Starting phenix.real_space_refine on Sat Aug 8 00:18:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12jz_76501/08_2026/12jz_76501.cif Found real_map, /net/cci-nas-00/data/ceres_data/12jz_76501/08_2026/12jz_76501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/12jz_76501/08_2026/12jz_76501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12jz_76501/08_2026/12jz_76501.map" model { file = "/net/cci-nas-00/data/ceres_data/12jz_76501/08_2026/12jz_76501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12jz_76501/08_2026/12jz_76501.cif" } resolution = 2.35 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 101 5.16 5 C 15331 2.51 5 N 3886 2.21 5 O 4595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 23913 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7788 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 56, 'TRANS': 933} Chain breaks: 10 Chain: "B" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7713 Classifications: {'peptide': 980} Link IDs: {'PTRANS': 56, 'TRANS': 923} Chain breaks: 13 Chain: "C" Number of atoms: 7782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7782 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 56, 'TRANS': 934} Chain breaks: 9 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.10, per 1000 atoms: 0.21 Number of scatterers: 23913 At special positions: 0 Unit cell: (132.288, 126.464, 170.56, 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 101 16.00 O 4595 8.00 N 3886 7.00 C 15331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 390 " - pdb=" SG CYS C 524 " distance=2.03 Simple disulfide: pdb=" SG CYS C 479 " - pdb=" SG CYS C 487 " distance=2.03 Simple disulfide: pdb=" SG CYS C 537 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 661 " - pdb=" SG CYS C 670 " distance=2.03 Simple disulfide: pdb=" SG CYS C 737 " - pdb=" SG CYS C 759 " distance=2.03 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 748 " distance=2.03 Simple disulfide: pdb=" SG CYS C1031 " - pdb=" SG CYS C1042 " distance=2.03 Simple disulfide: pdb=" SG CYS C1081 " - pdb=" SG CYS C1125 " 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 M 1 " - " NAG M 2 " NAG-ASN " NAG A1301 " - " ASN A 529 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 529 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B 61 " " NAG C1301 " - " ASN C 281 " " NAG C1302 " - " ASN C 800 " " NAG C1303 " - " ASN C1097 " " NAG C1304 " - " ASN C1073 " " NAG C1305 " - " ASN C 708 " " NAG C1306 " - " ASN C 330 " " NAG C1307 " - " ASN C 342 " " NAG C1308 " - " ASN C 528 " " NAG C1309 " - " ASN C 233 " " NAG C1311 " - " ASN C 615 " " NAG C1312 " - " ASN C 656 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN B 282 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN C 716 " " NAG M 1 " - " ASN C1133 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 950.4 milliseconds 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5566 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 44 sheets defined 26.8% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.717A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.147A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.286A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.757A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) 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: 3.632A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.560A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.289A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.709A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) 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: 4.662A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.237A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.948A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.683A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 417 through 421 removed outlier: 3.801A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 421' Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.564A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.012A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.593A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.525A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.696A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.312A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.582A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) 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: 4.085A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.409A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.542A pdb=" N VAL C 340 " --> pdb=" O PRO C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.596A pdb=" N TRP C 352 " --> pdb=" O VAL C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.547A pdb=" N TYR C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 388 removed outlier: 4.715A pdb=" N ASN C 387 " --> pdb=" O THR C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 629 through 635 removed outlier: 3.961A pdb=" N TYR C 635 " --> pdb=" O THR C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 743 Processing helix chain 'C' and resid 745 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 757 through 782 removed outlier: 3.597A pdb=" N ASP C 774 " --> pdb=" O ALA C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 825 Processing helix chain 'C' and resid 865 through 883 Processing helix chain 'C' and resid 885 through 889 Processing helix chain 'C' and resid 896 through 908 Processing helix chain 'C' and resid 912 through 917 Processing helix chain 'C' and resid 918 through 940 removed outlier: 3.700A pdb=" N GLN C 934 " --> pdb=" O ILE C 930 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP C 935 " --> pdb=" O GLY C 931 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 940 " --> pdb=" O SER C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 964 Processing helix chain 'C' and resid 965 through 967 No H-bonds generated for 'chain 'C' and resid 965 through 967' Processing helix chain 'C' and resid 975 through 983 Processing helix chain 'C' and resid 984 through 1032 removed outlier: 4.749A pdb=" N VAL C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 