Starting phenix.real_space_refine on Sun Sep 13 19:28:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h0y_34418/09_2026/8h0y_34418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0y_34418/09_2026/8h0y_34418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8h0y_34418/09_2026/8h0y_34418.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h0y_34418/09_2026/8h0y_34418.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h0y_34418/09_2026/8h0y_34418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0y_34418/09_2026/8h0y_34418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h0y_34418/09_2026/8h0y_34418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0y_34418/09_2026/8h0y_34418.map" } resolution = 2.85 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= 0.006 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 141 5.16 5 C 15977 2.51 5 N 4056 2.21 5 O 4825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24999 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7974 Classifications: {'peptide': 1019} Link IDs: {'PTRANS': 49, 'TRANS': 969} Chain breaks: 9 Chain: "A" Number of atoms: 8143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8143 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 50, 'TRANS': 993} Chain breaks: 6 Chain: "C" Number of atoms: 8049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8049 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 49, 'TRANS': 981} Chain breaks: 6 Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 287 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 273 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 15} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 273 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 15} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 5.22, per 1000 atoms: 0.21 Number of scatterers: 24999 At special positions: 0 Unit cell: (121.545, 125.925, 174.105, 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 141 16.00 O 4825 8.00 N 4056 7.00 C 15977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.05 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS C 967 " distance=2.05 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.05 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS C 370 " distance=2.05 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.05 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.07 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " 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 NAG-ASN " NAG A1302 " - " ASN A1056 " " NAG A1303 " - " ASN A 65 " " NAG A1304 " - " ASN A1080 " " NAG A1305 " - " ASN A 109 " " NAG A1306 " - " ASN A 119 " " NAG A1307 " - " ASN A 158 " " NAG A1308 " - " ASN A 227 " " NAG A1309 " - " ASN A 269 " " NAG A1310 " - " ASN A 318 " " NAG A1311 " - " ASN A 330 " " NAG A1312 " - " ASN A 357 " " NAG A1313 " - " ASN A 602 " " NAG A1314 " - " ASN A 699 " " NAG A1315 " - " ASN A 783 " " NAG A1316 " - " ASN A1116 " " NAG B1302 " - " ASN B1056 " " NAG B1303 " - " ASN B 65 " " NAG B1304 " - " ASN B1080 " " NAG B1305 " - " ASN B 109 " " NAG B1306 " - " ASN B 119 " " NAG B1307 " - " ASN B 158 " " NAG B1308 " - " ASN B 227 " " NAG B1309 " - " ASN B 269 " " NAG B1310 " - " ASN B 318 " " NAG B1311 " - " ASN B 330 " " NAG B1312 " - " ASN B 357 " " NAG B1313 " - " ASN B 602 " " NAG B1314 " - " ASN B 691 " " NAG B1315 " - " ASN B 699 " " NAG B1316 " - " ASN B 783 " " NAG B1317 " - " ASN B1116 " " NAG C1302 " - " ASN C1056 " " NAG C1303 " - " ASN C 65 " " NAG C1304 " - " ASN C1080 " " NAG C1305 " - " ASN C 109 " " NAG C1306 " - " ASN C 119 " " NAG C1307 " - " ASN C 158 " " NAG C1308 " - " ASN C 227 " " NAG C1309 " - " ASN C 269 " " NAG C1310 " - " ASN C 318 " " NAG C1311 " - " ASN C 357 " " NAG C1312 " - " ASN C 602 " " NAG C1313 " - " ASN C 691 " " NAG C1314 " - " ASN C 699 " " NAG C1315 " - " ASN C 783 " " NAG C1316 " - " ASN C1116 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5796 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 44 sheets defined 26.