Starting phenix.real_space_refine on Sat Aug 8 02:16:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ysj_73393/08_2026/9ysj_73393.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ysj_73393/08_2026/9ysj_73393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ysj_73393/08_2026/9ysj_73393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ysj_73393/08_2026/9ysj_73393.map" model { file = "/net/cci-nas-00/data/ceres_data/9ysj_73393/08_2026/9ysj_73393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ysj_73393/08_2026/9ysj_73393.cif" } resolution = 2.62 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= 0.015 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 105 5.16 5 C 15636 2.51 5 N 3974 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 24413 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7814 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 56, 'TRANS': 937} Chain breaks: 9 Chain: "B" Number of atoms: 8058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8058 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 57, 'TRANS': 969} Chain breaks: 7 Chain: "C" Number of atoms: 7883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7883 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 56, 'TRANS': 946} Chain breaks: 8 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 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: 4.84, per 1000 atoms: 0.20 Number of scatterers: 24413 At special positions: 0 Unit cell: (127.296, 128.96, 168.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4698 8.00 N 3974 7.00 C 15636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.02 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=2.04 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 B 234 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " 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: 1.70 Conformation dependent library (CDL) restraints added in 759.7 milliseconds 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5674 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 46 sheets defined 27.3% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 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 349 through 353 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.960A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.209A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.311A 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 630 through 636 Processing helix chain 'A' and resid 737 through 743 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 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 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.039A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.685A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.534A 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: 4.470A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.580A 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 349 through 353 removed outlier: 3.991A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.662A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.020A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.844A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.252A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.609A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.575A 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: 3.716A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 834 removed outlier: 4.093A pdb=" N ALA B 829 " --> pdb=" O LYS B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.012A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.046A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.771A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (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: 3.977A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.333A 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 Processing helix chain 'C' and resid 348 through 352 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.655A pdb=" N ASN C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 removed outlier: 4.401A 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 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 444 through 448 removed outlier: 4.123A pdb=" N TYR C 448 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 635 removed outlier: 4.257A 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 754 removed outlier: 3.661A pdb=" N GLN C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 782 Processing helix chain 'C' and resid 815 through 825 Processing helix chain 'C' and resid 849 through 855 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 911 through 917 removed outlier: 4.058A pdb=" N LEU C 915 " --> pdb=" O THR C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 940 removed outlier: 3.708A pdb=" N GLN C 934 " --> pdb=" O ILE C 930 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP C 935 " --> pdb=" O GLY C 931 " (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: 4.657A pdb=" N VAL C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.084A 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.822A pdb=" N VAL A 37 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N LEU A 223 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N HIS A 208 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER A 206 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 229 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.768A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 