8.199A pdb=" N ASN A 62 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR A 269 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER A 206 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.972A 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 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA6, first strand: chain 'A' and resid 131 through 133 removed outlier: 3.662A pdb=" N PHE A 169 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU A 133 " --> pdb=" O CYS A 167 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS A 167 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.409A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.242A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.881A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.647A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.566A pdb=" N LYS A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.876A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.876A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.563A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.047A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.222A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.596A pdb=" N GLY C 565 " --> pdb=" O ASP C 573 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP C 573 " --> pdb=" O ILE C 586 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.475A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.526A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.484A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.919A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR B 376 " --> pdb=" O SER B 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.509A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.959A pdb=" N LYS B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR B 696 " --> pdb=" O LYS B 654 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.851A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.851A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.592A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 790 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.136A pdb=" N ASN C 61 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR C 268 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE C 201 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP C 227 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 203 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.003A pdb=" N ASP C 286 " --> pdb=" O LYS C 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.540A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 310 through 318 removed outlier: 7.143A pdb=" N VAL C 594 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN C 316 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY C 592 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY C 593 " --> pdb=" O GLN C 612 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.607A pdb=" N ASN C 353 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN C 393 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.524A pdb=" N CYS C 360 " --> pdb=" O CYS C 524 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 653 through 654 removed outlier: 6.106A pdb=" N LYS C 653 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR C 695 " --> pdb=" O LYS C 653 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 669 " --> pdb=" O ILE C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 710 through 727 removed outlier: 6.870A pdb=" N GLN C1070 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE C 717 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C 719 " --> pdb=" O TYR C1066 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR C1066 " --> pdb=" O ILE C 719 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 721 " --> pdb=" O VAL C1064 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C1064 " --> pdb=" O VAL C 721 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR C 723 " --> pdb=" O LEU C1062 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C1062 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 725 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL C1060 " --> pdb=" O ILE C 725 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY C1058 " --> pdb=" O PRO C 727 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR C1066 " --> pdb=" O HIS C1047 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1047 " --> pdb=" O TYR C1066 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 710 through 727 removed outlier: 6.870A pdb=" N GLN C1070 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE C 717 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C 719 " --> pdb=" O TYR C1066 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR C1066 " --> pdb=" O ILE C 719 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 721 " --> pdb=" O VAL C1064 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C1064 " --> pdb=" O VAL C 721 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR C 723 " --> pdb=" O LEU C1062 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C1062 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 725 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL C1060 " --> pdb=" O ILE C 725 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY C1058 " --> pdb=" O PRO C 727 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C1075 " --> pdb=" O SER C1096 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 732 through 735 removed outlier: 4.518A pdb=" N LYS C 732 " --> pdb=" O LEU C 860 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1119 through 1121 1000 hydrogen bonds defined for protein. 