Starting phenix.real_space_refine on Mon Aug 25 04:21:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h10_34420/08_2025/8h10_34420.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h10_34420/08_2025/8h10_34420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h10_34420/08_2025/8h10_34420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h10_34420/08_2025/8h10_34420.map" model { file = "/net/cci-nas-00/data/ceres_data/8h10_34420/08_2025/8h10_34420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h10_34420/08_2025/8h10_34420.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 15894 2.51 5 N 4035 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24882 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8007 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 6 Chain: "B" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8007 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 6 Chain: "C" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8007 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 5.13, per 1000 atoms: 0.21 Number of scatterers: 24882 At special positions: 0 Unit cell: (122.64, 127.02, 177.39, 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 135 16.00 O 4818 8.00 N 4035 7.00 C 15894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 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=2.04 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=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 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 B 128 " - pdb=" SG CYS B 159 " distance=2.04 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 378 " - pdb=" SG CYS B 511 " distance=2.04 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=2.03 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 C 128 " - pdb=" SG CYS C 159 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 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=2.03 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A1080 " " NAG A1303 " - " ASN A 109 " " NAG A1304 " - " ASN A 119 " " NAG A1305 " - " ASN A 158 " " NAG A1306 " - " ASN A 269 " " NAG A1307 " - " ASN A 318 " " NAG A1308 " - " ASN A 357 " " NAG A1309 " - " ASN A 602 " " NAG A1310 " - " ASN A 691 " " NAG A1311 " - " ASN A 699 " " NAG A1312 " - " ASN A 783 " " NAG A1313 " - " ASN A1056 " " NAG A1315 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 109 " " NAG B1304 " - " ASN B 119 " " NAG B1305 " - " ASN B 158 " " NAG B1306 " - " ASN B 269 " " NAG B1307 " - " ASN B 318 " " NAG B1308 " - " ASN B 357 " " NAG B1309 " - " ASN B 602 " " NAG B1310 " - " ASN B 691 " " NAG B1311 " - " ASN B 699 " " NAG B1312 " - " ASN B 783 " " NAG B1313 " - " ASN B1056 " " NAG B1315 " - " ASN B1116 " " NAG C1302 " - " ASN C 65 " " NAG C1303 " - " ASN C1080 " " NAG C1304 " - " ASN C 109 " " NAG C1305 " - " ASN C 119 " " NAG C1306 " - " ASN C 158 " " NAG C1307 " - " ASN C 269 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 357 " " NAG C1310 " - " ASN C 602 " " NAG C1311 " - " ASN C 691 " " NAG C1312 " - " ASN C 699 " " NAG C1313 " - " ASN C 783 " " NAG C1314 " - " ASN C1056 " " NAG C1316 " - " ASN C1116 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 999.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 26.8% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 353 through 357 removed outlier: 3.568A pdb=" N TYR A 356 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 357 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 357' Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.656A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.515A pdb=" N ASP A 393 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.706A pdb=" N ASP A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 430' Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.542A pdb=" N TYR A 491 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 492 " --> pdb=" O ILE A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 492' Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 605 through 611 removed outlier: 3.611A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 615 removed outlier: 3.505A pdb=" N LEU A 615 " --> pdb=" O ALA A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.620A pdb=" N ILE A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.934A pdb=" N GLN A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 765 removed outlier: 3.744A pdb=" N ASN A 746 " --> pdb=" O CYS A 742 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 748 " --> pdb=" O GLN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 788 removed outlier: 3.799A 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 805 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.347A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.573A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) 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 963 removed outlier: 3.743A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 958 through 963' Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.739A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.568A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN B 357 