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 removed outlier: 3.513A pdb=" N VAL B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.658A pdb=" N LEU B 355 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 357 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.555A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.278A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 739 through 765 removed outlier: 4.465A pdb=" N THR B 743 " --> pdb=" O GLY B 739 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.738A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 838 removed outlier: 3.604A pdb=" N ASN B 838 " --> pdb=" O ALA B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 Processing helix chain 'B' and resid 879 through 890 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.855A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.666A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 965 removed outlier: 3.829A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.621A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.682A pdb=" N VAL A 354 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.752A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.665A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 739 through 765 removed outlier: 4.026A pdb=" N THR A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 745 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 788 removed outlier: 3.529A pdb=" N LEU A 788 " --> pdb=" O SER A 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 785 through 788' Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.792A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 830 through 837 removed outlier: 3.514A pdb=" N ALA A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 867 Processing helix chain 'A' and resid 868 through 873 removed outlier: 4.504A pdb=" N ALA A 872 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.759A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.758A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 947 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.775A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.896A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 329 removed outlier: 3.512A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.764A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.760A pdb=" N LEU C 355 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.558A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.513A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.686A pdb=" N LEU C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 765 removed outlier: 3.931A pdb=" N THR C 743 " --> pdb=" O GLY C 739 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 788 removed outlier: 3.600A pdb=" N LEU C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 806 Processing helix chain 'C' and resid 818 through 824 Processing helix chain 'C' and resid 830 through 837 Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.556A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 removed outlier: 4.226A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 964 removed outlier: 3.823A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.600A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.360A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 93 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.912A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.727A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 298 through 302 removed outlier: 4.642A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.809A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.162A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.633A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 510 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.568A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.798A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.752A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.752A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.443A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AB7, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AB8, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.394A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 93 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N TYR A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LEU A 216 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.963A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.162A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AC3, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.514A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.232A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.667A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 510 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AC7, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.384A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.634A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.634A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.499A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 769 through 771 removed outlier: 3.657A pdb=" N SER C 685 " --> pdb=" O MET A 770 