2748 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: 4.88 Time building geometry restraints manager: 2.55 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: 6309 1.33 - 1.46: 5157 1.46 - 1.58: 12882 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24473 Sorted by residual: bond pdb=" N ILE A 198 " pdb=" CA ILE A 198 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 1.01e+01 bond pdb=" N PHE C 897 " pdb=" CA PHE C 897 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.80e+00 bond pdb=" N ASN C 342 " pdb=" CA ASN C 342 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.12e-02 7.97e+03 8.97e+00 bond pdb=" N ILE B 197 " pdb=" CA ILE B 197 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.22e-02 6.72e+03 8.39e+00 bond pdb=" N VAL C 910 " pdb=" CA VAL C 910 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.20e-02 6.94e+03 8.28e+00 ... (remaining 24468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 32555 1.88 - 3.77: 702 3.77 - 5.65: 42 5.65 - 7.53: 10 7.53 - 9.42: 4 Bond angle restraints: 33313 Sorted by residual: angle pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" O GLY B 107 " ideal model delta sigma weight residual 120.91 118.26 2.65 6.90e-01 2.10e+00 1.48e+01 angle pdb=" CA GLY A 593 " pdb=" C GLY A 593 " pdb=" O GLY A 593 " ideal model delta sigma weight residual 121.75 118.10 3.65 1.02e+00 9.61e-01 1.28e+01 angle pdb=" N PHE C 905 " pdb=" CA PHE C 905 " pdb=" C PHE C 905 " ideal model delta sigma weight residual 111.36 107.47 3.89 1.09e+00 8.42e-01 1.28e+01 angle pdb=" N VAL B1128 " pdb=" CA VAL B1128 " pdb=" C VAL B1128 " ideal model delta sigma weight residual 113.53 110.08 3.45 9.80e-01 1.04e+00 1.24e+01 angle pdb=" N THR B 236 " pdb=" CA THR B 236 " pdb=" C THR B 236 " ideal model delta sigma weight residual 114.04 109.72 4.32 1.24e+00 6.50e-01 1.21e+01 ... (remaining 33308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 13672 17.72 - 35.45: 1119 35.45 - 53.17: 216 53.17 - 70.89: 117 70.89 - 88.61: 11 Dihedral angle restraints: 15135 sinusoidal: 6501 harmonic: 8634 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.29 -73.29 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CB CYS C 479 " pdb=" SG CYS C 479 " pdb=" SG CYS C 487 " pdb=" CB CYS C 487 " ideal model delta sinusoidal sigma weight residual -86.00 -156.98 70.98 1 1.00e+01 1.00e-02 6.47e+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 -15.06 -70.94 1 1.00e+01 1.00e-02 6.47e+01 ... (remaining 15132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3091 0.051 - 0.103: 619 0.103 - 0.154: 191 0.154 - 0.206: 15 0.206 - 0.257: 1 Chirality restraints: 3917 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.85e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.05e+00 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.92e+00 ... (remaining 3914 not shown) Planarity restraints: 4249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 356 " 0.263 9.50e-02 1.11e+02 1.18e-01 8.53e+00 pdb=" NE ARG C 356 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 356 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 356 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 356 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 454 " -0.181 9.50e-02 1.11e+02 8.09e-02 4.02e+00 pdb=" NE ARG A 454 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 454 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 454 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 454 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO B 373 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " -0.025 5.00e-02 4.00e+02 ... (remaining 4246 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 11561 2.96 - 3.45: 21549 3.45 - 3.93: 39198 3.93 - 4.42: 43895 4.42 - 4.90: 73248 Nonbonded interactions: 189451 Sorted by model distance: nonbonded pdb=" O SER A 443 " pdb=" OG SER A 443 " model vdw 2.480 3.040 nonbonded pdb=" O ASN C1097 " pdb=" OD1 ASN C1097 " model vdw 2.509 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.521 3.040 nonbonded pdb=" O SER A 496 " pdb=" OG SER A 496 " model vdw 2.552 3.040 nonbonded pdb=" OG1 THR C 911 " pdb=" OD1 ASN C 913 " model vdw 2.552 3.040 ... (remaining 189446 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 29 through 136 or resid 164 through 173 or resid 188 throu \ gh 413 or resid 417 through 439 or resid 442 or resid 450 through 469 or resid 4 \ 72 through 473 or resid 489 through 500 or resid 506 through 518 or resid 520 th \ rough 827 or resid 856 through 1306)) selection = (chain 'B' and (resid 28 through 67 or resid 82 through 110 or resid 115 through \ 135 or resid 163 through 172 or resid 187 through 210 or resid 214 through 241 \ or resid 264 through 439 or resid 442 or resid 450 through 827 or resid 856 thro \ ugh 1306)) selection = (chain 'C' and (resid 28 through 67 or resid 82 through 172 or resid 187 through \ 210 or resid 213 through 240 or resid 263 through 412 or resid 416 through 438 \ or resid 445 or resid 449 through 468 or resid 471 through 472 or resid 488 thro \ ugh 499 or resid 505 through 517 or resid 519 through 1306)) } 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' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.900 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: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.800 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 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 24553 Z= 0.231 Angle : 0.611 9.416 33516 Z= 0.370 Chirality : 0.047 0.257 3917 Planarity : 0.005 0.118 4216 Dihedral : 13.915 88.615 9458 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.69 % Allowed : 11.44 % Favored : 87.87 % 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: 0.22 (0.15), residues: 2891 helix: 2.15 (0.21), residues: 677 sheet: 0.54 (0.20), residues: 652 loop : -0.96 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 633 TYR 0.018 0.001 TYR B 421 PHE 0.028 0.001 PHE B 939 TRP 0.006 0.001 TRP B 886 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.23 (24473) covalent geometry : angle 0.60448 / 0.37 (33313) SS BOND : bond 0.00319 / 0.22 ( 37) SS BOND : angle 0.99864 / 0.68 ( 74) hydrogen bonds : bond 0.16181 / 10.23 ( 985) hydrogen bonds : angle 7.63527 / 5.34 ( 2748) link_BETA1-4 : bond 0.00227 / 0.11 ( 10) link_BETA1-4 : angle 1.33284 / 0.79 ( 30) link_NAG-ASN : bond 0.00170 / 0.10 ( 33) link_NAG-ASN : angle 1.52872 / 1.04 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9170 (tt0) cc_final: 0.8892 (tp40) REVERT: A 119 LEU cc_start: 0.9019 (tp) cc_final: 0.8709 (tm) REVERT: A 130 LYS cc_start: 0.8220 (mttt) cc_final: 0.7832 (mtmm) REVERT: A 161 TYR cc_start: 0.7764 (p90) cc_final: 0.7303 (p90) REVERT: A 169 PHE cc_start: 0.7601 (m-80) cc_final: 