424 / 0.25 (34254) SS BOND : bond 0.00228 / 0.14 ( 35) SS BOND : angle 0.82729 / 0.50 ( 70) hydrogen bonds : bond 0.04457 / 2.89 ( 1013) hydrogen bonds : angle 5.06447 / 3.44 ( 2820) link_BETA1-4 : bond 0.00637 / 0.32 ( 9) link_BETA1-4 : angle 2.01043 / 1.41 ( 27) link_NAG-ASN : bond 0.00206 / 0.13 ( 34) link_NAG-ASN : angle 1.61292 / 1.10 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8540 (tppt) REVERT: A 529 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7194 (mp10) REVERT: A 675 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: A 1142 GLN cc_start: 0.8909 (tp40) cc_final: 0.8527 (tm-30) REVERT: B 52 GLN cc_start: 0.8941 (tt0) cc_final: 0.8528 (tm-30) REVERT: B 214 ARG cc_start: 0.7340 (ttt180) cc_final: 0.7065 (ttt180) REVERT: B 314 GLN cc_start: 0.8843 (tt0) cc_final: 0.8437 (tp40) REVERT: B 440 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8435 (mtp-110) REVERT: B 471 GLU cc_start: 0.8043 (tt0) cc_final: 0.7397 (pm20) REVERT: B 828 LEU cc_start: 0.8432 (tp) cc_final: 0.8108 (tm) REVERT: B 1038 LYS cc_start: 0.9546 (mmmm) cc_final: 0.9263 (mmtm) REVERT: C 41 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7171 (mttt) REVERT: C 52 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 198 ILE cc_start: 0.7902 (pt) cc_final: 0.7575 (pp) REVERT: C 567 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8136 (mtm-85) REVERT: C 629 LEU cc_start: 0.7691 (mm) cc_final: 0.7454 (mt) REVERT: C 1038 LYS cc_start: 0.9456 (mttm) cc_final: 0.9195 (mmtm) outliers start: 40 outliers final: 25 residues processed: 138 average time/residue: 0.5824 time to fit residues: 94.8366 Evaluate side-chains 133 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 245 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B1005 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063351 restraints weight = 48197.787| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.67 r_work: 0.2779 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25258 Z= 0.165 Angle : 0.522 9.948 34453 Z= 0.269 Chirality : 0.045 0.229 4016 Planarity : 0.004 0.059 4337 Dihedral : 5.512 58.897 4199 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.49 % Allowed : 12.27 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 2985 helix: 2.48 (0.20), residues: 694 sheet: 0.71 (0.19), residues: 722 loop : -1.02 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.018 0.001 TYR B1067 PHE 0.032 0.001 PHE A 375 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (25180) covalent geometry : angle 0.51008 / 0.27 (34254) SS BOND : bond 0.00278 / 0.18 ( 35) SS BOND : angle 0.91528 / 0.57 ( 70) hydrogen bonds : bond 0.05141 / 3.33 ( 1013) hydrogen bonds : angle 5.18833 / 3.52 ( 2820) link_BETA1-4 : bond 0.00579 / 0.29 ( 9) link_BETA1-4 : angle 2.09487 / 1.47 ( 27) link_NAG-ASN : bond 0.00232 / 0.16 ( 34) link_NAG-ASN : angle 1.72393 / 1.17 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8526 (tppt) REVERT: A 529 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7266 (mp10) REVERT: A 675 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: A 1142 GLN cc_start: 0.8951 (tp40) cc_final: 0.8545 (tm-30) REVERT: B 52 GLN cc_start: 0.8956 (tt0) cc_final: 0.8526 (tm-30) REVERT: B 170 TYR cc_start: 0.8107 (t80) cc_final: 0.7895 (t80) REVERT: B 214 ARG cc_start: 0.7345 (ttt180) cc_final: 0.7066 (ttt180) REVERT: B 314 GLN cc_start: 0.8835 (tt0) cc_final: 0.8406 (tp40) REVERT: B 440 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8457 (mtp-110) REVERT: B 471 GLU cc_start: 0.7998 (tt0) cc_final: 0.7338 (pm20) REVERT: B 828 LEU cc_start: 0.8450 (tp) cc_final: 0.8130 (tm) REVERT: B 1038 LYS cc_start: 0.9551 (mmmm) cc_final: 0.9263 (mmtm) REVERT: C 41 