131 through 133 removed outlier: 3.947A pdb=" N PHE A 169 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLU A 133 " --> pdb=" O CYS A 167 " (cutoff:3.500A) removed outlier: 6.632A 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: 6.826A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.325A 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: 5.349A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.667A 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: 4.046A 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: 6.673A 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 655 removed outlier: 5.976A pdb=" N LYS A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR A 696 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (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: 6.541A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.444A 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 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.429A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 30 removed outlier: 7.895A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.704A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.753A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.724A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.363A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.536A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.423A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.397A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.327A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 Processing sheet with id=AD4, first strand: chain 'B' and resid 840 through 841 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 29 through 30 Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.837A 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 Processing sheet with id=AD9, first strand: chain 'C' and resid 223 through 228 removed outlier: 5.248A pdb=" N SER C 205 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 310 through 318 removed outlier: 6.720A pdb=" N VAL C 594 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN C 316 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY C 592 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY C 593 " --> pdb=" O GLN C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.679A pdb=" N PHE C 542 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP C 573 " --> pdb=" O ILE C 586 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.700A pdb=" N ASN C 393 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.408A pdb=" N CYS C 360 " --> pdb=" O CYS C 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AE6, first strand: chain 'C' and resid 653 through 654 removed outlier: 5.938A pdb=" N LYS C 653 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR C 695 " --> pdb=" O LYS C 653 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA C 671 " --> pdb=" O PRO C 664 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 710 through 727 removed outlier: 6.536A pdb=" N SER C 710 " --> pdb=" O THR C1075 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C1075 " --> pdb=" O SER C 710 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA C 712 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN C1073 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU C1071 " --> pdb=" O PRO C 714 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY C1058 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER C1054 " --> pdb=" O GLY C1058 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C1060 " --> pdb=" O PRO C1052 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C1062 " --> pdb=" O SER C1050 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER C1050 " --> pdb=" O LEU C1062 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C1064 " --> pdb=" O LEU C1048 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 710 through 727 removed outlier: 6.536A pdb=" N SER C 710 " --> pdb=" O THR C1075 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C1075 " --> pdb=" O SER C 710 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA C 712 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN C1073 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU C1071 " --> pdb=" O PRO C 714 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C1075 " --> pdb=" O SER C1096 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 732 through 735 removed outlier: 4.428A pdb=" N LYS C 732 " --> pdb=" O LEU C 860 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1119 through 1121 1044 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.64 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7617 1.34 - 1.46: 5834 1.46 - 1.58: 11408 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 24988 Sorted by residual: bond pdb=" N ILE A 211 " pdb=" CA ILE A 211 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.68e+00 bond pdb=" N ALA B 27 " pdb=" CA ALA B 27 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ALA C 27 " pdb=" CA ALA C 27 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N TYR A 29 " pdb=" CA TYR A 29 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" CB CYS C 737 " pdb=" SG CYS C 737 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.51e+00 ... (remaining 24983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 33076 1.30 - 2.60: 682 2.60 - 3.89: 225 3.89 - 5.19: 31 5.19 - 6.49: 3 Bond angle restraints: 34017 Sorted by residual: angle pdb=" CA LYS B 835 " pdb=" CB LYS B 835 " pdb=" CG LYS B 835 