0.6647 (m-10) REVERT: A 198 ILE cc_start: 0.7627 (pt) cc_final: 0.7010 (pp) REVERT: A 231 ILE cc_start: 0.9065 (mt) cc_final: 0.8739 (mm) REVERT: A 460 LYS cc_start: 0.9032 (mmtp) cc_final: 0.8630 (mmtm) REVERT: B 131 CYS cc_start: 0.6535 (OUTLIER) cc_final: 0.5927 (m) REVERT: B 172 PHE cc_start: 0.7951 (t80) cc_final: 0.7510 (t80) REVERT: B 492 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6170 (mm) REVERT: B 495 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.5910 (p90) REVERT: C 197 ILE cc_start: 0.8958 (pt) cc_final: 0.8653 (pp) REVERT: C 213 ARG cc_start: 0.7830 (tpp80) cc_final: 0.7550 (tpp80) REVERT: C 345 ARG cc_start: 0.8950 (mtp-110) cc_final: 0.8326 (mtp85) REVERT: C 477 ASN cc_start: 0.8461 (m-40) cc_final: 0.8125 (t0) REVERT: C 492 GLN cc_start: 0.8166 (tp40) cc_final: 0.7962 (tp40) REVERT: C 515 GLU cc_start: 0.8063 (tp30) cc_final: 0.7668 (tp30) outliers start: 18 outliers final: 12 residues processed: 152 average time/residue: 0.5422 time to fit residues: 97.3943 Evaluate side-chains 120 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 938 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS B 234 ASN B 949 GLN C 207 HIS C 906 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.091561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058534 restraints weight = 49756.895| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.95 r_work: 0.2728 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24553 Z= 0.227 Angle : 0.575 9.226 33516 Z= 0.296 Chirality : 0.047 0.260 3917 Planarity : 0.004 0.047 4216 Dihedral : 5.698 59.898 4137 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.03 % Allowed : 10.98 % Favored : 86.99 % 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: 0.17 (0.15), residues: 2891 helix: 2.16 (0.20), residues: 688 sheet: 0.47 (0.19), residues: 668 loop : -1.05 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1106 TYR 0.017 0.002 TYR A 171 PHE 0.018 0.002 PHE B 65 TRP 0.030 0.001 TRP B 452 HIS 0.006 0.001 HIS C1063 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (24473) covalent geometry : angle 0.56488 / 0.29 (33313) SS BOND : bond 0.00387 / 0.26 ( 37) SS BOND : angle 1.24311 / 0.88 ( 74) hydrogen bonds : bond 0.05808 / 3.80 ( 985) hydrogen bonds : angle 5.74684 / 3.99 ( 2748) link_BETA1-4 : bond 0.00126 / 0.06 ( 10) link_BETA1-4 : angle 1.44958 / 0.86 ( 30) link_NAG-ASN : bond 0.00264 / 0.17 ( 33) link_NAG-ASN : angle 1.69043 / 1.15 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 111 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9150 (tt0) cc_final: 0.8844 (tp40) REVERT: A 97 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6140 (mt-10) REVERT: A 119 LEU cc_start: 0.9167 (tp) cc_final: 0.8914 (tm) REVERT: A 130 LYS cc_start: 0.8455 (mttt) cc_final: 0.8054 (mtmm) REVERT: A 161 TYR cc_start: 0.7737 (p90) cc_final: 0.7246 (p90) REVERT: A 169 PHE cc_start: 0.7714 (m-80) cc_final: 0.7195 (m-10) REVERT: A 198 ILE cc_start: 0.8082 (pt) cc_final: 0.7842 (pp) REVERT: A 231 ILE cc_start: 0.9128 (mt) cc_final: 0.8866 (mp) REVERT: A 493 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: A 985 ASP cc_start: 0.7955 (p0) cc_final: 0.7755 (p0) REVERT: A 988 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8753 (tm-30) REVERT: A 994 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: A 1050 MET cc_start: 0.9242 (ptm) cc_final: 0.8992 (ptm) REVERT: B 172 PHE cc_start: 0.8016 (t80) cc_final: 0.7607 (t80) REVERT: B 314 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: B 452 TRP cc_start: 0.8621 (m100) cc_final: 0.8106 (m100) REVERT: B 495 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.5512 (p90) REVERT: C 213 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7582 (tpp80) REVERT: C 345 ARG cc_start: 0.8996 (mtp-110) cc_final: 0.8338 (mtp85) REVERT: C 423 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8739 (tppt) REVERT: C 459 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9125 (mtpm) REVERT: C 477 ASN cc_start: 0.8441 (m-40) cc_final: 0.8157 (t0) REVERT: C 515 GLU cc_start: 0.7997 (tp30) cc_final: 0.7599 (tp30) outliers start: 53 outliers final: 24 residues processed: 149 average time/residue: 0.4871 time to fit residues: 87.5750 Evaluate side-chains 136 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 915 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 61 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 295 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.092799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.060104 restraints weight = 49478.300| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.93 r_work: 0.2768 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24553 Z= 0.110 Angle : 0.499 9.449 33516 Z= 0.254 Chirality : 0.043 0.258 3917 Planarity : 0.004 0.044 4216 Dihedral : 5.442 58.893 4124 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.99 % Allowed : 11.21 % Favored : 86.80 % 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: 0.32 (0.15), residues: 2891 helix: 2.39 (0.20), residues: 678 sheet: 0.58 (0.19), residues: 661 loop : -0.99 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 236 TYR 0.017 0.001 TYR A 171 PHE 0.014 0.001 PHE B 65 TRP 0.021 0.001 TRP B 452 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (24473) covalent geometry : angle 0.48978 / 0.25 (33313) SS BOND : bond 0.00314 / 0.22 ( 37) SS BOND : angle 1.01928 / 0.71 ( 74) hydrogen bonds : bond 0.04757 / 3.10 ( 985) hydrogen bonds : angle 5.35781 / 3.71 ( 2748) link_BETA1-4 : bond 0.00227 / 0.11 ( 10) link_BETA1-4 : angle 1.30318 / 0.77 ( 30) link_NAG-ASN : bond 0.00209 / 0.13 ( 33) link_NAG-ASN : angle 1.55323 / 1.06 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9158 (tt0) cc_final: 0.8869 (tp40) REVERT: A 119 LEU cc_start: 0.9170 (tp) cc_final: 0.8905 (tm) REVERT: A 130 LYS cc_start: 0.8386 (mttt) cc_final: 0.7986 (mtmm) REVERT: A 161 TYR cc_start: 0.7758 (p90) cc_final: 0.7248 (p90) REVERT: A 169 PHE cc_start: 0.7706 (m-80) cc_final: 0.7165 (m-10) REVERT: A 198 ILE cc_start: 0.8138 (pt) cc_final: 0.7901 (pp) REVERT: A 231 ILE cc_start: 0.9136 (mt) cc_final: 0.8861 (mp) REVERT: A 493 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: A 995 