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AD4, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AD5, first strand: chain 'C' and resid 33 through 34 removed outlier: 7.552A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 93 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.023A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.767A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AD9, first strand: chain 'C' and resid 312 through 315 removed outlier: 5.458A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 341 through 345 removed outlier: 4.175A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.585A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 435 through 441 removed outlier: 5.900A pdb=" N TYR C 436 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE C 483 " --> pdb=" O TYR C 436 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR C 438 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.428A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.549A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.549A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.520A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1102 through 1104 1026 hydrogen bonds defined for protein. 2817 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: 7.11 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 4683 1.33 - 1.48: 10003 1.48 - 1.63: 10687 1.63 - 1.78: 22 1.78 - 1.93: 167 Bond restraints: 25562 Sorted by residual: bond pdb=" ND BLA B1318 " pdb=" C1D BLA B1318 " ideal model delta sigma weight residual 1.319 1.484 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" ND BLA C1317 " pdb=" C1D BLA C1317 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C1C BLA B1318 " pdb=" NC BLA B1318 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" ND BLA A1317 " pdb=" C1D BLA A1317 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C4C BLA C1317 " pdb=" NC BLA C1317 " ideal model delta sigma weight residual 1.375 1.535 -0.160 2.00e-02 2.50e+03 6.39e+01 ... (remaining 25557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 34643 4.98 - 9.96: 98 9.96 - 14.93: 1 14.93 - 19.91: 1 19.91 - 24.89: 1 Bond angle restraints: 34744 Sorted by residual: angle pdb=" CA CYS C 366 " pdb=" CB CYS C 366 " pdb=" SG CYS C 366 " ideal model delta sigma weight residual 114.40 139.29 -24.89 2.30e+00 1.89e-01 1.17e+02 angle pdb=" CA CYS B 159 " pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " ideal model delta sigma weight residual 114.40 132.91 -18.51 2.30e+00 1.89e-01 6.48e+01 angle pdb=" C CYS A 467 " pdb=" N THR A 468 " pdb=" CA THR A 468 " ideal model delta sigma weight residual 120.49 128.80 -8.31 1.42e+00 4.96e-01 3.42e+01 angle pdb=" N CYS C 366 " pdb=" CA CYS C 366 " pdb=" C CYS C 366 " ideal model delta sigma weight residual 108.96 116.53 -7.57 1.49e+00 4.50e-01 2.58e+01 angle pdb=" C ASN B 158 " pdb=" N CYS B 159 " pdb=" CA CYS B 159 " ideal model delta sigma weight residual 122.81 114.43 8.38 1.68e+00 3.54e-01 2.49e+01 ... (remaining 34739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13499 17.99 - 35.97: 1076 35.97 - 53.96: 182 53.96 - 71.94: 45 71.94 - 89.93: 16 Dihedral angle restraints: 14818 sinusoidal: 5808 harmonic: 9010 Sorted by residual: dihedral pdb=" CB CYS C1064 " pdb=" SG CYS C1064 " pdb=" SG CYS C1108 " pdb=" CB CYS C1108 " ideal model delta sinusoidal sigma weight residual -86.00 -0.55 -85.45 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS A1064 " pdb=" SG CYS A1064 " pdb=" SG CYS A1108 " pdb=" CB CYS A1108 " ideal model delta sinusoidal sigma weight residual -86.00 -3.97 -82.03 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual -86.00 -5.56 -80.44 1 1.00e+01 1.00e-02 8.01e+01 ... (remaining 14815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3551 0.088 - 0.176: 448 0.176 - 0.264: 14 0.264 - 0.352: 6 0.352 - 0.440: 8 Chirality restraints: 4027 Sorted by residual: chirality pdb=" C1 NAG B1315 " pdb=" ND2 ASN B 699 " pdb=" C2 NAG B1315 " pdb=" O5 NAG B1315 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C1 NAG A1314 " pdb=" ND2 ASN A 699 " pdb=" C2 NAG A1314 " pdb=" O5 NAG A1314 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CB ILE C 152 " pdb=" CA ILE C 152 " pdb=" CG1 ILE C 152 " pdb=" CG2 ILE C 152 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 4024 not shown) Planarity restraints: 4468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA B1318 " -0.223 2.00e-02 2.50e+03 2.75e-01 1.89e+03 pdb=" C1A BLA B1318 " 0.643 2.00e-02 2.50e+03 pdb=" C1D BLA B1318 " -0.037 2.00e-02 2.50e+03 pdb=" C2D BLA B1318 " 0.061 2.00e-02 2.50e+03 pdb=" C3D BLA B1318 " -0.071 2.00e-02 2.50e+03 pdb=" C4D BLA B1318 " -0.252 2.00e-02 2.50e+03 pdb=" CAD