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" N THR A 581 " pdb=" CA THR A 581 " pdb=" CB THR A 581 " ideal model delta sigma weight residual 114.17 110.72 3.45 1.14e+00 7.69e-01 9.14e+00 angle pdb=" N THR B 581 " pdb=" CA THR B 581 " pdb=" CB THR B 581 " ideal model delta sigma weight residual 114.17 110.78 3.39 1.14e+00 7.69e-01 8.87e+00 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 111.85 114.91 -3.06 1.06e+00 8.90e-01 8.35e+00 angle pdb=" C ASP B 848 " pdb=" CA ASP B 848 " pdb=" CB ASP B 848 " ideal model delta sigma weight residual 110.42 115.52 -5.10 1.99e+00 2.53e-01 6.58e+00 ... (remaining 34012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 13906 17.73 - 35.45: 1205 35.45 - 53.18: 256 53.18 - 70.91: 87 70.91 - 88.63: 22 Dihedral angle restraints: 15476 sinusoidal: 6661 harmonic: 8815 Sorted by residual: 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 2.63 -88.63 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C1081 " pdb=" SG CYS C1081 " pdb=" SG CYS C1125 " pdb=" CB CYS C1125 " ideal model delta sinusoidal sigma weight residual 93.00 14.99 78.01 1 1.00e+01 1.00e-02 7.61e+01 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 93.00 161.13 -68.13 1 1.00e+01 1.00e-02 6.02e+01 ... (remaining 15473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2563 0.032 - 0.065: 927 0.065 - 0.097: 245 0.097 - 0.129: 244 0.129 - 0.161: 13 Chirality restraints: 3992 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA ILE A 211 " pdb=" N ILE A 211 " pdb=" C ILE A 211 " pdb=" CB ILE A 211 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 3989 not shown) Planarity restraints: 4350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " -0.047 2.00e-02 2.50e+03 3.86e-02 1.86e+01 pdb=" C7 NAG C1303 " 0.014 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " 0.061 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1097 " -0.019 2.00e-02 2.50e+03 1.93e-02 4.67e+00 pdb=" CG ASN C1097 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C1097 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN C1097 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 987 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.026 5.00e-02 4.00e+02 ... (remaining 4347 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 228 2.59 - 3.17: 21341 3.17 - 3.75: 36911 3.75 - 4.32: 54262 4.32 - 4.90: 90316 Nonbonded interactions: 203058 Sorted by model distance: nonbonded pdb=" O ASN B 87 " pdb=" OD1 ASN B 87 " model vdw 2.014 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.073 3.040 nonbonded pdb=" O GLN A 580 " pdb=" OG1 THR A 581 " model vdw 2.088 3.040 nonbonded pdb=" O GLN B 580 " pdb=" OG1 THR B 581 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR B 376 " pdb=" OG SER B 435 " model vdw 2.129 3.040 ... (remaining 203053 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 500 or resid 506 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 827 or resid 855 through 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 499 or resid 505 through 826 \ or resid 854 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: 6.310 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 21.080 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 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 0.052 25072 Z= 0.181 Angle : 0.548 12.672 34230 Z= 0.280 Chirality : 0.043 0.161 3992 Planarity : 0.003 0.046 4315 Dihedral : 14.218 83.581 9685 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.60 % Allowed : 14.36 % Favored : 85.04 % 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: -0.00 (0.15), residues: 2970 helix: 2.14 (0.20), residues: 689 sheet: -0.17 (0.18), residues: 707 loop : -0.90 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.012 0.001 TYR A1067 PHE 0.015 0.001 PHE C 897 TRP 0.010 0.001 TRP B 452 HIS 0.003 0.001 HIS C1047 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (24988) covalent geometry : angle 0.52917 / 0.27 (34017) SS BOND : bond 0.00317 / 0.20 ( 39) SS BOND : angle 1.49821 / 0.95 ( 78) hydrogen bonds : bond 0.11454 / 7.36 ( 1008) hydrogen bonds : angle 6.67968 / 4.51 ( 2853) link_BETA1-4 : bond 0.00128 / 0.06 ( 10) link_BETA1-4 : angle 1.20369 / 0.71 ( 30) link_NAG-ASN : bond 0.00377 / 0.22 ( 35) link_NAG-ASN : angle 2.27009 / 1.41 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.9451 (pt) cc_final: 0.9129 (pp) REVERT: A 586 ASP cc_start: 0.8332 (m-30) cc_final: 0.7975 (m-30) REVERT: B 172 PHE cc_start: 0.8025 (t80) cc_final: 0.7718 (t80) REVERT: B 197 ILE cc_start: 0.9322 (pt) cc_final: 0.9060 (pp) REVERT: B 214 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7022 (ttp80) REVERT: B 421 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: C 345 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8495 (tpt90) REVERT: C 413 GLN cc_start: 0.9214 (mm-40) cc_final: 0.9004 (mp10) REVERT: C 457 LYS cc_start: 0.9336 (mttt) cc_final: 0.9055 (mppt) REVERT: C 461 LYS cc_start: 0.9321 (mtpt) cc_final: 0.9049 (mtmm) REVERT: C 470 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8450 (pp20) REVERT: C 473 GLN cc_start: 0.8842 (mt0) cc_final: 0.8542 (mm-40) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.5965 time to fit residues: 101.1049 Evaluate side-chains 120 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 476 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 ASN A 450 ASN A 762 GLN A1005 GLN B 87 ASN B 196 ASN B 218 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.086266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.058268 restraints weight = 56964.681| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.15 