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8130 (mtp180) REVERT: A 1050 MET cc_start: 0.9221 (ptm) cc_final: 0.8949 (ptm) REVERT: B 172 PHE cc_start: 0.8035 (t80) cc_final: 0.7620 (t80) REVERT: B 314 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8692 (tm-30) REVERT: B 452 TRP cc_start: 0.8598 (m100) cc_final: 0.7988 (m100) REVERT: B 495 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.5365 (p90) REVERT: C 83 VAL cc_start: 0.6209 (OUTLIER) cc_final: 0.5910 (p) REVERT: C 213 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7571 (tpp80) REVERT: C 345 ARG cc_start: 0.8954 (mtp-110) cc_final: 0.8355 (mtp85) REVERT: C 423 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8748 (tppt) REVERT: C 459 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9180 (mtpm) REVERT: C 477 ASN cc_start: 0.8464 (m-40) cc_final: 0.8185 (t0) REVERT: C 515 GLU cc_start: 0.7946 (tp30) cc_final: 0.7636 (tp30) outliers start: 52 outliers final: 19 residues processed: 152 average time/residue: 0.5294 time to fit residues: 96.5457 Evaluate side-chains 130 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 899 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 128 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 216 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 250 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.092610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.059904 restraints weight = 49333.238| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.92 r_work: 0.2764 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24553 Z= 0.122 Angle : 0.498 9.438 33516 Z= 0.252 Chirality : 0.044 0.262 3917 Planarity : 0.004 0.045 4216 Dihedral : 5.284 58.449 4120 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.18 % Allowed : 11.21 % Favored : 86.61 % 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: 2891 helix: 2.49 (0.20), residues: 672 sheet: 0.59 (0.20), residues: 651 loop : -0.95 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 236 TYR 0.016 0.001 TYR A 171 PHE 0.015 0.001 PHE B 65 TRP 0.017 0.001 TRP B 452 HIS 0.003 0.001 HIS C1063 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (24473) covalent geometry : angle 0.48828 / 0.25 (33313) SS BOND : bond 0.00295 / 0.21 ( 37) SS BOND : angle 0.98873 / 0.69 ( 74) hydrogen bonds : bond 0.04600 / 3.01 ( 985) hydrogen bonds : angle 5.12842 / 3.55 ( 2748) link_BETA1-4 : bond 0.00191 / 0.09 ( 10) link_BETA1-4 : angle 1.28392 / 0.76 ( 30) link_NAG-ASN : bond 0.00194 / 0.12 ( 33) link_NAG-ASN : angle 1.53856 / 1.06 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 110 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9167 (tt0) cc_final: 0.8875 (tp40) REVERT: A 119 LEU cc_start: 0.9165 (tp) cc_final: 0.8928 (tm) REVERT: A 130 LYS cc_start: 0.8407 (mttt) cc_final: 0.8007 (mtmm) REVERT: A 161 TYR cc_start: 0.7735 (p90) cc_final: 0.7229 (p90) REVERT: A 169 PHE cc_start: 0.7735 (m-80) cc_final: 0.7242 (m-10) REVERT: A 198 ILE cc_start: 0.8287 (pt) cc_final: 0.8058 (pp) REVERT: A 231 ILE cc_start: 0.9150 (mt) cc_final: 0.8873 (mp) REVERT: A 493 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: A 995 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8124 (mtp180) REVERT: A 1050 MET cc_start: 0.9200 (ptm) cc_final: 0.8894 (ptm) REVERT: B 172 PHE cc_start: 0.8057 (t80) cc_final: 0.7641 (t80) REVERT: B 186 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6848 (p90) REVERT: B 314 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8668 (tm-30) REVERT: B 452 TRP cc_start: 0.8500 (m100) cc_final: 0.7927 (m100) REVERT: C 345 ARG cc_start: 0.8964 (mtp-110) cc_final: 0.8340 (mtp85) REVERT: C 413 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8621 (mm-40) REVERT: C 423 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8751 (tppt) REVERT: C 459 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9176 (mtpm) REVERT: C 477 ASN cc_start: 0.8483 (m-40) cc_final: 0.8224 (t0) REVERT: C 515 GLU cc_start: 0.7985 (tp30) cc_final: 0.7631 (tp30) REVERT: C 580 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8580 (p) REVERT: C 585 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8544 (m-30) outliers start: 57 outliers final: 26 residues processed: 152 average time/residue: 0.5026 time to fit residues: 91.8467 Evaluate side-chains 140 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 ASP Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 915 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 255 optimal weight: 0.0370 chunk 202 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 chunk 216 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 293 optimal weight: 0.3980 chunk 284 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN C 486 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.061700 restraints weight = 48971.891| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.86 r_work: 0.2795 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24553 Z= 0.091 Angle : 0.474 9.501 33516 Z= 0.239 Chirality : 0.043 0.258 3917 Planarity : 0.004 0.044 4216 Dihedral : 5.087 58.044 4118 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.61 % Allowed : 12.17 % Favored : 86.22 % 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: 2891 helix: 2.61 (0.20), residues: 672 sheet: 0.71 (0.20), residues: 646 loop : -0.89 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 213 TYR 0.016 0.001 TYR A 171 PHE 0.022 0.001 PHE B 939 TRP 0.014 0.001 TRP B 452 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (24473) covalent geometry : angle 0.46558 / 0.24 (33313) SS BOND : bond 0.00283 / 0.18 ( 37) SS BOND : angle 0.87423 / 0.61 ( 74) hydrogen bonds : bond 0.03988 / 2.61 ( 985) hydrogen bonds : angle 4.90950 / 3.39 ( 2748) link_BETA1-4 : bond 0.00272 / 0.13 ( 10) link_BETA1-4 : angle 1.19799 / 0.71 ( 30) link_NAG-ASN : bond 0.00198 / 0.12 ( 33) link_NAG-ASN : angle 1.44633 / 1.00 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9160 (tt0) cc_final: 0.8869 (tp40) REVERT: A 119 LEU cc_start: 0.9159 (tp) cc_final: 0.8912 (tm) REVERT: A 130 LYS cc_start: 0.8407 (mttt) cc_final: 0.8010 (mtmm) REVERT: A 161 TYR cc_start: 0.7767 (p90) cc_final: 0.7271 (p90) REVERT: A 169 PHE cc_start: 