BLA B1318 " -0.026 2.00e-02 2.50e+03 pdb=" CHA BLA B1318 " -0.393 2.00e-02 2.50e+03 pdb=" CHD BLA B1318 " 0.046 2.00e-02 2.50e+03 pdb=" CMD BLA B1318 " 0.252 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1318 " -0.021 2.00e-02 2.50e+03 1.46e-01 5.30e+02 pdb=" C1D BLA B1318 " 0.331 2.00e-02 2.50e+03 pdb=" C2C BLA B1318 " 0.031 2.00e-02 2.50e+03 pdb=" C3C BLA B1318 " -0.030 2.00e-02 2.50e+03 pdb=" C4C BLA B1318 " -0.132 2.00e-02 2.50e+03 pdb=" CAC BLA B1318 " 0.000 2.00e-02 2.50e+03 pdb=" CHD BLA B1318 " -0.212 2.00e-02 2.50e+03 pdb=" CMC BLA B1318 " 0.146 2.00e-02 2.50e+03 pdb=" NC BLA B1318 " -0.127 2.00e-02 2.50e+03 pdb=" OC BLA B1318 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1317 " -0.098 2.00e-02 2.50e+03 1.12e-01 3.11e+02 pdb=" C1A BLA C1317 " 0.253 2.00e-02 2.50e+03 pdb=" C1D BLA C1317 " -0.021 2.00e-02 2.50e+03 pdb=" C2D BLA C1317 " 0.028 2.00e-02 2.50e+03 pdb=" C3D BLA C1317 " -0.023 2.00e-02 2.50e+03 pdb=" C4D BLA C1317 " -0.101 2.00e-02 2.50e+03 pdb=" CAD BLA C1317 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA C1317 " -0.162 2.00e-02 2.50e+03 pdb=" CHD BLA C1317 " 0.005 2.00e-02 2.50e+03 pdb=" CMD BLA C1317 " 0.111 2.00e-02 2.50e+03 ... (remaining 4465 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6275 2.80 - 3.32: 19982 3.32 - 3.85: 38803 3.85 - 4.37: 46179 4.37 - 4.90: 82281 Nonbonded interactions: 193520 Sorted by model distance: nonbonded pdb=" OH TYR C 436 " pdb=" OH TYR C 484 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR A 894 " pdb=" OD1 ASN A 896 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 436 " pdb=" OH TYR A 484 " model vdw 2.312 3.040 nonbonded pdb=" OG SER C 461 " pdb=" OD1 ASP C 463 " model vdw 2.315 3.040 nonbonded pdb=" O ASN A 960 " pdb=" OG SER A 964 " model vdw 2.323 3.040 ... (remaining 193515 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 31 through 93 or resid 96 through 250 or resid 252 through \ 603 or resid 619 through 810 or resid 815 through 823 or resid 829 through 1316 \ )) selection = (chain 'B' and resid 31 through 1316) selection = (chain 'C' and (resid 31 through 93 or resid 96 through 250 or resid 252 through \ 810 or resid 815 through 823 or resid 829 through 1316)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.480 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.008 0.165 25653 Z= 0.366 Angle : 0.899 24.890 34972 Z= 0.456 Chirality : 0.057 0.440 4027 Planarity : 0.008 0.275 4422 Dihedral : 13.298 89.931 8887 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3046 helix: -0.24 (0.19), residues: 697 sheet: 0.66 (0.19), residues: 695 loop : -1.75 (0.13), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 544 TYR 0.023 0.002 TYR C 481 PHE 0.053 0.002 PHE A 334 TRP 0.013 0.002 TRP B 423 HIS 0.006 0.001 HIS B 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00783 / 0.37 (25562) covalent geometry : angle 0.85197 / 0.44 (34744) SS BOND : bond 0.01084 / 0.74 ( 45) SS BOND : angle 2.71234 / 1.97 ( 90) hydrogen bonds : bond 0.14006 / 9.37 ( 990) hydrogen bonds : angle 6.54779 / 4.60 ( 2817) link_NAG-ASN : bond 0.00580 / 0.44 ( 46) link_NAG-ASN : angle 4.16040 / 2.79 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8231 (pttm) cc_final: 0.7432 (mmtt) outliers start: 0 outliers final: 2 residues processed: 203 average time/residue: 0.6008 time to fit residues: 142.3228 Evaluate side-chains 154 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain C residue 643 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0070 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 984 GLN A 112 GLN A 122 ASN A 987 GLN C 889 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.092671 restraints weight = 34889.288| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.37 r_work: 0.2954 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25653 Z= 0.126 Angle : 0.562 13.661 34972 Z= 0.292 Chirality : 0.046 0.300 4027 Planarity : 0.005 0.059 4422 Dihedral : 5.891 81.553 3401 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 5.68 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3046 helix: 0.86 (0.20), residues: 688 sheet: 0.89 (0.19), residues: 680 loop : -1.50 (0.13), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.020 0.001 TYR C1049 PHE 0.018 0.001 PHE A 334 TRP 0.010 0.001 TRP B 423 HIS 0.002 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (25562) covalent geometry : angle 0.53444 / 0.28 (34744) SS BOND : bond 0.00533 / 0.37 ( 45) SS BOND : angle 1.74857 / 1.26 ( 90) hydrogen bonds : bond 0.05496 / 3.59 ( 990) hydrogen bonds : angle 5.21509 / 3.59 ( 2817) link_NAG-ASN : bond 0.00436 / 0.34 ( 46) link_NAG-ASN : angle 2.50527 / 1.69 