r_work: 0.2751 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25072 Z= 0.131 Angle : 0.525 9.370 34230 Z= 0.270 Chirality : 0.044 0.249 3992 Planarity : 0.004 0.040 4315 Dihedral : 5.300 58.191 4251 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.95 % Allowed : 13.64 % Favored : 84.40 % 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: 0.16 (0.15), residues: 2970 helix: 2.29 (0.20), residues: 685 sheet: -0.02 (0.18), residues: 710 loop : -0.82 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 213 TYR 0.022 0.001 TYR A 171 PHE 0.018 0.001 PHE A 169 TRP 0.012 0.001 TRP B 452 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (24988) covalent geometry : angle 0.51251 / 0.27 (34017) SS BOND : bond 0.00323 / 0.21 ( 39) SS BOND : angle 1.38519 / 0.86 ( 78) hydrogen bonds : bond 0.04006 / 2.55 ( 1008) hydrogen bonds : angle 5.42414 / 3.67 ( 2853) link_BETA1-4 : bond 0.00213 / 0.10 ( 10) link_BETA1-4 : angle 1.17685 / 0.71 ( 30) link_NAG-ASN : bond 0.00218 / 0.13 ( 35) link_NAG-ASN : angle 1.74477 / 1.20 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 114 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7339 (tp) cc_final: 0.7139 (tp) REVERT: A 450 ASN cc_start: 0.8685 (m110) cc_final: 0.8330 (p0) REVERT: A 516 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8468 (mt-10) REVERT: A 586 ASP cc_start: 0.8375 (m-30) cc_final: 0.7847 (m-30) REVERT: B 172 PHE cc_start: 0.7964 (t80) cc_final: 0.7571 (t80) REVERT: B 214 ARG cc_start: 0.7489 (ttp80) cc_final: 0.6903 (ttp80) REVERT: B 349 SER cc_start: 0.7327 (OUTLIER) cc_final: 0.7065 (p) REVERT: B 474 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6904 (tp40) REVERT: C 413 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8907 (mm-40) REVERT: C 457 LYS cc_start: 0.9356 (mttt) cc_final: 0.9013 (mppt) REVERT: C 470 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8471 (pp20) REVERT: C 499 THR cc_start: 0.8136 (p) cc_final: 0.7919 (p) REVERT: C 633 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7813 (mmp-170) REVERT: C 984 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8149 (m-30) outliers start: 52 outliers final: 16 residues processed: 157 average time/residue: 0.4126 time to fit residues: 77.9913 Evaluate side-chains 116 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 633 ARG Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 984 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 285 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A1002 GLN B 196 ASN B 218 GLN B 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.056564 restraints weight = 57228.297| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.15 r_work: 0.2728 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25072 Z= 0.222 Angle : 0.545 9.289 34230 Z= 0.277 Chirality : 0.045 0.251 3992 Planarity : 0.004 0.042 4315 Dihedral : 5.304 58.290 4235 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.41 % Allowed : 13.79 % Favored : 83.80 % 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: 0.11 (0.15), residues: 2970 helix: 2.25 (0.20), residues: 676 sheet: -0.04 (0.18), residues: 711 loop : -0.85 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.018 0.001 TYR C1066 PHE 0.016 0.001 PHE C 897 TRP 0.008 0.001 TRP B 452 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (24988) covalent geometry : angle 0.53137 / 0.27 (34017) SS BOND : bond 0.00358 / 0.23 ( 39) SS BOND : angle 1.38744 / 0.85 ( 78) hydrogen bonds : bond 0.04249 / 2.71 ( 1008) hydrogen bonds : angle 5.31091 / 3.60 ( 2853) link_BETA1-4 : bond 0.00125 / 0.06 ( 10) link_BETA1-4 : angle 1.19770 / 0.71 ( 30) link_NAG-ASN : bond 0.00322 / 0.19 ( 35) link_NAG-ASN : angle 1.85094 / 1.27 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 103 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ASN cc_start: 0.8584 (m110) cc_final: 0.8262 (p0) REVERT: A 586 ASP cc_start: 0.8328 (m-30) cc_final: 0.7833 (m-30) REVERT: A 780 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8890 (mm-30) REVERT: B 172 PHE cc_start: 0.7922 (t80) cc_final: 0.7496 (t80) REVERT: B 214 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7043 (ttp80) REVERT: B 349 SER cc_start: 0.7373 (OUTLIER) cc_final: 0.7111 (p) REVERT: B 424 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7591 (mmtm) REVERT: B 474 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6856 (tp40) REVERT: B 571 ASP cc_start: 0.8415 (m-30) cc_final: 0.7564 (t0) REVERT: C 413 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8879 (mm-40) REVERT: C 457 LYS cc_start: 0.9350 (mttt) cc_final: 0.9008 (mppt) REVERT: C 470 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8466 (pp20) REVERT: C 473 GLN cc_start: 0.8772 (mt0) cc_final: 0.8321 (tp-100) REVERT: C 499 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7845 (p) REVERT: C 984 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8177 (m-30) outliers start: 64 outliers final: 25 residues processed: 156 average time/residue: 0.4169 time to fit residues: 78.9389 Evaluate side-chains 127 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain C residue 1105 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 126 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 34 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN B 196 ASN B 218 GLN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.057556 restraints weight = 56958.215| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.14 r_work: 0.2739 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25072 Z= 0.155 Angle : 0.524 10.140 