Starting phenix.real_space_refine on Sat May 24 10:31:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0y_34418/05_2025/8h0y_34418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0y_34418/05_2025/8h0y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h0y_34418/05_2025/8h0y_34418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0y_34418/05_2025/8h0y_34418.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0y_34418/05_2025/8h0y_34418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0y_34418/05_2025/8h0y_34418.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 1.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 48 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 dihedrals: 45 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 dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 15.62, per 1000 atoms: 0.62 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: 6.38 Conformation dependent library (CDL) restraints added in 3.5 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: 3.83 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: 11.74 Time building geometry restraints manager: 7.34 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: 14379 17.99 - 35.97: 1134 35.97 - 53.96: 245 53.96 - 71.94: 58 71.94 - 89.93: 16 Dihedral angle restraints: 15832 sinusoidal: 6822 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 15829 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 1123 \ or resid 1301 through 1316)) selection = (chain 'B' and (resid 31 through 1123 or resid 1301 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 1123 or resid 1301 through 13 \ 16)) } 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 59.310 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.100 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 13.440 89.931 9901 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (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 TRP 0.013 0.002 TRP B 423 HIS 0.006 0.001 HIS B 661 PHE 0.053 0.002 PHE A 334 TYR 0.023 0.002 TYR C 481 ARG 0.018 0.001 ARG C 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 46) link_NAG-ASN : angle 4.16040 ( 138) hydrogen bonds : bond 0.14006 ( 990) hydrogen bonds : angle 6.54779 ( 2817) SS BOND : bond 0.01084 ( 45) SS BOND : angle 2.71234 ( 90) covalent geometry : bond 0.00783 (25562) covalent geometry : angle 0.85197 (34744) *********************** 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 : 2.954 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: 1.2745 time to fit residues: 304.1646 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 : 6.873 ------------------------------------------------------------------------------- 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 260 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3530 r_free = 0.3530 target = 0.121335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.091350 restraints weight = 34721.386| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.38 r_work: 0.2927 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25653 Z= 0.151 Angle : 0.596 13.452 34972 Z= 0.309 Chirality : 0.048 0.324 4027 Planarity : 0.005 0.057 4422 Dihedral : 7.915 81.824 4415 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.12 % Allowed : 6.16 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3046 helix: 0.73 (0.20), residues: 692 sheet: 0.85 (0.19), residues: 691 loop : -1.57 (0.13), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 423 HIS 0.004 0.001 HIS A1030 PHE 0.025 0.001 PHE A 334 TYR 0.021 0.001 TYR B1049 ARG 0.006 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 46) link_NAG-ASN : angle 2.73447 ( 138) hydrogen bonds : bond 0.06126 ( 990) hydrogen bonds : angle 5.29839 ( 2817) SS BOND : bond 0.00618 ( 45) SS BOND : angle 1.90556 ( 90) covalent geometry : bond 0.00358 (25562) covalent geometry : angle 0.56445 (34744) *********************** 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 205 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 976 ASP cc_start: 0.8205 (m-30) cc_final: 0.7647 (m-30) REVERT: A 305 PHE cc_start: 0.7686 (m-10) cc_final: 0.7485 (m-10) REVERT: A 606 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7858 (t) REVERT: C 632 GLN cc_start: 0.8189 (tt0) cc_final: 0.7917 (mp10) outliers start: 30 outliers final: 4 residues processed: 191 average time/residue: 1.1780 time to fit residues: 267.5464 Evaluate side-chains 157 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 46 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 300 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3522 r_free = 0.3522 target = 0.120723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.090946 restraints weight = 34790.198| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.43 r_work: 0.2920 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25653 Z= 0.149 Angle : 0.574 14.580 34972 Z= 0.298 Chirality : 0.048 0.303 4027 Planarity : 0.004 0.054 4422 Dihedral : 7.130 82.469 4411 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.05 % Allowed : 8.70 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3046 helix: 1.11 (0.20), residues: 688 sheet: 0.89 (0.19), residues: 684 loop : -1.48 