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 818 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.5812 (mp10) REVERT: B 976 ASP cc_start: 0.8110 (m-30) cc_final: 0.7600 (m-30) REVERT: A 606 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7862 (t) REVERT: C 632 GLN cc_start: 0.8227 (tt0) cc_final: 0.7940 (mp10) outliers start: 29 outliers final: 4 residues processed: 195 average time/residue: 0.5141 time to fit residues: 119.6520 Evaluate side-chains 158 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 818 GLN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 97 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 234 optimal weight: 0.0370 chunk 208 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN A 987 GLN C 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.090244 restraints weight = 35016.288| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.39 r_work: 0.2933 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25653 Z= 0.139 Angle : 0.562 14.501 34972 Z= 0.292 Chirality : 0.047 0.290 4027 Planarity : 0.004 0.053 4422 Dihedral : 5.715 80.806 3397 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.05 % Allowed : 8.36 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3046 helix: 1.15 (0.20), residues: 691 sheet: 0.94 (0.19), residues: 682 loop : -1.45 (0.13), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 449 TYR 0.019 0.001 TYR C1049 PHE 0.021 0.001 PHE A 334 TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS B 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (25562) covalent geometry : angle 0.53409 / 0.28 (34744) SS BOND : bond 0.00573 / 0.40 ( 45) SS BOND : angle 1.89458 / 1.34 ( 90) hydrogen bonds : bond 0.05711 / 3.74 ( 990) hydrogen bonds : angle 5.05951 / 3.48 ( 2817) link_NAG-ASN : bond 0.00400 / 0.32 ( 46) link_NAG-ASN : angle 2.43734 / 1.66 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 903 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8139 (mppt) REVERT: B 976 ASP cc_start: 0.8173 (m-30) cc_final: 0.7538 (m-30) REVERT: C 449 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8113 (mtp85) REVERT: C 632 GLN cc_start: 0.8178 (tt0) cc_final: 0.7896 (mp10) REVERT: C 1011 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.7913 (tpp) outliers start: 28 outliers final: 9 residues processed: 188 average time/residue: 0.5552 time to fit residues: 124.4880 Evaluate side-chains 168 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1011 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 286 optimal weight: 3.9990 chunk 296 optimal weight: 0.7980 chunk 259 optimal weight: 0.4980 chunk 148 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 34 optimal weight: 0.0070 chunk 120 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.092120 restraints weight = 34825.190| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.45 r_work: 0.2941 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25653 Z= 0.123 Angle : 0.532 12.512 34972 Z= 0.277 Chirality : 0.046 0.286 4027 Planarity : 0.004 0.045 4422 Dihedral : 5.480 79.107 3397 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.57 % Allowed : 9.48 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3046 helix: 1.36 (0.20), residues: 691 sheet: 0.90 (0.20), residues: 652 loop : -1.31 (0.13), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 449 TYR 0.021 0.001 TYR A1120 PHE 0.014 0.001 PHE A 334 TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS B 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (25562) covalent geometry : angle 0.50514 / 0.27 (34744) SS BOND : bond 0.00522 / 0.36 ( 45) SS BOND : angle 1.76047 / 1.20 ( 90) hydrogen bonds : bond 0.05283 / 3.44 ( 990) hydrogen bonds : angle 4.92419 / 3.38 ( 2817) link_NAG-ASN : bond 0.00404 / 0.32 ( 46) link_NAG-ASN : angle 2.32545 / 1.59 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.6738 (p90) REVERT: B 708 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8990 (m) REVERT: B 768 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8279 (mttp) REVERT: B 850 ASP cc_start: 0.8622 (m-30) cc_final: 0.8335 (m-30) REVERT: B 976 ASP cc_start: 0.8200 (m-30) cc_final: 0.7614 (m-30) REVERT: A 37 MET cc_start: 0.6826 (ttp) cc_final: 0.6461 (ttt) REVERT: A 274 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: A 305 PHE cc_start: 0.7778 (m-10) cc_final: 0.7553 (m-10) REVERT: A 708 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8735 (t) REVERT: C 449 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8112 (mtp85) REVERT: C 632 GLN cc_start: 0.8202 (tt0) cc_final: 0.7922 (mp10) REVERT: C 1011 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.7850 (tpp) outliers start: 42 outliers final: 18 