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 357' Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.657A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 3.514A pdb=" N ASP B 393 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.446A 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 removed outlier: 3.706A pdb=" N ASP B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 430' Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.543A pdb=" N TYR B 491 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 488 through 492' Processing helix chain 'B' and resid 602 through 604 No H-bonds generated for 'chain 'B' and resid 602 through 604' Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.612A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 removed outlier: 3.506A pdb=" N LEU B 615 " --> pdb=" O ALA B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.621A pdb=" N ILE B 621 " --> pdb=" O PRO B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.934A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 765 removed outlier: 3.742A pdb=" N ASN B 746 " --> pdb=" O CYS B 742 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 747 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 788 removed outlier: 3.799A pdb=" N LEU B 788 " --> pdb=" O SER B 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 785 through 788' Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 879 through 890 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.347A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.573A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 963 removed outlier: 3.743A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 958 through 963' Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.738A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 353 through 357 removed outlier: 3.568A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 357 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 357' Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.657A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 3.514A pdb=" N ASP C 393 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.446A 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 removed outlier: 3.707A pdb=" N ASP C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 430' Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.543A pdb=" N TYR C 491 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN C 492 " --> pdb=" O ILE C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 492' Processing helix chain 'C' and resid 602 through 604 No H-bonds generated for 'chain 'C' and resid 602 through 604' Processing helix chain 'C' and resid 605 through 611 removed outlier: 3.612A pdb=" N ALA C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 3.505A pdb=" N LEU C 615 " --> pdb=" O ALA C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 616 through 621 removed outlier: 3.620A pdb=" N ILE C 621 " --> pdb=" O PRO C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.935A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 765 removed outlier: 3.742A pdb=" N ASN C 746 " --> pdb=" O CYS C 742 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 747 " --> pdb=" O THR C 743 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 748 " --> pdb=" O GLN C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 788 removed outlier: 3.800A pdb=" N LEU C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 785 through 788' Processing helix chain 'C' and resid 798 through 805 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.347A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.573A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (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 963 removed outlier: 3.743A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 958 through 963' Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.738A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.789A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.941A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.073A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.516A pdb=" N PHE A 529 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.954A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 502 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.643A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'A' and resid 537 through 540 removed outlier: 5.211A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.063A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.718A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.684A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.684A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.519A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB7, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB8, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.789A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.941A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 7.073A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN B 118 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 315 removed