0.7715 (m-80) cc_final: 0.7259 (m-10) REVERT: A 198 ILE cc_start: 0.8334 (pt) cc_final: 0.8110 (pp) REVERT: A 231 ILE cc_start: 0.9153 (mt) cc_final: 0.8870 (mp) REVERT: A 493 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: A 995 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8087 (mtp180) REVERT: A 1050 MET cc_start: 0.9175 (ptm) cc_final: 0.8876 (ptm) REVERT: B 172 PHE cc_start: 0.8112 (t80) cc_final: 0.7660 (t80) REVERT: B 186 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6847 (p90) REVERT: B 314 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.8726 (tm-30) REVERT: B 495 TYR cc_start: 0.5929 (t80) cc_final: 0.4913 (t80) REVERT: C 345 ARG cc_start: 0.8973 (mtp-110) cc_final: 0.8425 (mtp85) REVERT: C 413 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8635 (mm-40) REVERT: C 423 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8808 (tppt) REVERT: C 477 ASN cc_start: 0.8496 (m-40) cc_final: 0.8130 (t0) REVERT: C 515 GLU cc_start: 0.7957 (tp30) cc_final: 0.7611 (tp30) REVERT: C 580 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8618 (p) REVERT: C 585 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8540 (m-30) outliers start: 42 outliers final: 18 residues processed: 145 average time/residue: 0.4406 time to fit residues: 77.3699 Evaluate side-chains 132 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 ASP Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 915 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 272 optimal weight: 0.0000 chunk 103 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.061267 restraints weight = 49442.460| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.87 r_work: 0.2785 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24553 Z= 0.100 Angle : 0.475 9.454 33516 Z= 0.240 Chirality : 0.043 0.259 3917 Planarity : 0.004 0.045 4216 Dihedral : 5.067 58.989 4118 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.88 % Allowed : 12.02 % Favored : 86.11 % 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: 0.56 (0.15), residues: 2891 helix: 2.64 (0.20), residues: 672 sheet: 0.72 (0.20), residues: 648 loop : -0.84 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 213 TYR 0.015 0.001 TYR A 171 PHE 0.022 0.001 PHE A 939 TRP 0.012 0.001 TRP B 452 HIS 0.003 0.000 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (24473) covalent geometry : angle 0.46604 / 0.24 (33313) SS BOND : bond 0.00267 / 0.18 ( 37) SS BOND : angle 0.90403 / 0.62 ( 74) hydrogen bonds : bond 0.04091 / 2.68 ( 985) hydrogen bonds : angle 4.83596 / 3.33 ( 2748) link_BETA1-4 : bond 0.00247 / 0.12 ( 10) link_BETA1-4 : angle 1.19882 / 0.71 ( 30) link_NAG-ASN : bond 0.00177 / 0.11 ( 33) link_NAG-ASN : angle 1.45447 / 1.01 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9162 (tt0) cc_final: 0.8873 (tp40) REVERT: A 119 LEU cc_start: 0.9157 (tp) cc_final: 0.8935 (tm) REVERT: A 130 LYS cc_start: 0.8394 (mttt) cc_final: 0.8008 (mtmm) REVERT: A 161 TYR cc_start: 0.7765 (p90) cc_final: 0.7252 (p90) REVERT: A 169 PHE cc_start: 0.7730 (m-80) cc_final: 0.7294 (m-10) REVERT: A 198 ILE cc_start: 0.8364 (pt) cc_final: 0.8137 (pp) REVERT: A 231 ILE cc_start: 0.9132 (mt) cc_final: 0.8853 (mp) REVERT: A 493 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: A 995 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8101 (mtp180) REVERT: A 1050 MET cc_start: 0.9177 (ptm) cc_final: 0.8855 (ptm) REVERT: B 172 PHE cc_start: 0.8122 (t80) cc_final: 0.7666 (t80) REVERT: B 186 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6870 (p90) REVERT: B 314 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8718 (tm-30) REVERT: B 495 TYR cc_start: 0.5887 (t80) cc_final: 0.4889 (t80) REVERT: C 345 ARG cc_start: 0.8975 (mtp-110) cc_final: 0.8392 (mtp85) REVERT: C 413 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8638 (mm-40) REVERT: C 423 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8812 (tppt) REVERT: C 477 ASN cc_start: 0.8364 (m-40) cc_final: 0.8135 (t0) REVERT: C 580 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8598 (p) REVERT: C 585 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8550 (m-30) REVERT: C 633 ARG cc_start: 0.7993 (mpt-90) cc_final: 0.7705 (mpt-90) outliers start: 49 outliers final: 24 residues processed: 147 average time/residue: 0.4999 time to fit residues: 88.6961 Evaluate side-chains 139 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 ASP Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 915 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 192 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 215 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061224 restraints weight = 49312.825| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.89 r_work: 0.2783 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24553 Z= 0.103 Angle : 0.478 9.442 33516 Z= 0.242 Chirality : 0.043 0.258 3917 Planarity : 0.004 0.045 4216 Dihedral : 5.067 58.637 4118 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.57 % Allowed : 12.40 % Favored : 86.03 % 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: 0.60 (0.15), residues: 2891 helix: 2.73 (0.20), residues: 666 sheet: 0.69 (0.20), residues: 649 loop : -0.80 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 213 TYR 0.015 0.001 TYR A 171 PHE 0.013 0.001 PHE B 65 TRP 0.010 0.001 TRP B 452 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (24473) covalent geometry : angle 0.46962 / 0.24 (33313) SS BOND : bond 0.00254 / 0.18 ( 37) SS BOND : angle 0.97689 / 0.69 ( 74) hydrogen bonds : bond 0.04085 / 2.68 ( 985) hydrogen bonds : angle 4.80907 / 3.31 ( 2748) link_BETA1-4 : bond 0.00247 / 0.12 ( 10) link_BETA1-4 : angle 1.18347 / 0.70 ( 30) link_NAG-ASN : bond 0.00173 / 0.11 ( 33) link_NAG-ASN : angle 1.44574 / 1.00 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9152 (tt0) cc_final: 0.8857 (tp40) REVERT: A 119 LEU cc_start: 0.9172 (tp) cc_final: 0.8944 (tm) REVERT: A 130 LYS cc_start: 0.8404 (mttt) cc_final: 0.8006 (mtmm) REVERT: A 161 TYR cc_start: 0.7761 (p90) cc_final: 0.7231 (p90) REVERT: A 169 PHE cc_start: 0.7748 (m-80) cc_final: 0.7314 (m-10) REVERT: A 198 ILE cc_start: 0.8370 (pt) cc_final: 0.8140 (pp) REVERT: A 231 ILE cc_start: 