residues processed: 198 average time/residue: 0.5358 time to fit residues: 127.0209 Evaluate side-chains 179 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1011 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 230 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 301 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 786 GLN B 960 ASN A 304 ASN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.088076 restraints weight = 34968.629| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.45 r_work: 0.2864 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 25653 Z= 0.258 Angle : 0.670 17.138 34972 Z= 0.346 Chirality : 0.052 0.359 4027 Planarity : 0.005 0.053 4422 Dihedral : 6.011 83.636 3397 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.02 % Allowed : 10.90 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3046 helix: 1.04 (0.20), residues: 692 sheet: 0.90 (0.19), residues: 684 loop : -1.42 (0.13), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 449 TYR 0.028 0.002 TYR C 738 PHE 0.022 0.002 PHE A 83 TRP 0.010 0.002 TRP C 423 HIS 0.006 0.002 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.26 (25562) covalent geometry : angle 0.63606 / 0.34 (34744) SS BOND : bond 0.00941 / 0.66 ( 45) SS BOND : angle 2.39326 / 1.62 ( 90) hydrogen bonds : bond 0.07397 / 4.86 ( 990) hydrogen bonds : angle 5.21656 / 3.60 ( 2817) link_NAG-ASN : bond 0.00349 / 0.27 ( 46) link_NAG-ASN : angle 2.83214 / 1.91 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.6441 (p90) REVERT: B 768 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8428 (mttp) REVERT: B 976 ASP cc_start: 0.8474 (m-30) cc_final: 0.8239 (m-30) REVERT: B 1105 SER cc_start: 0.9120 (t) cc_final: 0.8786 (m) REVERT: A 37 MET cc_start: 0.6819 (ttp) cc_final: 0.6442 (ttt) REVERT: A 274 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: A 987 GLN cc_start: 0.8354 (mt0) cc_final: 0.7995 (mm110) REVERT: C 152 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8097 (tp) REVERT: C 449 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8206 (mtp85) REVERT: C 632 GLN cc_start: 0.8164 (tt0) cc_final: 0.7873 (mp10) outliers start: 54 outliers final: 27 residues processed: 197 average time/residue: 0.5540 time to fit residues: 130.3098 Evaluate side-chains 184 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1009 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 135 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 306 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 299 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092064 restraints weight = 34917.881| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.42 r_work: 0.2939 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25653 Z= 0.118 Angle : 0.531 14.320 34972 Z= 0.276 Chirality : 0.046 0.294 4027 Planarity : 0.004 0.044 4422 Dihedral : 5.448 81.934 3397 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.49 % Allowed : 12.32 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z 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: -0.18 (0.14), residues: 3046 helix: 1.45 (0.20), residues: 693 sheet: 0.94 (0.20), residues: 636 loop : -1.27 (0.13), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 449 TYR 0.021 0.001 TYR A1120 PHE 0.013 0.001 PHE A 137 TRP 0.010 0.001 TRP B 423 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (25562) covalent geometry : angle 0.50509 / 0.27 (34744) SS BOND : bond 0.00538 / 0.38 ( 45) SS BOND : angle 1.76941 / 1.20 ( 90) hydrogen bonds : bond 0.05197 / 3.38 ( 990) hydrogen bonds : angle 4.86538 / 3.35 ( 2817) link_NAG-ASN : bond 0.00418 / 0.33 ( 46) link_NAG-ASN : angle 2.30049 / 1.56 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.6740 (p90) REVERT: B 818 GLN cc_start: 0.7044 (mm110) cc_final: 0.5639 (mp10) REVERT: B 903 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8155 (mppt) REVERT: B 976 ASP cc_start: 0.8303 (m-30) cc_final: 0.7671 (m-30) REVERT: A 37 MET cc_start: 0.6662 (ttp) cc_final: 0.6311 (ttt) REVERT: A 274 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: A 708 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8713 (t) REVERT: C 449 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8073 (mtp85) REVERT: C 632 GLN cc_start: 0.8159 (tt0) cc_final: 0.7896 (mp10) outliers start: 40 outliers final: 17 residues processed: 191 average time/residue: 0.5093 time to fit residues: 117.3278 Evaluate side-chains 176 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 96 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 299 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 164 optimal weight: 0.0370 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.090664 