34230 Z= 0.265 Chirality : 0.044 0.259 3992 Planarity : 0.004 0.042 4315 Dihedral : 5.234 58.319 4233 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.44 % Allowed : 14.43 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 2970 helix: 2.25 (0.20), residues: 678 sheet: -0.00 (0.19), residues: 699 loop : -0.83 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.024 0.001 TYR A 171 PHE 0.015 0.001 PHE C 897 TRP 0.007 0.001 TRP C 64 HIS 0.002 0.000 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (24988) covalent geometry : angle 0.51153 / 0.26 (34017) SS BOND : bond 0.00313 / 0.20 ( 39) SS BOND : angle 1.37379 / 0.87 ( 78) hydrogen bonds : bond 0.03900 / 2.48 ( 1008) hydrogen bonds : angle 5.15281 / 3.49 ( 2853) link_BETA1-4 : bond 0.00174 / 0.08 ( 10) link_BETA1-4 : angle 1.13026 / 0.68 ( 30) link_NAG-ASN : bond 0.00227 / 0.13 ( 35) link_NAG-ASN : angle 1.72634 / 1.21 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 107 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ASN cc_start: 0.8608 (m110) cc_final: 0.8210 (p0) REVERT: A 516 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 586 ASP cc_start: 0.8331 (m-30) cc_final: 0.7884 (m-30) REVERT: B 172 PHE cc_start: 0.7916 (t80) cc_final: 0.7525 (t80) REVERT: B 214 ARG cc_start: 0.7561 (ttp80) cc_final: 0.7001 (ttp80) REVERT: B 349 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.7115 (p) REVERT: B 424 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7485 (mptt) REVERT: B 452 TRP cc_start: 0.6948 (m-90) cc_final: 0.6345 (m-90) REVERT: B 474 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6929 (tp40) REVERT: B 571 ASP cc_start: 0.8336 (m-30) cc_final: 0.7502 (t0) REVERT: C 413 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8834 (mm-40) REVERT: C 457 LYS cc_start: 0.9349 (mttt) cc_final: 0.9004 (mppt) REVERT: C 470 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8435 (pp20) REVERT: C 473 GLN cc_start: 0.8777 (mt0) cc_final: 0.8377 (tp-100) REVERT: C 499 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7907 (p) REVERT: C 868 MET cc_start: 0.9252 (mtt) cc_final: 0.8808 (mtt) REVERT: C 984 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8192 (m-30) outliers start: 65 outliers final: 32 residues processed: 160 average time/residue: 0.3946 time to fit residues: 77.0787 Evaluate side-chains 136 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain C residue 1105 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 123 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN B 218 GLN C 612 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.084777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056692 restraints weight = 57089.744| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.15 r_work: 0.2750 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25072 Z= 0.210 Angle : 0.547 9.381 34230 Z= 0.276 Chirality : 0.044 0.256 3992 Planarity : 0.004 0.043 4315 Dihedral : 5.303 58.326 4233 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.41 % Allowed : 14.88 % Favored : 82.71 % 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: 0.09 (0.15), residues: 2970 helix: 2.20 (0.20), residues: 677 sheet: -0.03 (0.18), residues: 710 loop : -0.85 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.018 0.001 TYR C1066 PHE 0.020 0.001 PHE A 169 TRP 0.008 0.001 TRP C 64 HIS 0.002 0.001 HIS C1087 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (24988) covalent geometry : angle 0.53345 / 0.27 (34017) SS BOND : bond 0.00349 / 0.23 ( 39) SS BOND : angle 1.54746 / 0.96 ( 78) hydrogen bonds : bond 0.04100 / 2.62 ( 1008) hydrogen bonds : angle 5.17043 / 3.50 ( 2853) link_BETA1-4 : bond 0.00107 / 0.05 ( 10) link_BETA1-4 : angle 1.16029 / 0.69 ( 30) link_NAG-ASN : bond 0.00296 / 0.17 ( 35) link_NAG-ASN : angle 1.77381 / 1.24 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 101 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ASN cc_start: 0.8626 (m110) cc_final: 0.8129 (p0) REVERT: A 516 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8298 (mt-10) REVERT: A 586 ASP cc_start: 0.8314 (m-30) cc_final: 0.7881 (m-30) REVERT: A 780 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8893 (mm-30) REVERT: B 131 CYS cc_start: 0.5319 (OUTLIER) cc_final: 0.4608 (m) REVERT: B 172 PHE cc_start: 0.7894 (t80) cc_final: 0.7462 (t80) REVERT: B 214 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7085 (ttp80) REVERT: B 349 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.7142 (p) REVERT: B 424 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7512 (mptt) REVERT: B 452 TRP cc_start: 0.6860 (m-90) cc_final: 0.6309 (m-90) REVERT: B 474 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6824 (tp40) REVERT: B 571 ASP cc_start: 0.8334 (m-30) cc_final: 0.7552 (OUTLIER) REVERT: C 457 LYS cc_start: 0.9341 (mttt) cc_final: 0.8998 (mppt) REVERT: C 470 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8488 (pp20) REVERT: C 499 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7938 (p) REVERT: C 984 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8162 (m-30) outliers start: 64 outliers final: 36 residues processed: 155 average time/residue: 0.3913 time to fit residues: 75.3784 Evaluate side-chains 137 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain C residue 1105 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 260 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 230 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN B 196 ASN B 751 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.085930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.058064 