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7233 (mttt) REVERT: C 52 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8148 (tm-30) REVERT: C 198 ILE cc_start: 0.7809 (pt) cc_final: 0.7527 (pp) REVERT: C 567 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7928 (mtt-85) REVERT: C 629 LEU cc_start: 0.7655 (mm) cc_final: 0.7422 (mt) REVERT: C 1038 LYS cc_start: 0.9468 (mttm) cc_final: 0.9179 (mmtm) outliers start: 40 outliers final: 28 residues processed: 133 average time/residue: 0.5835 time to fit residues: 91.3751 Evaluate side-chains 128 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 35 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 301 optimal weight: 0.6980 chunk 154 optimal weight: 0.0070 chunk 240 optimal weight: 3.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN B1005 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.095260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064258 restraints weight = 48066.904| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.65 r_work: 0.2801 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25258 Z= 0.122 Angle : 0.497 9.817 34453 Z= 0.256 Chirality : 0.044 0.227 4016 Planarity : 0.004 0.060 4337 Dihedral : 5.422 58.775 4199 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.45 % Allowed : 12.42 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 2985 helix: 2.63 (0.20), residues: 684 sheet: 0.72 (0.19), residues: 722 loop : -0.96 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 319 TYR 0.013 0.001 TYR B1067 PHE 0.034 0.001 PHE A 375 TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (25180) covalent geometry : angle 0.48538 / 0.25 (34254) SS BOND : bond 0.00229 / 0.15 ( 35) SS BOND : angle 0.84680 / 0.52 ( 70) hydrogen bonds : bond 0.04642 / 3.01 ( 1013) hydrogen bonds : angle 5.05875 / 3.43 ( 2820) link_BETA1-4 : bond 0.00622 / 0.31 ( 9) link_BETA1-4 : angle 2.02652 / 1.42 ( 27) link_NAG-ASN : bond 0.00203 / 0.13 ( 34) link_NAG-ASN : angle 1.64571 / 1.12 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: A 1142 GLN cc_start: 0.8941 (tp40) cc_final: 0.8534 (tm-30) REVERT: B 52 GLN cc_start: 0.8941 (tt0) cc_final: 0.8503 (tm-30) REVERT: B 170 TYR cc_start: 0.8081 (t80) cc_final: 0.7833 (t80) REVERT: B 214 ARG cc_start: 0.7379 (ttt180) cc_final: 0.7116 (ttt180) REVERT: B 314 GLN cc_start: 0.8814 (tt0) cc_final: 0.8384 (tp40) REVERT: B 440 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8446 (mtp-110) REVERT: B 471 GLU cc_start: 0.7978 (tt0) cc_final: 0.7317 (pm20) REVERT: B 828 LEU cc_start: 0.8409 (tp) cc_final: 0.8076 (tm) REVERT: B 1038 LYS cc_start: 0.9543 (mmmm) cc_final: 0.9243 (mmtm) REVERT: C 41 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7151 (mttt) REVERT: C 52 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8133 (tm-30) REVERT: C 198 ILE cc_start: 0.7773 (pt) cc_final: 0.7490 (pp) REVERT: C 567 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7863 (mtt-85) REVERT: C 629 LEU cc_start: 0.7679 (mm) cc_final: 0.7442 (mt) REVERT: C 1038 LYS cc_start: 0.9450 (mttm) cc_final: 0.9149 (mmtm) outliers start: 39 outliers final: 28 residues processed: 131 average time/residue: 0.5455 time to fit residues: 83.7703 Evaluate side-chains 129 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 130 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 222 optimal weight: 4.9990 chunk 217 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1005 GLN C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.096297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065521 restraints weight = 47895.083| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.63 r_work: 0.2830 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25258 