restraints weight = 34870.336| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.45 r_work: 0.2913 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25653 Z= 0.147 Angle : 0.579 19.451 34972 Z= 0.295 Chirality : 0.048 0.550 4027 Planarity : 0.004 0.045 4422 Dihedral : 5.488 79.760 3397 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.42 % Allowed : 12.81 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3046 helix: 1.44 (0.20), residues: 689 sheet: 1.00 (0.20), residues: 647 loop : -1.27 (0.13), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 449 TYR 0.018 0.001 TYR B1049 PHE 0.015 0.001 PHE A 137 TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (25562) covalent geometry : angle 0.53612 / 0.28 (34744) SS BOND : bond 0.00632 / 0.44 ( 45) SS BOND : angle 1.89811 / 1.30 ( 90) hydrogen bonds : bond 0.05785 / 3.77 ( 990) hydrogen bonds : angle 4.91207 / 3.38 ( 2817) link_NAG-ASN : bond 0.00474 / 0.37 ( 46) link_NAG-ASN : angle 3.17929 / 2.22 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.6619 (p90) REVERT: B 818 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.5616 (mp10) REVERT: B 976 ASP cc_start: 0.8324 (m-30) cc_final: 0.7730 (m-30) REVERT: B 1105 SER cc_start: 0.9093 (t) cc_final: 0.8719 (m) REVERT: A 37 MET cc_start: 0.6691 (ttp) cc_final: 0.6330 (ttt) REVERT: A 274 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: C 449 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8123 (mtp85) REVERT: C 632 GLN cc_start: 0.8156 (tt0) cc_final: 0.7889 (mp10) outliers start: 38 outliers final: 21 residues processed: 190 average time/residue: 0.5137 time to fit residues: 117.3727 Evaluate side-chains 177 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 818 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN A 301 GLN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.092115 restraints weight = 34749.424| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.42 r_work: 0.2941 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25653 Z= 0.124 Angle : 0.549 16.001 34972 Z= 0.282 Chirality : 0.047 0.501 4027 Planarity : 0.004 0.045 4422 Dihedral : 5.350 80.858 3397 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.53 % Allowed : 13.11 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3046 helix: 1.53 (0.20), residues: 693 sheet: 0.99 (0.20), residues: 625 loop : -1.19 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 449 TYR 0.022 0.001 TYR A1120 PHE 0.015 0.001 PHE A 137 TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (25562) covalent geometry : angle 0.51573 / 0.27 (34744) SS BOND : bond 0.00673 / 0.43 ( 45) SS BOND : angle 1.85841 / 1.33 ( 90) hydrogen bonds : bond 0.05211 / 3.38 ( 990) hydrogen bonds : angle 4.80678 / 3.31 ( 2817) link_NAG-ASN : bond 0.00457 / 0.36 ( 46) link_NAG-ASN : angle 2.65808 / 1.83 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.6696 (p90) REVERT: B 802 ASP cc_start: 0.8544 (m-30) cc_final: 0.8318 (m-30) REVERT: B 818 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.5589 (mp10) REVERT: B 903 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8149 (mppt) REVERT: B 976 ASP cc_start: 0.8275 (m-30) cc_final: 0.7635 (m-30) REVERT: B 1105 SER cc_start: 0.9046 (t) cc_final: 0.8678 (m) REVERT: A 37 MET cc_start: 0.6684 (ttp) cc_final: 0.6326 (ttt) REVERT: A 274 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: A 708 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8733 (t) REVERT: C 449 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8095 (mtp85) REVERT: C 632 GLN cc_start: 0.8170 (tt0) cc_final: 0.7893 (mp10) outliers start: 41 outliers final: 21 residues processed: 197 average time/residue: 0.5384 time to fit residues: 127.2527 Evaluate side-chains 181 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 818 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 chunk 105 optimal weight: 0.0570 chunk 234 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 786 GLN B 960 ASN A 987 GLN C 889 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.091252 restraints weight = 34752.433| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.38 r_work: 0.2910 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 25653 Z= 0.151 Angle : 0.568 15.986 34972 Z= 0.294 Chirality : 0.047 0.298 4027 Planarity : 0.004 0.045 4422 Dihedral : 5.497 87.218 3397 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.42 % Allowed : 13.37 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3046 helix: 1.45 (0.20), residues: 695 sheet: 1.00 (0.20), residues: 649 loop : -1.23 (0.13), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 449 TYR 0.019 0.001 TYR B1049 PHE 0.016 0.001 PHE A 137 