outlier: 3.517A pdb=" N PHE B 529 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.954A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.642A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC8, first strand: chain 'B' and resid 537 through 540 removed outlier: 5.211A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.064A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.829A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.685A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.685A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.521A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD6, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.789A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.941A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 7.073A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AE2, first strand: chain 'C' and resid 312 through 315 removed outlier: 3.517A pdb=" N PHE C 529 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.955A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.643A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE6, first strand: chain 'C' and resid 537 through 540 removed outlier: 5.211A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.063A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.684A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.684A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AF1, 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=AF2, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF3, first strand: chain 'C' and resid 1102 through 1104 968 hydrogen bonds defined for protein. 2661 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4011 1.31 - 1.44: 7158 1.44 - 1.58: 14097 1.58 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 25446 Sorted by residual: bond pdb=" C1C BLA B1314 " pdb=" NC BLA B1314 " ideal model delta sigma weight residual 1.368 1.534 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" C1C BLA C1315 " pdb=" NC BLA C1315 " ideal model delta sigma weight residual 1.368 1.534 -0.166 2.00e-02 2.50e+03 6.85e+01 bond pdb=" C1C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.368 1.533 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" C4C BLA B1314 " pdb=" NC BLA B1314 " ideal model delta sigma weight residual 1.375 1.538 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C4C BLA C1315 " pdb=" NC BLA C1315 " ideal model delta sigma weight residual 1.375 1.538 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 25441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 33622 2.34 - 4.68: 840 4.68 - 7.02: 101 7.02 - 9.35: 30 9.35 - 11.69: 18 Bond angle restraints: 34611 Sorted by residual: angle pdb=" N ASN A 589 " pdb=" CA ASN A 589 " pdb=" C ASN A 589 " ideal model delta sigma weight residual 114.64 106.26 8.38 1.52e+00 4.33e-01 3.04e+01 angle pdb=" N ASN C 589 " pdb=" CA ASN C 589 " pdb=" C ASN C 589 " ideal model delta sigma weight residual 114.64 106.27 8.37 1.52e+00 4.33e-01 3.03e+01 angle pdb=" N ASN B 589 " pdb=" CA ASN B 589 " pdb=" C ASN B 589 " ideal model delta sigma weight residual 114.64 106.31 8.33 1.52e+00 4.33e-01 3.00e+01 angle pdb=" CA GLN C1124 " pdb=" CB GLN C1124 " pdb=" CG GLN C1124 " ideal model delta sigma weight residual 114.10 123.72 -9.62 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA GLN A1124 " pdb=" CB GLN A1124 " pdb=" CG GLN A1124 " ideal model delta sigma weight residual 114.10 123.69 -9.59 2.00e+00 2.50e-01 2.30e+01 ... (remaining 34606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 14072 15.24 - 30.47: 1258 30.47 - 45.71: 324 45.71 - 60.94: 99 60.94 - 76.18: 36 Dihedral angle restraints: 15789 sinusoidal: 6813 harmonic: 8976 Sorted by residual: dihedral pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " pdb=" SG CYS B 474 " pdb=" CB CYS B 474 " ideal model delta sinusoidal sigma weight residual -86.00 -154.63 68.63 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS A 467 " pdb=" SG CYS A 467 " pdb=" SG CYS A 474 " pdb=" CB CYS A 474 " ideal model delta sinusoidal sigma weight residual -86.00 -154.61 68.61 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS C 467 " pdb=" SG CYS C 467 " pdb=" SG CYS C 474 " pdb=" CB CYS C 474 " ideal model delta sinusoidal sigma weight residual -86.00 -154.60 68.60 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 15786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3436 0.077 - 0.153: 549 0.153 - 0.230: 44 0.230 - 0.306: 0 0.306 - 0.383: 3 Chirality restraints: 4032 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.77e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 65 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 65 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 4029 not shown) Planarity restraints: 4449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA C1315 " -0.221 2.00e-02 2.50e+03 2.63e-01 1.72e+03 pdb=" C1A BLA C1315 " 0.613 2.00e-02 2.50e+03 pdb=" C1D BLA C1315 " -0.045 2.00e-02 2.50e+03 pdb=" C2D BLA C1315 " 0.058 2.00e-02 2.50e+03 pdb=" C3D BLA C1315 " -0.061 2.00e-02 2.50e+03 pdb=" C4D BLA C1315 " -0.244 2.00e-02 2.50e+03 pdb=" CAD BLA C1315 " -0.011 2.00e-02 2.50e+03 pdb=" CHA BLA C1315 " -0.369 2.00e-02 2.50e+03 pdb=" CHD BLA C1315 " 0.036 2.00e-02 2.50e+03 pdb=" CMD BLA C1315 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1314 " -0.221 2.00e-02 2.50e+03 2.62e-01 1.72e+03 pdb=" C1A BLA B1314 " 0.612 2.00e-02 2.50e+03 pdb=" C1D BLA B1314 " -0.045 2.00e-02 2.50e+03 pdb=" C2D BLA B1314 " 0.057 2.00e-02 2.50e+03 pdb=" C3D BLA B1314 " -0.060 2.00e-02 2.50e+03 pdb=" C4D BLA B1314 " -0.243 2.00e-02 2.50e+03 pdb=" CAD BLA B1314 " -0.010 2.00e-02 2.50e+03 pdb=" CHA BLA B1314 " -0.370 2.00e-02 2.50e+03 pdb=" CHD BLA B1314 " 0.037 2.00e-02 2.50e+03 pdb=" CMD BLA B1314 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA A1314 " -0.221 2.00e-02 2.50e+03 2.62e-01 1.72e+03 pdb=" C1A BLA A1314 " 0.612 2.00e-02 2.50e+03 pdb=" C1D BLA A1314 " -0.045 2.00e-02 2.50e+03 pdb=" C2D BLA A1314 " 0.058 2.00e-02 2.50e+03 pdb=" C3D BLA A1314 " -0.061 2.00e-02 2.50e+03 pdb=" C4D BLA A1314 " -0.243 2.00e-02 2.50e+03 pdb=" CAD BLA A1314 " -0.011 2.00e-02 2.50e+03 pdb=" CHA BLA A1314 " -0.369 2.00e-02 2.50e+03 pdb=" CHD BLA A1314 " 0.037 2.00e-02 2.50e+03 pdb=" CMD BLA A1314 " 0.243 2.00e-02 2.50e+03 ... (remaining 4446 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7537 2.82 - 3.34: 20022 3.34 - 3.86: 38480 3.86 - 4.38: 44658 4.38 - 4.90: 79807 Nonbonded interactions: 190504 Sorted by model distance: nonbonded pdb=" OH TYR C 436 " pdb=" OH TYR C 484 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR A 436 " pdb=" OH TYR A 484 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR B 436 " pdb=" OH TYR B 484 " model vdw 2.305 3.040 nonbonded pdb=" NH1 ARG A1073 " pdb=" O ASP A1100 " model vdw 2.325 3.120 nonbonded pdb=" NH1 ARG B1073 " pdb=" O ASP B1100 " model vdw 2.326 3.120 ... (remaining 190499 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 1125 or resid 1302 through 1313)) selection = (chain 'B' and (resid 31 through 1125 or resid 1302 through 1313)) selection = (chain 'C' and (resid 31 through 1125 or resid 1302 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.270 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 0.166 25533 Z= 0.371 Angle : 0.956 15.073 34833 Z= 0.486 Chirality : 0.055 0.383 4032 Planarity : 0.010 0.263 4404 Dihedral : 12.960 76.178 9894 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.64 % Allowed : 1.05 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.14), residues: 3036 helix: -0.06 (0.20), residues: 684 sheet: 0.91 (0.20), residues: 717 loop : -1.84 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 183 TYR 0.039 0.002 TYR C1120 PHE 0.038 0.002 PHE A 888 TRP 0.036 0.002 TRP B 868 HIS 0.005 0.001 HIS B1040 Details of bonding type rmsd covalent geometry : bond 0.00789 (25446) covalent geometry : angle 0.90066 (34611) SS BOND : bond 0.00676 ( 39) SS BOND : angle 1.69297 ( 78) hydrogen bonds : bond 0.13588 ( 932) hydrogen bonds : angle 6.52358 ( 2661) link_BETA1-4 : bond 0.01102 ( 3) link_BETA1-4 : angle 2.25654 ( 9) link_NAG-ASN : bond 0.00565 ( 45) link_NAG-ASN : angle 5.06044 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 273 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: C 543 LYS cc_start: 0.7849 (tttm) cc_final: 0.7595 (mttt) REVERT: C 679 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7485 (ptp) REVERT: C 1032 MET cc_start: 0.8791 (ptm) cc_final: 0.8464 (ptp) outliers start: 17 outliers final: 0 residues processed: 279 average time/residue: 0.6354 time to fit residues: 204.5613 Evaluate side-chains 162 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 679 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 632 GLN A 746 ASN A 883 GLN A 889 ASN B 96 ASN B 523 GLN B 632 GLN B 746 ASN B 889 ASN C 96 ASN C 155 ASN C 523 GLN C 632 GLN C 746 ASN C 883 GLN C 889 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093853 restraints weight = 36137.088| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.53 r_work: 0.3033 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 25533 Z= 0.199 Angle : 0.675 11.918 34833 Z= 0.336 Chirality : 0.047 0.345 4032 Planarity : 0.006 0.108 4404 Dihedral : 8.124 89.921 4437 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.46 % Allowed : 9.06 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.15), residues: 3036 helix: 0.82 (0.21), residues: 669 sheet: 0.77 (0.19), residues: 744 loop : -1.68 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 449 TYR 0.025 0.002 TYR A 352 PHE 0.031 0.002 PHE A 888 TRP 0.021 0.002 TRP B 868 HIS 0.007 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00481 (25446) covalent geometry : angle 0.62443 (34611) SS BOND : bond 0.00639 ( 39) SS BOND : angle 1.58490 ( 78) hydrogen bonds : bond 0.06521 ( 932) hydrogen bonds : angle 5.30583 ( 2661) link_BETA1-4 : bond 0.00729 ( 3) link_BETA1-4 : angle 1.93363 ( 9) link_NAG-ASN : bond 0.00411 ( 45) link_NAG-ASN : angle 3.98140 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8151 (mtpt) REVERT: B 520 ILE cc_start: 0.8530 (mt) cc_final: 0.8300 (mm) REVERT: B 768 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8433 (mmtp) REVERT: C 56 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.7133 (pt0) REVERT: C 850 ASP cc_start: 0.8494 (m-30) cc_final: 0.8287 (m-30) REVERT: C 918 GLU cc_start: 0.8008 (tt0) cc_final: 0.7648 (mm-30) REVERT: C 1073 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7730 (mtt180) outliers start: 39 outliers final: 21 residues processed: 182 average time/residue: 0.5341 time to fit residues: 116.9960 Evaluate side-chains 173 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 967 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 298 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 733 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095042 restraints weight = 36280.823| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.57 r_work: 0.3020 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25533 Z= 0.147 Angle : 0.605 10.667 34833 Z= 0.303 Chirality : 0.045 0.333 4032 Planarity : 0.005 0.104 4404 Dihedral : 7.387 88.904 4434 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.91 % Allowed : 10.82 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.15), residues: 3036 helix: 1.31 (0.22), residues: 663 sheet: 0.72 (0.19), residues: 747 loop : -1.55 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 183 TYR 0.021 0.001 TYR A 352 PHE 0.018 0.001 PHE B 888 TRP 0.016 0.001 TRP B 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00350 (25446) covalent geometry : angle 0.55834 (34611) SS BOND : bond 0.00519 ( 39) SS BOND : angle 1.36312 ( 78) hydrogen bonds : bond 0.05704 ( 932) hydrogen bonds : angle 5.02447 ( 2661) link_BETA1-4 : bond 0.00706 ( 3) link_BETA1-4 : angle 1.51414 ( 9) link_NAG-ASN : bond 0.00410 ( 45) link_NAG-ASN : angle 3.65717 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8107 (pptt) REVERT: A 1047 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.9048 (t) REVERT: B 53 TYR cc_start: 0.8061 (t80) cc_final: 0.7806 (t80) REVERT: B 200 TYR cc_start: 0.6339 (t80) cc_final: 0.6134 (t80) REVERT: B 520 ILE cc_start: 0.8503 (mt) cc_final: 0.8269 (mm) REVERT: B 546 GLN cc_start: 0.7433 (tp-100) cc_final: 0.7202 (mm110) REVERT: B 768 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8485 (mmtp) REVERT: C 56 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: C 687 ILE cc_start: 0.8795 (pt) cc_final: 0.8539 (pt) REVERT: C 918 GLU cc_start: 0.8040 (tt0) cc_final: 0.7711 (mm-30) outliers start: 51 outliers final: 27 residues processed: 197 average time/residue: 0.5580 time to fit residues: 130.9012 Evaluate side-chains 179 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 98 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 277 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 883 GLN B 733 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.093495 restraints weight = 36160.182| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.62 r_work: 0.2946 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 25533 Z= 0.272 Angle : 0.712 12.031 34833 Z= 0.358 Chirality : 0.049 0.345 4032 Planarity : 0.005 0.100 4404 Dihedral : 7.387 89.506 4434 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.85 % Allowed : 12.73 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.15), residues: 3036 helix: 0.98 (0.21), residues: 693 sheet: 0.65 (0.19), residues: 744 loop : -1.66 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1021 TYR 0.027 0.002 TYR A 352 PHE 0.028 0.002 PHE B 888 TRP 0.022 0.002 TRP A 868 HIS 0.008 0.002 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00671 (25446) covalent geometry : angle 0.66126 (34611) SS BOND : bond 0.00850 ( 39) SS BOND : angle 1.85629 ( 78) hydrogen bonds : bond 0.07472 ( 932) hydrogen bonds : angle 5.20773 ( 2661) link_BETA1-4 : bond 0.00638 ( 3) link_BETA1-4 : angle 1.57865 ( 9) link_NAG-ASN : bond 0.00446 ( 45) link_NAG-ASN : angle 4.05680 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 164 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7899 (p) REVERT: A 264 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7191 (mt) REVERT: A 333 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8110 (pptt) REVERT: A 544 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7566 (ttt-90) REVERT: B 53 TYR cc_start: 0.8225 (t80) cc_final: 0.7888 (t80) REVERT: B 546 GLN cc_start: 0.7567 (tp-100) cc_final: 0.7267 (mm110) REVERT: B 762 GLU cc_start: 0.8709 (pp20) cc_final: 0.8482 (pp20) REVERT: B 768 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8588 (mmtp) REVERT: B 941 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8239 (mp) REVERT: C 56 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: C 151 MET cc_start: 0.3392 (OUTLIER) cc_final: 0.2370 (ptp) REVERT: C 762 GLU cc_start: 0.8613 (pp20) cc_final: 0.8413 (pp20) REVERT: C 850 ASP cc_start: 0.8604 (m-30) cc_final: 0.8399 (m-30) REVERT: C 918 GLU cc_start: 0.8061 (tt0) cc_final: 0.7597 (mm-30) outliers start: 76 outliers final: 42 residues processed: 224 average time/residue: 0.5007 time to fit residues: 136.2079 Evaluate side-chains 201 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 206 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 201 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 274 optimal weight: 0.9990 chunk 264 