0.9141 (mt) cc_final: 0.8862 (mp) REVERT: A 493 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: A 995 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8103 (mtp180) REVERT: A 1050 MET cc_start: 0.9185 (ptm) cc_final: 0.8894 (ptm) REVERT: B 172 PHE cc_start: 0.8121 (t80) cc_final: 0.7665 (t80) REVERT: B 186 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6837 (p90) REVERT: B 314 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: B 495 TYR cc_start: 0.5947 (t80) cc_final: 0.4954 (t80) REVERT: C 345 ARG cc_start: 0.8971 (mtp-110) cc_final: 0.8409 (mtp85) REVERT: C 413 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8625 (mm-40) REVERT: C 423 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8805 (tppt) REVERT: C 477 ASN cc_start: 0.8393 (m-40) cc_final: 0.8162 (t0) REVERT: C 580 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8589 (p) outliers start: 41 outliers final: 24 residues processed: 140 average time/residue: 0.5198 time to fit residues: 87.8610 Evaluate side-chains 138 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 915 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 91 optimal weight: 0.9990 chunk 236 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.092411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060153 restraints weight = 49123.139| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.86 r_work: 0.2757 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24553 Z= 0.134 Angle : 0.499 9.373 33516 Z= 0.255 Chirality : 0.044 0.259 3917 Planarity : 0.004 0.046 4216 Dihedral : 5.156 59.330 4118 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.65 % Allowed : 12.36 % Favored : 85.99 % 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: 0.52 (0.15), residues: 2891 helix: 2.62 (0.20), residues: 672 sheet: 0.64 (0.20), residues: 653 loop : -0.84 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 213 TYR 0.015 0.001 TYR A 171 PHE 0.015 0.001 PHE C 172 TRP 0.009 0.001 TRP B 452 HIS 0.004 0.001 HIS C1063 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (24473) covalent geometry : angle 0.48942 / 0.25 (33313) SS BOND : bond 0.00327 / 0.22 ( 37) SS BOND : angle 1.00273 / 0.71 ( 74) hydrogen bonds : bond 0.04601 / 3.02 ( 985) hydrogen bonds : angle 4.90941 / 3.38 ( 2748) link_BETA1-4 : bond 0.00180 / 0.09 ( 10) link_BETA1-4 : angle 1.21176 / 0.72 ( 30) link_NAG-ASN : bond 0.00170 / 0.11 ( 33) link_NAG-ASN : angle 1.53803 / 1.06 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9174 (tt0) cc_final: 0.8918 (tp40) REVERT: A 119 LEU cc_start: 0.9171 (tp) cc_final: 0.8958 (tm) REVERT: A 130 LYS cc_start: 0.8390 (mttt) cc_final: 0.8002 (mtmm) REVERT: A 161 TYR cc_start: 0.7722 (p90) cc_final: 0.7188 (p90) REVERT: A 169 PHE cc_start: 0.7768 (m-80) cc_final: 0.7328 (m-10) REVERT: A 198 ILE cc_start: 0.8437 (pt) cc_final: 0.8206 (pp) REVERT: A 231 ILE cc_start: 0.9145 (mt) cc_final: 0.8883 (mp) REVERT: A 493 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: A 995 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8116 (mtp180) REVERT: A 1050 MET cc_start: 0.9196 (ptm) cc_final: 0.8883 (ptm) REVERT: B 172 PHE cc_start: 0.8104 (t80) cc_final: 0.7651 (t80) REVERT: B 186 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6769 (p90) REVERT: B 242 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8130 (mm) REVERT: B 314 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8690 (tm-30) REVERT: B 495 TYR cc_start: 0.5978 (t80) cc_final: 0.4968 (t80) REVERT: C 345 ARG cc_start: 0.8981 (mtp-110) cc_final: 0.8421 (mtp85) REVERT: C 413 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8617 (mm-40) REVERT: C 423 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8802 (tppt) REVERT: C 477 ASN cc_start: 0.8245 (m-40) cc_final: 0.7990 (t0) REVERT: C 580 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8570 (p) REVERT: C 633 ARG cc_start: 0.7995 (mpt-90) cc_final: 0.7652 (mpt-90) outliers start: 43 outliers final: 26 residues processed: 136 average time/residue: 0.4813 time to fit residues: 79.3710 Evaluate side-chains 138 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 915 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 192 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 293 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.093498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.061438 restraints weight = 49341.091| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.87 r_work: 0.2787 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24553 Z= 0.095 Angle : 0.473 9.483 33516 Z= 0.240 Chirality : 0.043 0.258 3917 Planarity : 0.004 0.046 4216 Dihedral : 5.067 59.239 4118 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.34 % Allowed : 12.82 % Favored : 85.84 % 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: 0.63 (0.15), residues: 2891 helix: 2.80 (0.20), residues: 660 sheet: 0.72 (0.20), residues: 644 loop : -0.78 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 213 TYR 0.015 0.001 TYR A 171 PHE 0.012 0.001 PHE C 172 TRP 0.010 0.001 TRP B 452 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (24473) covalent geometry : angle 0.46508 / 0.24 (33313) SS BOND : bond 0.00252 / 0.17 ( 37) SS BOND : angle 0.89312 / 0.63 ( 74) hydrogen bonds : bond 0.03999 / 2.62 ( 985) hydrogen bonds : angle 4.75011 / 3.27 ( 2748) link_BETA1-4 : bond 0.00279 / 0.14 ( 10) link_BETA1-4 : angle 1.14538 / 0.68 ( 30) link_NAG-ASN : bond 0.00188 / 0.12 ( 33) link_NAG-ASN : angle 1.42719 / 0.99 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9156 (tt0) cc_final: 0.8865 (tp40) REVERT: A 119 LEU cc_start: 0.9168 (tp) cc_final: 0.8947 (tm) REVERT: A 130 LYS cc_start: 0.8366 (mttt) cc_final: 0.7960 (mtmm) REVERT: A 161 TYR cc_start: 0.7777 (p90) cc_final: 0.7229 (p90) REVERT: A 169 PHE cc_start: 0.7750 (m-80) cc_final: 0.7338 (m-10) REVERT: A 198 ILE cc_start: 0.8494 (pt) cc_final: 0.8264 (pp) REVERT: A 231 ILE cc_start: 0.9143 (mt) cc_final: 0.8891 (mp) REVERT: A 493 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: A 995 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8108 (mtp180) REVERT: A 1050 MET cc_start: 0.9178 (ptm) cc_final: 0.8881 (ptm) REVERT: B 172 PHE cc_start: 0.8087 (t80) cc_final: 0.7643 (t80) REVERT: B 186 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6733 (p90) REVERT: B 242 LEU cc_start: 0.8443 (mm) cc_final: 0.8018 (mm) REVERT: B 314 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8719 (tm-30) REVERT: B 900 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8828 (mtp) REVERT: B 1142 GLN cc_start: 0.8483 (mm110) cc_final: 0.8282 (tm-30) REVERT: C 186 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7773 (p90) REVERT: C 345 ARG cc_start: 0.8969 (mtp-110) cc_final: 0.8446 (mtp85) REVERT: C 413 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8611 (mm-40) REVERT: C 423 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8829 (tppt) REVERT: C 477 ASN cc_start: 0.8315 (m-40) cc_final: 0.8073 (t0) REVERT: C 580 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8600 (p) REVERT: C 901 MET cc_start: 0.9422 (tpt) cc_final: 0.9185 (tpp) outliers start: 35 outliers final: 25 residues processed: 132 average time/residue: 0.4412 time to fit residues: 70.3877 Evaluate side-chains 141 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 915 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 27 optimal weight: 0.0870 chunk 224 optimal weight: 0.0370 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 292 optimal weight: 0.9990 chunk 265 optimal weight: 0.0370 chunk 272 optimal weight: 0.0030 chunk 192 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.095035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063266 restraints weight = 49235.111| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.88 r_work: 0.2831 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24553 Z= 0.084 Angle : 0.467 9.540 33516 Z= 0.235 Chirality : 0.043 0.257 3917 Planarity : 0.004 0.046 4216 Dihedral : 4.925 59.864 4118 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.11 % Allowed : 13.13 % Favored : 85.76 % 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: 0.77 (0.16), residues: 2891 helix: 2.91 (0.20), residues: 661 sheet: 0.86 (0.19), residues: 668 loop : -0.75 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 213 TYR 0.016 0.001 TYR B 495 PHE 0.013 0.001 PHE C 172 TRP 0.010 0.001 TRP B 452 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 (24473) covalent geometry : angle 0.46022 / 0.23 (33313) SS BOND : bond 0.00212 / 0.14 ( 37) SS BOND : angle 0.78756 / 0.55 ( 74) hydrogen bonds : bond 0.03450 / 2.25 ( 985) hydrogen bonds : angle 4.59730 / 3.17 ( 2748) link_BETA1-4 : bond 0.00310 / 0.15 ( 10) link_BETA1-4 : angle 1.08740 / 0.64 ( 30) link_NAG-ASN : bond 0.00202 / 0.12 ( 33) link_NAG-ASN : angle 1.32582 / 0.93 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5782 Ramachandran restraints generated. 2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9158 (tt0) cc_final: 0.8869 (tp40) REVERT: A 119 LEU cc_start: 0.9135 (tp) cc_final: 0.8908 (tm) REVERT: A 130 LYS cc_start: 0.8338 (mttt) cc_final: 0.7923 (mtmm) REVERT: A 161 TYR cc_start: 0.7757 (p90) cc_final: 0.7211 (p90) REVERT: A 169 PHE cc_start: 0.7745 (m-80) cc_final: 0.7322 (m-10) REVERT: A 198 ILE cc_start: 0.8515 (pt) cc_final: 0.8290 (pp) REVERT: A 231 ILE cc_start: 0.9094 (mt) cc_final: 0.8831 (mp) REVERT: A 427 ASP cc_start: 0.8871 (m-30) cc_final: 0.8516 (m-30) REVERT: A 493 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: A 634 ARG cc_start: 0.7372 (mmt180) cc_final: 0.7112 (mmt-90) REVERT: A 995 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8095 (mtp180) REVERT: A 1050 MET cc_start: 0.9178 (ptm) cc_final: 0.8883 (ptm) REVERT: B 172 PHE cc_start: 0.8105 (t80) cc_final: 0.7678 (t80) REVERT: B 186 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6761 (p90) REVERT: B 200 TYR cc_start: 0.8869 (m-80) cc_final: 0.8545 (m-80) REVERT: B 242 LEU cc_start: 0.8428 (mm) cc_final: 0.7992 (mm) REVERT: B 314 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: B 900 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8816 (mtp) REVERT: C 186 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7805 (p90) REVERT: C 345 ARG cc_start: 0.8959 (mtp-110) cc_final: 0.8438 (mtp85) REVERT: C 413 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8633 (mm-40) REVERT: C 470 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8125 (pt0) REVERT: C 477 ASN cc_start: 0.8336 (m-40) cc_final: 0.8074 (t0) REVERT: C 580 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8608 (p) REVERT: C 633 ARG cc_start: 0.8123 (mpt180) cc_final: 0.7715 (mmt90) REVERT: C 822 PHE cc_start: 0.8148 (t80) cc_final: 0.7778 (m-80) outliers start: 29 outliers final: 19 residues processed: 135 average time/residue: 0.4814 time to fit residues: 78.4952 Evaluate side-chains 130 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 915 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 288 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 256 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.092785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.060512 restraints weight = 49324.357| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.87 r_work: 0.2765 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24553 Z= 0.135 Angle : 0.502 9.353 33516 Z= 0.255 Chirality : 0.044 0.258 3917 Planarity : 0.004 0.047 4216 Dihedral : 5.061 59.833 4118 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.11 % Allowed : 13.43 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 2891 helix: 2.77 (0.20), residues: 660 sheet: 0.77 (0.19), residues: 672 loop : -0.83 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 213 TYR 0.018 0.001 TYR B 495 PHE 0.014 0.001 PHE C 172 TRP 0.007 0.001 TRP A 65 HIS 0.004 0.001 HIS C1063 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (24473) covalent geometry : angle 0.49334 / 0.25 (33313) SS BOND : bond 0.00303 / 0.21 ( 37) SS BOND : angle 0.95530 / 0.68 ( 74) hydrogen bonds : bond 0.04462 / 2.93 ( 985) hydrogen bonds : angle 4.80419 / 3.31 ( 2748) link_BETA1-4 : bond 0.00212 / 0.10 ( 10) link_BETA1-4 : angle 1.16339 / 0.69 ( 30) link_NAG-ASN : bond 0.00163 / 0.10 ( 33) link_NAG-ASN : angle 1.49013 / 1.03 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10411.14 seconds wall clock time: 177 minutes 20.12 seconds (10640.12 seconds total)