restraints weight = 56879.270| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.15 r_work: 0.2789 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25072 Z= 0.118 Angle : 0.515 9.546 34230 Z= 0.259 Chirality : 0.043 0.261 3992 Planarity : 0.004 0.042 4315 Dihedral : 5.169 58.227 4233 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 2.18 % Allowed : 15.60 % Favored : 82.22 % 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: 0.21 (0.15), residues: 2970 helix: 2.34 (0.20), residues: 671 sheet: 0.12 (0.19), residues: 671 loop : -0.81 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 237 TYR 0.022 0.001 TYR A 171 PHE 0.014 0.001 PHE B 65 TRP 0.006 0.001 TRP B 452 HIS 0.002 0.000 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (24988) covalent geometry : angle 0.50238 / 0.26 (34017) SS BOND : bond 0.00262 / 0.16 ( 39) SS BOND : angle 1.49922 / 0.94 ( 78) hydrogen bonds : bond 0.03677 / 2.34 ( 1008) hydrogen bonds : angle 5.01384 / 3.40 ( 2853) link_BETA1-4 : bond 0.00222 / 0.11 ( 10) link_BETA1-4 : angle 1.08130 / 0.64 ( 30) link_NAG-ASN : bond 0.00199 / 0.12 ( 35) link_NAG-ASN : angle 1.64071 / 1.16 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 105 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ASN cc_start: 0.8620 (m110) cc_final: 0.8100 (p0) REVERT: A 516 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8276 (mt-10) REVERT: A 586 ASP cc_start: 0.8293 (m-30) cc_final: 0.7834 (m-30) REVERT: A 780 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8845 (mm-30) REVERT: B 131 CYS cc_start: 0.5181 (OUTLIER) cc_final: 0.4470 (m) REVERT: B 172 PHE cc_start: 0.7899 (t80) cc_final: 0.7477 (t80) REVERT: B 214 ARG cc_start: 0.7503 (ttp80) cc_final: 0.6933 (ttp80) REVERT: B 349 SER cc_start: 0.7331 (OUTLIER) cc_final: 0.7089 (p) REVERT: B 423 TYR cc_start: 0.7954 (t80) cc_final: 0.7619 (t80) REVERT: B 424 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7474 (mptt) REVERT: B 452 TRP cc_start: 0.6748 (m-90) cc_final: 0.6185 (m-90) REVERT: B 474 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6927 (tp40) REVERT: B 571 ASP cc_start: 0.8317 (m-30) cc_final: 0.7539 (OUTLIER) REVERT: B 1050 MET cc_start: 0.9405 (ptm) cc_final: 0.9183 (ptm) REVERT: C 413 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8799 (mm-40) REVERT: C 457 LYS cc_start: 0.9334 (mttt) cc_final: 0.8986 (mppt) REVERT: C 470 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8477 (pp20) REVERT: C 499 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7976 (p) REVERT: C 868 MET cc_start: 0.9232 (mtt) cc_final: 0.8789 (mtt) REVERT: C 984 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8146 (m-30) outliers start: 58 outliers final: 28 residues processed: 153 average time/residue: 0.3814 time to fit residues: 72.3878 Evaluate side-chains 132 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 984 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 173 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 258 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN A 762 GLN B 188 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.087050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.059288 restraints weight = 56670.787| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.16 r_work: 0.2816 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25072 Z= 0.098 Angle : 0.500 9.563 34230 Z= 0.252 Chirality : 0.043 0.259 3992 Planarity : 0.004 0.043 4315 Dihedral : 4.970 57.602 4233 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 1.95 % Allowed : 15.78 % Favored : 82.26 % 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: 0.33 (0.15), residues: 2970 helix: 2.43 (0.20), residues: 673 sheet: 0.25 (0.19), residues: 671 loop : -0.76 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 237 TYR 0.019 0.001 TYR A1067 PHE 0.026 0.001 PHE A 486 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (24988) covalent geometry : angle 0.48970 / 0.25 (34017) SS BOND : bond 0.00286 / 0.19 ( 39) SS BOND : angle 1.21835 / 0.77 ( 78) hydrogen bonds : bond 0.03404 / 2.17 ( 1008) hydrogen bonds : angle 4.80674 / 3.27 ( 2853) link_BETA1-4 : bond 0.00298 / 0.15 ( 10) link_BETA1-4 : angle 1.06973 / 0.63 ( 30) link_NAG-ASN : bond 0.00188 / 0.11 ( 35) link_NAG-ASN : angle 1.53594 / 1.09 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 104 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ASN cc_start: 0.8578 (m110) cc_final: 0.8042 (p0) REVERT: A 516 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 586 ASP cc_start: 0.8247 (m-30) cc_final: 0.7756 (m-30) REVERT: A 740 MET cc_start: 0.8948 (mmm) cc_final: 0.8492 (tpp) REVERT: A 825 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8654 (ttpt) REVERT: B 131 CYS cc_start: 0.5071 (OUTLIER) cc_final: 0.4373 (m) REVERT: B 172 PHE cc_start: 0.7895 (t80) cc_final: 0.7478 (t80) REVERT: B 214 ARG cc_start: 0.7452 (ttp80) cc_final: 0.6881 (ttp80) REVERT: B 423 TYR cc_start: 0.7939 (t80) cc_final: 0.7663 (t80) REVERT: B 424 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7457 (mptt) REVERT: B 474 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6941 (tp40) REVERT: B 571 ASP cc_start: 0.8313 (m-30) cc_final: 0.7657 (t70) REVERT: B 1050 MET cc_start: 0.9348 (ptm) cc_final: 0.9129 (ptm) REVERT: C 170 TYR cc_start: 0.7651 (t80) cc_final: 0.7347 (t80) REVERT: C 413 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8694 (mm-40) REVERT: C 422 TYR cc_start: 0.8909 (t80) cc_final: 0.8683 (t80) REVERT: C 457 LYS cc_start: 0.9333 (mttt) cc_final: 0.8984 (mppt) REVERT: C 470 