TRP 0.009 0.001 TRP C 423 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (25562) covalent geometry : angle 0.53898 / 0.29 (34744) SS BOND : bond 0.00685 / 0.46 ( 45) SS BOND : angle 2.02775 / 1.44 ( 90) hydrogen bonds : bond 0.05741 / 3.75 ( 990) hydrogen bonds : angle 4.88897 / 3.36 ( 2817) link_NAG-ASN : bond 0.00371 / 0.29 ( 46) link_NAG-ASN : angle 2.45081 / 1.73 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.6504 (p90) REVERT: B 802 ASP cc_start: 0.8574 (m-30) cc_final: 0.8342 (m-30) REVERT: B 818 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.5651 (mp10) REVERT: B 976 ASP cc_start: 0.8376 (m-30) cc_final: 0.7732 (m-30) REVERT: B 1105 SER cc_start: 0.9095 (t) cc_final: 0.8709 (m) REVERT: A 37 MET cc_start: 0.6686 (ttp) cc_final: 0.6327 (ttt) REVERT: A 108 ASN cc_start: 0.7951 (t0) cc_final: 0.7597 (t0) REVERT: A 274 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: C 449 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8126 (mtp85) REVERT: C 632 GLN cc_start: 0.8184 (tt0) cc_final: 0.7882 (mp10) outliers start: 38 outliers final: 29 residues processed: 189 average time/residue: 0.5449 time to fit residues: 123.6623 Evaluate side-chains 185 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 818 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 282 optimal weight: 6.9990 chunk 305 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 232 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN A 987 GLN C 889 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089729 restraints weight = 34790.425| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.38 r_work: 0.2886 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 25653 Z= 0.192 Angle : 0.616 16.643 34972 Z= 0.318 Chirality : 0.049 0.324 4027 Planarity : 0.004 0.047 4422 Dihedral : 5.738 89.089 3397 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.49 % Allowed : 13.37 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3046 helix: 1.31 (0.20), residues: 693 sheet: 1.00 (0.19), residues: 668 loop : -1.31 (0.13), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 449 TYR 0.023 0.002 TYR A1120 PHE 0.017 0.001 PHE A 83 TRP 0.010 0.001 TRP C 423 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (25562) covalent geometry : angle 0.58444 / 0.31 (34744) SS BOND : bond 0.00796 / 0.54 ( 45) SS BOND : angle 2.22231 / 1.55 ( 90) hydrogen bonds : bond 0.06515 / 4.26 ( 990) hydrogen bonds : angle 5.03014 / 3.46 ( 2817) link_NAG-ASN : bond 0.00361 / 0.28 ( 46) link_NAG-ASN : angle 2.65921 / 1.85 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.6325 (p90) REVERT: B 818 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.5737 (mp10) REVERT: B 976 ASP cc_start: 0.8465 (m-30) cc_final: 0.8230 (m-30) REVERT: B 1105 SER cc_start: 0.9102 (t) cc_final: 0.8739 (m) REVERT: A 37 MET cc_start: 0.6691 (ttp) cc_final: 0.6324 (ttt) REVERT: A 108 ASN cc_start: 0.8032 (t0) cc_final: 0.7637 (t0) REVERT: A 274 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: C 449 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8155 (mtp85) REVERT: C 632 GLN cc_start: 0.8174 (tt0) cc_final: 0.7861 (mp10) outliers start: 40 outliers final: 28 residues processed: 184 average time/residue: 0.5571 time to fit residues: 122.7712 Evaluate side-chains 180 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 818 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 139 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN A 987 GLN C 889 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.090486 restraints weight = 34785.643| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.44 r_work: 0.2913 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 25653 Z= 0.160 Angle : 0.581 16.111 34972 Z= 0.300 Chirality : 0.048 0.304 4027 Planarity : 0.004 0.046 4422 Dihedral : 5.609 89.731 3397 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.27 % Allowed : 13.78 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3046 helix: 1.40 (0.20), residues: 693 sheet: 0.98 (0.19), residues: 665 loop : -1.28 (0.13), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 449 TYR 0.019 0.001 TYR B1049 PHE 0.017 0.001 PHE A 137 TRP 0.009 0.001 TRP C 423 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (25562) covalent geometry : angle 0.55096 / 0.29 (34744) SS BOND : bond 0.00695 / 0.47 ( 45) SS BOND : angle 2.03988 / 1.42 ( 90) hydrogen bonds : bond 0.05870 / 3.83 ( 990) hydrogen bonds : angle 4.93192 / 3.39 ( 2817) link_NAG-ASN : bond 0.00365 / 0.29 ( 46) link_NAG-ASN : angle 2.52912 / 1.77 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7269.15 seconds wall clock time: 124 minutes 48.57 seconds (7488.57 seconds total)