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 GLN B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.093909 restraints weight = 36225.549| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.57 r_work: 0.3009 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25533 Z= 0.141 Angle : 0.598 10.295 34833 Z= 0.299 Chirality : 0.045 0.319 4032 Planarity : 0.005 0.094 4404 Dihedral : 6.886 86.679 4434 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.70 % Allowed : 14.34 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.15), residues: 3036 helix: 1.49 (0.22), residues: 666 sheet: 0.73 (0.19), residues: 744 loop : -1.47 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 183 TYR 0.021 0.001 TYR C 352 PHE 0.012 0.001 PHE B1103 TRP 0.019 0.001 TRP B 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00335 (25446) covalent geometry : angle 0.55163 (34611) SS BOND : bond 0.00509 ( 39) SS BOND : angle 1.37897 ( 78) hydrogen bonds : bond 0.05624 ( 932) hydrogen bonds : angle 4.92257 ( 2661) link_BETA1-4 : bond 0.00716 ( 3) link_BETA1-4 : angle 1.39986 ( 9) link_NAG-ASN : bond 0.00385 ( 45) link_NAG-ASN : angle 3.60459 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 148 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7960 (p) REVERT: A 264 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7186 (mt) REVERT: A 333 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8314 (pttp) REVERT: A 544 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7588 (ttt-90) REVERT: B 53 TYR cc_start: 0.8154 (t80) cc_final: 0.7821 (t80) REVERT: B 546 GLN cc_start: 0.7545 (tp-100) cc_final: 0.7090 (mm110) REVERT: B 762 GLU cc_start: 0.8482 (pp20) cc_final: 0.8001 (tm-30) REVERT: C 151 MET cc_start: 0.3282 (OUTLIER) cc_final: 0.2353 (ptp) REVERT: C 918 GLU cc_start: 0.8077 (tt0) cc_final: 0.7633 (mm-30) outliers start: 72 outliers final: 40 residues processed: 205 average time/residue: 0.5217 time to fit residues: 129.0080 Evaluate side-chains 186 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 901 ASN Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 303 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 273 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093554 restraints weight = 36225.500| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.57 r_work: 0.3006 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25533 Z= 0.160 Angle : 0.612 10.151 34833 Z= 0.307 Chirality : 0.046 0.323 4032 Planarity : 0.005 0.091 4404 Dihedral : 6.793 89.428 4434 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.96 % Allowed : 14.61 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 3036 helix: 1.48 (0.22), residues: 675 sheet: 0.74 (0.19), residues: 744 loop : -1.47 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 99 TYR 0.022 0.001 TYR A 352 PHE 0.013 0.001 PHE A 83 TRP 0.021 0.001 TRP B 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00388 (25446) covalent geometry : angle 0.56627 (34611) SS BOND : bond 0.00631 ( 39) SS BOND : angle 1.74377 ( 78) hydrogen bonds : bond 0.05788 ( 932) hydrogen bonds : angle 4.88928 ( 2661) link_BETA1-4 : bond 0.00588 ( 3) link_BETA1-4 : angle 1.34135 ( 9) link_NAG-ASN : bond 0.00392 ( 45) link_NAG-ASN : angle 3.56496 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 143 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7160 (mt) REVERT: A 333 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8307 (pttp) REVERT: A 544 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7572 (ttt-90) REVERT: A 551 PHE cc_start: 0.6131 (OUTLIER) cc_final: 0.5114 (p90) REVERT: B 37 MET cc_start: 0.6914 (mtp) cc_final: 0.6668 (mtm) REVERT: B 53 TYR cc_start: 0.8119 (t80) cc_final: 0.7703 (t80) REVERT: B 132 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7236 (mm) REVERT: B 546 GLN cc_start: 0.7512 (tp-100) cc_final: 0.7080 (mm110) REVERT: B 762 GLU cc_start: 0.8418 (pp20) cc_final: 0.8066 (tm-30) REVERT: C 32 GLN cc_start: 0.7721 (mp-120) cc_final: 0.7494 (mp10) REVERT: C 151 MET cc_start: 0.3310 (OUTLIER) cc_final: 0.2370 (ptp) REVERT: C 918 GLU cc_start: 0.8089 (tt0) cc_final: 0.7761 (pt0) outliers start: 79 outliers final: 53 residues processed: 208 average time/residue: 0.4886 time to fit residues: 124.0505 Evaluate side-chains 202 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 901 ASN Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 275 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.093131 restraints weight = 36416.426| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.58 r_work: 0.3001 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25533 Z= 0.172 Angle : 0.622 10.125 34833 Z= 0.312 Chirality : 0.046 0.322 4032 Planarity : 0.005 0.090 4404 Dihedral : 6.691 83.746 4434 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.15 % Allowed : 14.87 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 3036 helix: 1.40 (0.21), residues: 690 sheet: 0.74 (0.19), residues: 744 loop : -1.48 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.022 0.001 TYR A 352 PHE 0.014 0.001 PHE A 83 TRP 0.018 0.001 TRP B 868 HIS 0.006 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00420 (25446) covalent geometry : angle 0.57589 (34611) SS BOND : bond 0.00657 ( 39) SS BOND : angle 1.83842 ( 78) hydrogen bonds : bond 0.05965 ( 932) hydrogen bonds : angle 4.89864 ( 2661) link_BETA1-4 : bond 0.00647 ( 3) link_BETA1-4 : angle 1.29454 ( 9) link_NAG-ASN : bond 0.00385 ( 45) link_NAG-ASN : angle 3.57800 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 150 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7680 (mp-120) cc_final: 0.7457 (mp10) REVERT: A 264 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7169 (mt) REVERT: A 333 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8351 (pttp) REVERT: A 544 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7560 (ttt-90) REVERT: A 551 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5184 (p90) REVERT: B 32 GLN cc_start: 0.7565 (mp-120) cc_final: 0.7221 (mp10) REVERT: B 37 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6717 (mtm) REVERT: B 53 TYR cc_start: 0.8169 (t80) cc_final: 0.7705 (t80) REVERT: B 132 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7250 (mm) REVERT: B 546 GLN cc_start: 0.7514 (tp-100) cc_final: 0.7020 (mm-40) REVERT: B 762 GLU cc_start: 0.8496 (pp20) cc_final: 0.8083 (tm-30) REVERT: C 151 MET cc_start: 0.3300 (OUTLIER) cc_final: 0.2271 (ptp) REVERT: C 850 ASP cc_start: 0.8502 (m-30) cc_final: 0.8302 (m-30) REVERT: C 918 GLU cc_start: 0.8109 (tt0) cc_final: 0.7773 (pt0) outliers start: 84 outliers final: 57 residues processed: 217 average time/residue: 0.4891 time to fit residues: 129.6674 Evaluate side-chains 207 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 143 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 901 ASN Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 293 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 275 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 296 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.096595 restraints weight = 36184.779| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.58 r_work: 0.3052 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25533 Z= 0.099 Angle : 0.551 9.640 34833 Z= 0.277 Chirality : 0.043 0.306 4032 Planarity : 0.004 0.090 4404 Dihedral : 6.305 74.892 4434 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.36 % Allowed : 15.92 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 3036 helix: 2.09 (0.22), residues: 642 sheet: 0.78 (0.19), residues: 750 loop : -1.37 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.019 0.001 TYR B1049 PHE 0.010 0.001 PHE B 909 TRP 0.023 0.001 TRP B 868 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00220 (25446) covalent geometry : angle 0.51002 (34611) SS BOND : bond 0.00457 ( 39) SS BOND : angle 1.37665 ( 78) hydrogen bonds : bond 0.04444 ( 932) hydrogen bonds : angle 4.65962 ( 2661) link_BETA1-4 : bond 0.00608 ( 3) link_BETA1-4 : angle 1.00117 ( 9) link_NAG-ASN : bond 0.00400 ( 45) link_NAG-ASN : angle 3.23921 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 149 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7668 (mp-120) cc_final: 0.7441 (mp10) REVERT: A 264 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7172 (mt) REVERT: A 333 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8354 (pttp) REVERT: A 544 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7580 (ttt-90) REVERT: A 551 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5140 (p90) REVERT: A 1047 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8986 (t) REVERT: B 32 GLN cc_start: 0.7611 (mp-120) cc_final: 0.7284 (mp10) REVERT: B 37 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6698 (mtm) REVERT: B 53 TYR cc_start: 0.8225 (t80) cc_final: 0.7752 (t80) REVERT: B 546 GLN cc_start: 0.7491 (tp-100) cc_final: 0.7070 (mm-40) REVERT: B 762 GLU cc_start: 0.8378 (pp20) cc_final: 0.8178 (tm-30) REVERT: C 32 GLN cc_start: 0.7633 (mp-120) cc_final: 0.7367 (mp10) REVERT: C 918 GLU cc_start: 0.8064 (tt0) cc_final: 0.7780 (pt0) outliers start: 63 outliers final: 36 residues processed: 200 average time/residue: 0.5018 time to fit residues: 121.5968 Evaluate side-chains 176 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1123 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 303 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 GLN B 733 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.132016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.094091 restraints weight = 36215.810| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.58 r_work: 0.3016 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25533 Z= 0.153 Angle : 0.593 9.766 34833 Z= 0.299 Chirality : 0.045 0.317 4032 Planarity : 0.005 0.091 4404 Dihedral : 6.346 67.021 4434 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.36 % Allowed : 16.22 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 3036 helix: 1.62 (0.21), residues: 690 sheet: 0.79 (0.20), residues: 747 loop : -1.40 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.021 0.001 TYR A 352 PHE 0.012 0.001 PHE A 83 TRP 0.022 0.001 TRP A 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00370 (25446) covalent geometry : angle 0.55120 (34611) SS BOND : bond 0.00595 ( 39) SS BOND : angle 