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8495 (pp20) REVERT: C 499 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7982 (p) REVERT: C 868 MET cc_start: 0.9220 (mtt) cc_final: 0.8742 (mtt) REVERT: C 984 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8107 (m-30) outliers start: 52 outliers final: 27 residues processed: 149 average time/residue: 0.4107 time to fit residues: 75.0833 Evaluate side-chains 127 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 984 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 56 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 235 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN A 762 GLN B 218 GLN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.085714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057711 restraints weight = 56869.122| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.15 r_work: 0.2784 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25072 Z= 0.165 Angle : 0.523 10.172 34230 Z= 0.263 Chirality : 0.044 0.253 3992 Planarity : 0.004 0.043 4315 Dihedral : 5.010 57.403 4232 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 1.77 % Allowed : 16.23 % Favored : 82.00 % 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: 0.31 (0.15), residues: 2970 helix: 2.39 (0.20), residues: 672 sheet: 0.20 (0.19), residues: 684 loop : -0.74 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.025 0.001 TYR A 171 PHE 0.015 0.001 PHE C 897 TRP 0.009 0.001 TRP C 64 HIS 0.002 0.000 HIS C1047 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (24988) covalent geometry : angle 0.51245 / 0.26 (34017) SS BOND : bond 0.00294 / 0.18 ( 39) SS BOND : angle 1.24181 / 0.79 ( 78) hydrogen bonds : bond 0.03764 / 2.41 ( 1008) hydrogen bonds : angle 4.90830 / 3.34 ( 2853) link_BETA1-4 : bond 0.00153 / 0.07 ( 10) link_BETA1-4 : angle 1.11057 / 0.66 ( 30) link_NAG-ASN : bond 0.00219 / 0.13 ( 35) link_NAG-ASN : angle 1.59952 / 1.13 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 98 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ASN cc_start: 0.8604 (m110) cc_final: 0.7979 (p0) REVERT: A 516 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 586 ASP cc_start: 0.8310 (m-30) cc_final: 0.7826 (m-30) REVERT: A 825 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8637 (ttpt) REVERT: B 131 CYS cc_start: 0.5183 (OUTLIER) cc_final: 0.4491 (m) REVERT: B 172 PHE cc_start: 0.7905 (t80) cc_final: 0.7486 (t80) REVERT: B 214 ARG cc_start: 0.7539 (ttp80) cc_final: 0.6994 (ttp80) REVERT: B 349 SER cc_start: 0.7376 (OUTLIER) cc_final: 0.7141 (p) REVERT: B 398 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: B 474 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6961 (tp40) REVERT: B 571 ASP cc_start: 0.8335 (m-30) cc_final: 0.7702 (t70) REVERT: C 170 TYR cc_start: 0.7809 (t80) cc_final: 0.7450 (t80) REVERT: C 413 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8735 (mm-40) REVERT: C 422 TYR cc_start: 0.8932 (t80) cc_final: 0.8655 (t80) REVERT: C 457 LYS cc_start: 0.9358 (mttt) cc_final: 0.8995 (mppt) REVERT: C 470 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8502 (pp20) REVERT: C 499 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7989 (p) REVERT: C 984 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8157 (m-30) outliers start: 47 outliers final: 25 residues processed: 137 average time/residue: 0.4010 time to fit residues: 67.6461 Evaluate side-chains 128 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 984 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 148 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 273 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 275 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN B 196 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.085717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.057621 restraints weight = 56900.796| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.16 r_work: 0.2783 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25072 Z= 0.153 Angle : 0.522 9.526 34230 Z= 0.263 Chirality : 0.044 0.256 3992 Planarity : 0.004 0.043 4315 Dihedral : 5.038 57.674 4232 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 1.35 % Allowed : 16.76 % Favored : 81.89 % 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: 0.31 (0.15), residues: 2970 helix: 2.38 (0.20), residues: 671 sheet: 0.22 (0.19), residues: 674 loop : -0.75 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.018 0.001 TYR A1067 PHE 0.027 0.001 PHE A 486 TRP 0.010 0.001 TRP C 64 HIS 0.002 0.000 HIS C1047 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (24988) covalent geometry : angle 0.51203 / 0.26 (34017) SS BOND : bond 0.00292 / 0.18 ( 39) SS BOND : angle 1.24055 / 0.78 ( 78) hydrogen bonds : bond 0.03735 / 2.38 ( 1008) hydrogen bonds : angle 4.92344 / 3.34 ( 2853) link_BETA1-4 : bond 0.00157 / 0.08 ( 10) link_BETA1-4 : angle 1.08405 / 0.64 ( 30) link_NAG-ASN : bond 0.00207 / 0.12 ( 35) link_NAG-ASN : angle 1.60350 / 1.13 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ASN cc_start: 0.8555 (m110) cc_final: 0.8015 (p0) REVERT: A 516 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8346 (mt-10) REVERT: A 586 ASP cc_start: 0.8315 (m-30) cc_final: 0.7836 (m-30) REVERT: A 740 MET cc_start: 0.9068 (mmm) cc_final: 0.8621 (tpp) REVERT: B 131 CYS cc_start: 0.5223 (OUTLIER) cc_final: 0.4516 (m) REVERT: B 172 PHE cc_start: 0.7908 (t80) cc_final: 0.7505 (t80) REVERT: B 214 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7006 (ttp80) REVERT: B 474 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6903 (tp40) REVERT: B 571 ASP cc_start: 0.8323 (m-30) cc_final: 0.7699 (t70) REVERT: C 169 GLU cc_start: 0.8254 (tp30) cc_final: 0.8045 (tp30) REVERT: C 170 TYR cc_start: 0.7849 (t80) cc_final: 0.7345 (t80) REVERT: C 413 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8728 (mm-40) REVERT: C 422 TYR cc_start: 0.8922 (t80) cc_final: 0.8640 (t80) REVERT: C 457 LYS cc_start: 0.9356 (mttt) cc_final: 0.8994 (mppt) REVERT: C 470 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8506 (pp20) REVERT: C 499 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8002 (p) REVERT: C 868 MET cc_start: 0.9249 (mtt) cc_final: 0.8826 (mtt) REVERT: C 984 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8136 (m-30) outliers start: 36 outliers final: 23 residues processed: 127 average time/residue: 0.4102 time to fit residues: 64.0736 Evaluate side-chains 122 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 984 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 159 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 45 optimal weight: 0.0470 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.086659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.058715 restraints weight = 56735.035| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.16 r_work: 0.2808 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25072 Z= 0.112 Angle : 0.509 9.646 34230 Z= 0.256 Chirality : 0.043 0.259 3992 Planarity : 0.004 0.043 4315 Dihedral : 4.951 57.672 4232 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 1.32 % Allowed : 16.76 % Favored : 81.92 % 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: 0.36 (0.15), residues: 2970 helix: 2.43 (0.20), residues: 672 sheet: 0.26 (0.19), residues: 674 loop : -0.73 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE B 65 TRP 0.007 0.001 TRP C 64 HIS 0.002 0.000 HIS C1087 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (24988) covalent geometry : angle 0.50007 / 0.25 (34017) SS BOND : bond 0.00272 / 0.17 ( 39) SS BOND : angle 1.11993 / 0.70 ( 78) hydrogen bonds : bond 0.03479 / 2.22 ( 1008) hydrogen bonds : angle 4.80811 / 3.27 ( 2853) link_BETA1-4 : bond 0.00240 / 0.12 ( 10) link_BETA1-4 : angle 1.04571 / 0.62 ( 30) link_NAG-ASN : bond 0.00176 / 0.10 ( 35) link_NAG-ASN : angle 1.52313 / 1.08 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ASN cc_start: 0.8559 (m110) cc_final: 0.8015 (p0) REVERT: A 516 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 586 ASP cc_start: 0.8278 (m-30) cc_final: 0.7785 (m-30) REVERT: A 740 MET cc_start: 0.8999 (mmm) cc_final: 0.8562 (tpp) REVERT: A 825 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8649 (ttpt) REVERT: B 131 CYS cc_start: 0.5148 (OUTLIER) cc_final: 0.4442 (m) REVERT: B 172 PHE cc_start: 0.7894 (t80) cc_final: 0.7481 (t80) REVERT: B 214 ARG cc_start: 0.7556 (ttp80) cc_final: 0.6994 (ttp80) REVERT: B 349 SER cc_start: 0.7389 (OUTLIER) cc_final: 0.7162 (p) REVERT: B 378 LYS cc_start: 0.8750 (mmmm) cc_final: 0.8192 (tppp) REVERT: B 474 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6942 (tp40) REVERT: B 571 ASP cc_start: 0.8314 (m-30) cc_final: 0.7718 (t70) REVERT: C 169 GLU cc_start: 0.8214 (tp30) cc_final: 0.7984 (tp30) REVERT: C 170 TYR cc_start: 0.7844 (t80) cc_final: 0.7354 (t80) REVERT: C 413 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8678 (mm-40) REVERT: C 422 TYR cc_start: 0.8911 (t80) cc_final: 0.8686 (t80) REVERT: C 457 LYS cc_start: 0.9364 (mttt) cc_final: 0.8995 (mppt) REVERT: C 470 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8493 (pp20) REVERT: C 499 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8051 (p) REVERT: C 868 MET cc_start: 0.9236 (mtt) cc_final: 0.8795 (mtt) REVERT: C 984 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8096 (m-30) outliers start: 35 outliers final: 24 residues processed: 127 average time/residue: 0.3749 time to fit residues: 58.3723 Evaluate side-chains 124 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 984 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 255 optimal weight: 0.6980 chunk 147 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 286 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 235 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.086484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058531 restraints weight = 56974.470| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.17 r_work: 0.2798 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25072 Z= 0.119 Angle : 0.507 9.500 34230 Z= 0.255 Chirality : 0.043 0.256 3992 Planarity : 0.004 0.043 4315 Dihedral : 4.917 57.423 4232 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 1.24 % Allowed : 16.95 % Favored : 81.81 % 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: 0.36 (0.15), residues: 2970 helix: 2.44 (0.20), residues: 672 sheet: 0.28 (0.19), residues: 674 loop : -0.74 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.019 0.001 TYR A1067 PHE 0.034 0.001 PHE A 486 TRP 0.009 0.001 TRP C 64 HIS 0.002 0.000 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (24988) covalent geometry : angle 0.49787 / 0.25 (34017) SS BOND : bond 0.00267 / 0.17 ( 39) SS BOND : angle 1.12724 / 0.71 ( 78) hydrogen bonds : bond 0.03537 / 2.26 ( 1008) hydrogen bonds : angle 4.80308 / 3.27 ( 2853) link_BETA1-4 : bond 0.00226 / 0.11 ( 10) link_BETA1-4 : angle 1.07278 / 0.63 ( 30) link_NAG-ASN : bond 0.00179 / 0.10 ( 35) link_NAG-ASN : angle 1.51758 / 1.08 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5529.94 seconds wall clock time: 95 minutes 31.16 seconds (5731.16 seconds total)