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 423 HIS 0.003 0.001 HIS B 661 PHE 0.020 0.001 PHE A 334 TYR 0.019 0.001 TYR C1049 ARG 0.008 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 46) link_NAG-ASN : angle 2.56049 ( 138) hydrogen bonds : bond 0.05898 ( 990) hydrogen bonds : angle 5.09941 ( 2817) SS BOND : bond 0.00589 ( 45) SS BOND : angle 1.94007 ( 90) covalent geometry : bond 0.00355 (25562) covalent geometry : angle 0.54365 (34744) *********************** 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 198 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 903 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8203 (mppt) REVERT: B 976 ASP cc_start: 0.8269 (m-30) cc_final: 0.7659 (m-30) REVERT: C 632 GLN cc_start: 0.8176 (tt0) cc_final: 0.7923 (mp10) outliers start: 28 outliers final: 11 residues processed: 188 average time/residue: 1.1534 time to fit residues: 257.2703 Evaluate side-chains 171 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain A residue 209 LEU 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 722 MET Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 68 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 59 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 49 optimal weight: 0.0670 chunk 229 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 960 ASN B 984 GLN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.091766 restraints weight = 35019.799| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.46 r_work: 0.2938 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25653 Z= 0.121 Angle : 0.530 12.758 34972 Z= 0.276 Chirality : 0.046 0.290 4027 Planarity : 0.004 0.049 4422 Dihedral : 6.469 79.491 4411 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.57 % Allowed : 9.97 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3046 helix: 1.34 (0.20), residues: 692 sheet: 0.85 (0.20), residues: 657 loop : -1.31 (0.13), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS B 661 PHE 0.012 0.001 PHE A 334 TYR 0.021 0.001 TYR A1120 ARG 0.009 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 46) link_NAG-ASN : angle 2.38766 ( 138) hydrogen bonds : bond 0.05227 ( 990) hydrogen bonds : angle 4.92273 ( 2817) SS BOND : bond 0.00603 ( 45) SS BOND : angle 1.76201 ( 90) covalent geometry : bond 0.00283 (25562) covalent geometry : angle 0.50249 (34744) *********************** 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 215 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.6760 (p90) REVERT: B 768 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8405 (mttp) REVERT: B 796 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7767 (mmmt) REVERT: B 850 ASP cc_start: 0.8606 (m-30) cc_final: 0.8327 (m-30) REVERT: B 976 ASP cc_start: 0.8101 (m-30) cc_final: 0.7498 (m-30) REVERT: A 37 MET cc_start: 0.6751 (ttp) cc_final: 0.6367 (ttt) REVERT: A 274 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: A 708 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8733 (t) REVERT: C 449 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8048 (mtp85) REVERT: C 632 GLN cc_start: 0.8141 (tt0) cc_final: 0.7860 (mp10) outliers start: 42 outliers final: 17 residues processed: 203 average time/residue: 1.1289 time to fit residues: 274.2133 Evaluate side-chains 182 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 2.692 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 268 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 293 optimal weight: 0.5980 chunk 304 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 786 GLN B 960 ASN A 304 ASN A 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.088545 restraints weight = 34954.856| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.41 r_work: 0.2903 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1190 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= 0.167 Angle : 0.587 16.613 34972 Z= 0.301 Chirality : 0.049 0.605 4027 Planarity : 0.004 0.045 4422 Dihedral : 6.620 80.045 4411 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.72 % Allowed : 11.50 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3046 helix: 1.31 (0.20), residues: 692 sheet: 0.92 (0.19), residues: 679 loop : -1.32 (0.13), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.004 0.001 HIS B 661 PHE 0.015 0.001 PHE A 83 TYR 0.019 0.001 TYR B1049 ARG 0.007 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 46) link_NAG-ASN : angle 2.93879 ( 138) hydrogen bonds : bond 0.06052 ( 990) hydrogen bonds : angle 4.99201 ( 2817) SS BOND : bond 0.00746 ( 45) SS BOND : angle 2.01479 ( 90) covalent geometry : bond 0.00406 (25562) covalent geometry : angle 0.54990 (34744) *********************** 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 205 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.6566 (p90) REVERT: B 768 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8460 (mttp) REVERT: B 818 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.5643 (mp10) REVERT: B 850 ASP cc_start: 0.8667 (m-30) cc_final: 0.8424 (m-30) REVERT: B 976 ASP cc_start: 0.8244 (m-30) cc_final: 0.7654 (m-30) REVERT: B 1105 SER cc_start: 0.9082 (t) cc_final: 0.8693 (m) REVERT: A 37 MET cc_start: 0.6649 (ttp) cc_final: 0.6254 (ttt) REVERT: A 274 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: A 305 PHE cc_start: 0.7736 (m-10) cc_final: 0.7534 (m-10) REVERT: C 449 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8087 (mtp85) REVERT: C 632 GLN cc_start: 0.8146 (tt0) cc_final: 0.7855 (mp10) outliers start: 46 outliers final: 26 residues processed: 195 average time/residue: 1.1509 time to fit residues: 267.3627 Evaluate side-chains 187 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 2.700 ------------------------------------------------------------------------------- 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 818 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 946 LYS 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 592 SER 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 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 891 ILE Chi-restraints excluded: chain C residue 958 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 263 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 282 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 786 GLN B 960 ASN A 301 GLN A 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.088064 restraints weight = 34846.055| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.46 r_work: 0.2889 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 25653 Z= 0.193 Angle : 0.618 16.752 34972 Z= 0.317 Chirality : 0.051 0.874 4027 Planarity : 0.004 0.047 4422 Dihedral : 6.733 83.815 4411 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 12.17 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3046 helix: 1.24 (0.20), residues: 693 sheet: 0.91 (0.19), residues: 670 loop : -1.32 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 423 HIS 0.004 0.001 HIS A1046 PHE 0.017 0.001 PHE A 83 TYR 0.021 0.002 TYR A1120 ARG 0.007 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 46) link_NAG-ASN : angle 3.11496 ( 138) hydrogen bonds : bond 0.06520 ( 990) hydrogen bonds : angle 5.06094 ( 2817) SS BOND : bond 0.00766 ( 45) SS BOND : angle 2.13806 ( 90) covalent geometry : bond 0.00471 (25562) covalent geometry : angle 0.57760 (34744) *********************** 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 204 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.6393 (p90) REVERT: B 768 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8434 (mttp) REVERT: B 818 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.5584 (mp10) REVERT: B 850 ASP cc_start: 0.8680 (m-30) cc_final: 0.8393 (m-30) REVERT: B 976 ASP cc_start: 0.8342 (m-30) cc_final: 0.8080 (m-30) REVERT: A 37 MET cc_start: 0.6635 (ttp) cc_final: 0.6252 (ttt) REVERT: A 274 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: C 152 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8032 (tp) REVERT: C 449 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8088 (mtp85) REVERT: C 632 GLN cc_start: 0.8123 (tt0) cc_final: 0.7815 (mp10) outliers start: 45 outliers final: 29 residues processed: 193 average time/residue: 1.1063 time to fit residues: 256.7844 Evaluate side-chains 188 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 2.706 ------------------------------------------------------------------------------- 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 489 ILE Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 818 GLN Chi-restraints excluded: chain B residue 946 LYS 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 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 485 THR Chi-restraints excluded: chain C residue 557 ASP 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 891 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 69 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 303 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 278 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN B 984 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 = 0.3539 r_free = 0.3539 target = 0.122677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.091736 restraints weight = 34695.019| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.39 r_work: 0.2941 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25653 Z= 0.114 Angle : 0.529 13.420 34972 Z= 0.274 Chirality : 0.047 0.552 4027 Planarity : 0.004 0.044 4422 Dihedral : 6.208 82.617 4411 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.57 % Allowed : 12.70 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3046 helix: 1.58 (0.20), residues: 688 sheet: 0.93 (0.20), residues: 643 loop : -1.21 (0.13), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.002 0.001 HIS B1030 PHE 0.014 0.001 PHE A 137 TYR 0.019 0.001 TYR B1049 ARG 0.010 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 46) link_NAG-ASN : angle 2.45014 ( 138) hydrogen bonds : bond 0.04996 ( 990) hydrogen bonds : angle 4.79751 ( 2817) SS BOND : bond 0.00556 ( 45) SS BOND : angle 1.74313 ( 90) covalent geometry : bond 0.00261 (25562) covalent geometry : angle 0.49962 (34744) *********************** 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 210 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.6558 (p90) REVERT: B 708 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8960 (m) REVERT: B 818 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.5696 (mp10) REVERT: B 903 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8080 (mppt) REVERT: B 976 ASP cc_start: 0.8199 (m-30) cc_final: 0.7527 (m-30) REVERT: B 1105 SER cc_start: 0.9005 (t) cc_final: 0.8622 (m) REVERT: A 37 MET cc_start: 0.6660 (ttp) cc_final: 0.6302 (ttt) REVERT: A 274 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: C 449 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8021 (mtp85) REVERT: C 632 GLN cc_start: 0.8114 (tt0) cc_final: 0.7824 (mp10) outliers start: 42 outliers final: 19 residues processed: 200 average time/residue: 1.1134 time to fit residues: 266.7028 Evaluate side-chains 183 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 2.588 ------------------------------------------------------------------------------- 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 307 VAL 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 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 209 LEU 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 C residue 56 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 124 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 301 optimal weight: 0.8980 chunk 170 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3525 r_free = 0.3525 target = 0.121580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090503 restraints weight = 34721.517| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.40 r_work: 0.2919 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25653 Z= 0.137 Angle : 0.550 15.984 34972 Z= 0.285 Chirality : 0.047 0.488 4027 Planarity : 0.004 0.044 4422 Dihedral : 6.246 83.897 4411 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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 : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3046 helix: 1.51 (0.20), residues: 691 sheet: 0.98 (0.19), residues: 664 loop : -1.22 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS A1030 PHE 0.016 0.001 PHE A 137 TYR 0.022 0.001 TYR A1120 ARG 0.011 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 46) link_NAG-ASN : angle 2.44121 ( 138) hydrogen bonds : bond 0.05490 ( 990) hydrogen bonds : angle 4.84585 ( 2817) SS BOND : bond 0.00639 ( 45) SS BOND : angle 1.92485 ( 90) covalent geometry : bond 0.00326 (25562) covalent geometry : angle 0.52082 (34744) *********************** 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 206 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.6753 (p90) REVERT: B 818 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.5693 (mp10) REVERT: B 976 ASP cc_start: 0.8246 (m-30) cc_final: 0.7569 (m-30) REVERT: B 1105 SER cc_start: 0.9002 (t) cc_final: 0.8612 (m) REVERT: A 37 MET cc_start: 0.6676 (ttp) cc_final: 0.6309 (ttt) REVERT: A 274 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: C 449 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8046 (mtp85) REVERT: C 632 GLN cc_start: 0.8127 (tt0) cc_final: 0.7826 (mp10) outliers start: 41 outliers final: 25 residues processed: 197 average time/residue: 1.1164 time to fit residues: 264.3182 Evaluate side-chains 188 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 2.939 ------------------------------------------------------------------------------- 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 307 VAL 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 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 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 916 ILE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 124 VAL 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 720 CYS Chi-restraints excluded: chain C residue 891 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 304 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 228 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3534 r_free = 0.3534 target = 0.121772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.090721 restraints weight = 35002.798| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.38 r_work: 0.2938 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25653 Z= 0.130 Angle : 0.543 15.540 34972 Z= 0.281 Chirality : 0.047 0.461 4027 Planarity : 0.004 0.044 4422 Dihedral : 6.177 84.011 4411 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.42 % Allowed : 13.41 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3046 helix: 1.51 (0.20), residues: 690 sheet: 0.99 (0.20), residues: 629 loop : -1.19 (0.13), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.003 0.001 HIS A1046 PHE 0.017 0.001 PHE A 137 TYR 0.019 0.001 TYR B1049 ARG 0.011 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 46) link_NAG-ASN : angle 2.37190 ( 138) hydrogen bonds : bond 0.05316 ( 990) hydrogen bonds : angle 4.81813 ( 2817) SS BOND : bond 0.00618 ( 45) SS BOND : angle 1.85214 ( 90) covalent geometry : bond 0.00308 (25562) covalent geometry : angle 0.51510 (34744) *********************** 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 203 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.6547 (p90) REVERT: B 708 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8957 (m) REVERT: B 818 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.5647 (mp10) REVERT: B 903 LYS cc_start: 0.8380 (mtmt) cc_final: 