Z= 0.098 Angle : 0.478 9.721 34453 Z= 0.245 Chirality : 0.043 0.226 4016 Planarity : 0.004 0.063 4337 Dihedral : 5.262 56.117 4199 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.19 % Allowed : 12.68 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 2985 helix: 2.76 (0.20), residues: 678 sheet: 0.80 (0.19), residues: 722 loop : -0.91 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 319 TYR 0.011 0.001 TYR C1067 PHE 0.033 0.001 PHE A 375 TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (25180) covalent geometry : angle 0.46763 / 0.24 (34254) SS BOND : bond 0.00192 / 0.12 ( 35) SS BOND : angle 0.78663 / 0.48 ( 70) hydrogen bonds : bond 0.04107 / 2.65 ( 1013) hydrogen bonds : angle 4.88294 / 3.31 ( 2820) link_BETA1-4 : bond 0.00624 / 0.31 ( 9) link_BETA1-4 : angle 1.95140 / 1.37 ( 27) link_NAG-ASN : bond 0.00203 / 0.13 ( 34) link_NAG-ASN : angle 1.53153 / 1.05 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7418 (mp10) REVERT: A 675 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: A 1142 GLN cc_start: 0.8932 (tp40) cc_final: 0.8530 (tm-30) REVERT: B 52 GLN cc_start: 0.8935 (tt0) cc_final: 0.8499 (tm-30) REVERT: B 170 TYR cc_start: 0.8098 (t80) cc_final: 0.7886 (t80) REVERT: B 214 ARG cc_start: 0.7307 (ttt180) cc_final: 0.7074 (ttt180) REVERT: B 314 GLN cc_start: 0.8805 (tt0) cc_final: 0.8367 (tp40) REVERT: B 440 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8419 (mtp-110) REVERT: B 471 GLU cc_start: 0.8002 (tt0) cc_final: 0.7362 (pm20) REVERT: B 780 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8849 (mt-10) REVERT: B 828 LEU cc_start: 0.8334 (tp) cc_final: 0.8042 (tm) REVERT: B 1038 LYS cc_start: 0.9534 (mmmm) cc_final: 0.9231 (mmtm) REVERT: C 41 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7184 (mttt) REVERT: C 52 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 198 ILE cc_start: 0.7777 (pt) cc_final: 0.7507 (pp) REVERT: C 629 LEU cc_start: 0.7716 (mm) cc_final: 0.7477 (mt) REVERT: C 1038 LYS cc_start: 0.9446 (mttm) cc_final: 0.9149 (mmtm) outliers start: 32 outliers final: 23 residues processed: 134 average time/residue: 0.5534 time to fit residues: 87.5456 Evaluate side-chains 125 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 245 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 297 optimal weight: 0.2980 chunk 294 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B1005 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.094855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063787 restraints weight = 48111.839| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.64 r_work: 0.2790 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25258 Z= 0.157 Angle : 0.513 9.924 34453 Z= 0.264 Chirality : 0.045 0.229 4016 Planarity : 0.004 0.060 4337 Dihedral : 5.392 55.972 4199 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.30 % Allowed : 12.72 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 2985 helix: 2.62 (0.20), residues: 686 sheet: 0.76 (0.19), residues: 712 loop : -0.95 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 319 TYR 0.017 0.001 TYR B1067 PHE 0.034 0.001 PHE A 375 TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (25180) covalent geometry : angle 0.50175 / 0.26 (34254) SS BOND : bond 0.00258 / 0.17 ( 35) SS BOND : angle 0.86971 / 0.53 ( 70) hydrogen bonds : bond 0.04899 / 3.18 ( 1013) hydrogen bonds : angle 5.05047 / 3.43 ( 2820) link_BETA1-4 : bond 0.00570 / 0.29 ( 9) link_BETA1-4 : angle 2.03835 / 1.43 ( 27) link_NAG-ASN : bond 0.00219 / 0.15 ( 34) link_NAG-ASN : angle 1.65904 / 1.13 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9516.91 seconds wall clock time: 162 minutes 28.80 seconds (9748.80 seconds total)