1.64761 ( 78) hydrogen bonds : bond 0.05493 ( 932) hydrogen bonds : angle 4.76518 ( 2661) link_BETA1-4 : bond 0.00608 ( 3) link_BETA1-4 : angle 1.07739 ( 9) link_NAG-ASN : bond 0.00383 ( 45) link_NAG-ASN : angle 3.36747 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 143 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7163 (mt) REVERT: A 333 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8041 (tttt) REVERT: A 544 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7592 (ttt-90) REVERT: A 551 PHE cc_start: 0.6226 (OUTLIER) cc_final: 0.5150 (p90) REVERT: B 32 GLN cc_start: 0.7570 (mp-120) cc_final: 0.7277 (mp10) REVERT: B 37 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6661 (mtm) REVERT: B 53 TYR cc_start: 0.8262 (t80) cc_final: 0.7742 (t80) REVERT: B 132 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7233 (mm) REVERT: B 546 GLN cc_start: 0.7457 (tp-100) cc_final: 0.6996 (mm-40) REVERT: B 762 GLU cc_start: 0.8445 (pp20) cc_final: 0.8191 (tm-30) REVERT: C 151 MET cc_start: 0.3430 (OUTLIER) cc_final: 0.2390 (ptp) REVERT: C 918 GLU cc_start: 0.8105 (tt0) cc_final: 0.7754 (pt0) outliers start: 63 outliers final: 46 residues processed: 196 average time/residue: 0.4934 time to fit residues: 117.4681 Evaluate side-chains 193 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 140 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 901 ASN Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 251 optimal weight: 0.0770 chunk 246 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 266 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095412 restraints weight = 36271.130| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.58 r_work: 0.3036 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25533 Z= 0.119 Angle : 0.566 9.577 34833 Z= 0.285 Chirality : 0.044 0.310 4032 Planarity : 0.004 0.092 4404 Dihedral : 6.205 60.004 4434 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.99 % Allowed : 16.82 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 3036 helix: 1.79 (0.21), residues: 675 sheet: 0.84 (0.20), residues: 741 loop : -1.31 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.019 0.001 TYR C1049 PHE 0.011 0.001 PHE B1103 TRP 0.020 0.001 TRP A 868 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00278 (25446) covalent geometry : angle 0.52542 (34611) SS BOND : bond 0.00508 ( 39) SS BOND : angle 1.44834 ( 78) hydrogen bonds : bond 0.04901 ( 932) hydrogen bonds : angle 4.68349 ( 2661) link_BETA1-4 : bond 0.00606 ( 3) link_BETA1-4 : angle 1.03232 ( 9) link_NAG-ASN : bond 0.00384 ( 45) link_NAG-ASN : angle 3.26142 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7772 (mp-120) cc_final: 0.7524 (mp10) REVERT: A 264 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7165 (mt) REVERT: A 333 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8036 (tttt) REVERT: A 544 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7581 (ttt-90) REVERT: A 551 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.5193 (p90) REVERT: B 32 GLN cc_start: 0.7556 (mp-120) cc_final: 0.7268 (mp10) REVERT: B 37 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6670 (mtm) REVERT: B 53 TYR cc_start: 0.8249 (t80) cc_final: 0.7709 (t80) REVERT: B 546 GLN cc_start: 0.7465 (tp-100) cc_final: 0.6973 (mm-40) REVERT: B 762 GLU cc_start: 0.8391 (pp20) cc_final: 0.8186 (tm-30) REVERT: C 151 MET cc_start: 0.3406 (OUTLIER) cc_final: 0.2068 (ptp) REVERT: C 918 GLU cc_start: 0.8075 (tt0) cc_final: 0.7718 (pt0) outliers start: 53 outliers final: 43 residues processed: 186 average time/residue: 0.4938 time to fit residues: 111.8037 Evaluate side-chains 186 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 223 optimal weight: 4.9990 chunk 64 optimal weight: 0.0670 chunk 272 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 118 optimal weight: 0.0970 chunk 166 optimal weight: 3.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.132031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094208 restraints weight = 36168.252| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.57 r_work: 0.3020 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25533 Z= 0.147 Angle : 0.592 9.636 34833 Z= 0.297 Chirality : 0.045 0.315 4032 Planarity : 0.005 0.093 4404 Dihedral : 6.226 56.560 4434 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.25 % Allowed : 16.59 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.15), residues: 3036 helix: 1.67 (0.21), residues: 690 sheet: 0.83 (0.20), residues: 744 loop : -1.36 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.021 0.001 TYR A 352 PHE 0.012 0.001 PHE B 83 TRP 0.020 0.002 TRP A 868 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00355 (25446) covalent geometry : angle 0.55045 (34611) SS BOND : bond 0.00582 ( 39) SS BOND : angle 1.60009 ( 78) hydrogen bonds : bond 0.05440 ( 932) hydrogen bonds : angle 4.74691 ( 2661) link_BETA1-4 : bond 0.00601 ( 3) link_BETA1-4 : angle 1.08044 ( 9) link_NAG-ASN : bond 0.00381 ( 45) link_NAG-ASN : angle 3.33225 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7841.33 seconds wall clock time: 134 minutes 56.58 seconds (8096.58 seconds total)