0.8121 (mppt) REVERT: B 976 ASP cc_start: 0.8268 (m-30) cc_final: 0.7596 (m-30) REVERT: B 1105 SER cc_start: 0.9026 (t) cc_final: 0.8642 (m) REVERT: A 37 MET cc_start: 0.6660 (ttp) cc_final: 0.6303 (ttt) REVERT: A 274 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: C 367 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8774 (m-80) REVERT: C 449 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8060 (mtp85) REVERT: C 632 GLN cc_start: 0.8132 (tt0) cc_final: 0.7846 (mp10) outliers start: 38 outliers final: 28 residues processed: 198 average time/residue: 1.0864 time to fit residues: 258.8495 Evaluate side-chains 191 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 2.693 ------------------------------------------------------------------------------- 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 307 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 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 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 538 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 708 VAL 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 124 VAL 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 367 TYR 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 891 ILE 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 134 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3525 r_free = 0.3525 target = 0.121067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.089994 restraints weight = 34913.273| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.37 r_work: 0.2928 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25653 Z= 0.145 Angle : 0.560 15.606 34972 Z= 0.290 Chirality : 0.048 0.458 4027 Planarity : 0.004 0.045 4422 Dihedral : 6.274 83.883 4411 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.61 % Allowed : 13.44 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3046 helix: 1.54 (0.20), residues: 687 sheet: 1.02 (0.19), residues: 657 loop : -1.19 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 423 HIS 0.003 0.001 HIS A1046 PHE 0.017 0.001 PHE A 137 TYR 0.021 0.001 TYR A1120 ARG 0.012 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 46) link_NAG-ASN : angle 2.41815 ( 138) hydrogen bonds : bond 0.05646 ( 990) hydrogen bonds : angle 4.87203 ( 2817) SS BOND : bond 0.00657 ( 45) SS BOND : angle 1.92149 ( 90) covalent geometry : bond 0.00347 (25562) covalent geometry : angle 0.53145 (34744) ********************** 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 205 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.6478 (p90) REVERT: B 818 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.5698 (mp10) REVERT: B 976 ASP cc_start: 0.8298 (m-30) cc_final: 0.7650 (m-30) REVERT: A 37 MET cc_start: 0.6674 (ttp) cc_final: 0.6323 (ttt) REVERT: A 108 ASN cc_start: 0.7906 (t0) cc_final: 0.7572 (t0) REVERT: A 274 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: C 449 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8076 (mtp85) REVERT: C 632 GLN cc_start: 0.8157 (tt0) cc_final: 0.7848 (mp10) outliers start: 43 outliers final: 31 residues processed: 199 average time/residue: 1.2170 time to fit residues: 297.7260 Evaluate side-chains 194 residues out of total 2678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 2.857 ------------------------------------------------------------------------------- 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 307 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 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 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 635 CYS Chi-restraints excluded: chain A residue 708 VAL 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 124 VAL 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 891 ILE 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 100 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 260 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN A 614 GLN 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 = 0.3498 r_free = 0.3498 target = 0.118940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.089122 restraints weight = 34894.696| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.39 r_work: 0.2876 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 25653 Z= 0.222 Angle : 0.641 16.246 34972 Z= 0.330 Chirality : 0.051 0.482 4027 Planarity : 0.004 0.046 4422 Dihedral : 6.748 88.447 4411 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.42 % Allowed : 13.93 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3046 helix: 1.23 (0.20), residues: 693 sheet: 0.97 (0.19), residues: 678 loop : -1.31 (0.13), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 423 HIS 0.005 0.001 HIS A1046 PHE 0.018 0.002 PHE A 137 TYR 0.023 0.002 TYR C 738 ARG 0.014 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 46) link_NAG-ASN : angle 2.76100 ( 138) hydrogen bonds : bond 0.06858 ( 990) hydrogen bonds : angle 5.08315 ( 2817) SS BOND : bond 0.00847 ( 45) SS BOND : angle 2.29337 ( 90) covalent geometry : bond 0.00550 (25562) covalent geometry : angle 0.60839 (34744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14680.04 seconds wall clock time: 254 minutes 17.71 seconds (15257.71 seconds total)