Starting phenix.real_space_refine on Thu Mar 5 13:59:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m0j_23612/03_2026/7m0j_23612.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m0j_23612/03_2026/7m0j_23612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m0j_23612/03_2026/7m0j_23612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m0j_23612/03_2026/7m0j_23612.map" model { file = "/net/cci-nas-00/data/ceres_data/7m0j_23612/03_2026/7m0j_23612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m0j_23612/03_2026/7m0j_23612.cif" } resolution = 3.52 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= 0.003 sd= 0.060 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 99 5.16 5 C 14604 2.51 5 N 3783 2.21 5 O 4341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22827 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7609 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7609 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7609 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Time building chain proxies: 5.12, per 1000 atoms: 0.22 Number of scatterers: 22827 At special positions: 0 Unit cell: (137.54, 136.482, 172.454, 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 99 16.00 O 4341 8.00 N 3783 7.00 C 14604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.99 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.99 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 950.4 milliseconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 48 sheets defined 27.5% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.542A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.179A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.551A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.652A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.750A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.114A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 868 through 885 removed outlier: 3.600A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.618A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.667A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.621A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.697A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.533A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.950A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.952A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.935A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.620A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.583A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.812A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.578A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.546A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.507A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.370A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.721A pdb=" N VAL B1129 " --> pdb=" O CYS B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.802A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.157A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.508A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.755A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.848A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.262A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 3.997A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.739A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.561A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.507A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.941A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.698A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.522A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.950A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.038A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 3.625A pdb=" N VAL C1129 " --> pdb=" O CYS C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.941A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.375A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.501A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.405A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.505A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.307A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.528A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.690A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.847A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.861A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.524A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.150A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.325A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.828A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.551A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.256A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.607A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.531A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.662A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.688A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.724A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.427A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.541A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.453A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.265A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.339A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.470A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.802A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.590A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.590A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 999 hydrogen bonds defined for protein. 2676 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: 4.75 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4479 1.32 - 1.45: 5721 1.45 - 1.57: 13008 1.57 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 23331 Sorted by residual: bond pdb=" CA ALA B 520 " pdb=" C ALA B 520 " ideal model delta sigma weight residual 1.524 1.565 -0.041 1.26e-02 6.30e+03 1.08e+01 bond pdb=" CZ ARG C1000 " pdb=" NH2 ARG C1000 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.07e+01 bond pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 1.517 1.547 -0.030 9.30e-03 1.16e+04 1.03e+01 bond pdb=" CA LEU C 229 " pdb=" C LEU C 229 " ideal model delta sigma weight residual 1.522 1.549 -0.027 8.40e-03 1.42e+04 1.02e+01 bond pdb=" CZ ARG A1039 " pdb=" NH2 ARG A1039 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 ... (remaining 23326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 20968 1.74 - 3.48: 8733 3.48 - 5.21: 1805 5.21 - 6.95: 211 6.95 - 8.69: 20 Bond angle restraints: 31737 Sorted by residual: angle pdb=" CA ASP A 427 " pdb=" CB ASP A 427 " pdb=" CG ASP A 427 " ideal model delta sigma weight residual 112.60 120.04 -7.44 1.00e+00 1.00e+00 5.53e+01 angle pdb=" CA ASP B 427 " pdb=" CB ASP B 427 " pdb=" CG ASP B 427 " ideal model delta sigma weight residual 112.60 119.73 -7.13 1.00e+00 1.00e+00 5.08e+01 angle pdb=" CA PHE A 643 " pdb=" CB PHE A 643 " pdb=" CG PHE A 643 " ideal model delta sigma weight residual 113.80 120.20 -6.40 1.00e+00 1.00e+00 4.10e+01 angle pdb=" CA ASP A1084 " pdb=" CB ASP A1084 " pdb=" CG ASP A1084 " ideal model delta sigma weight residual 112.60 118.92 -6.32 1.00e+00 1.00e+00 4.00e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.17 -7.47 1.22e+00 6.72e-01 3.75e+01 ... (remaining 31732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12801 17.94 - 35.89: 858 35.89 - 53.83: 180 53.83 - 71.78: 51 71.78 - 89.72: 27 Dihedral angle restraints: 13917 sinusoidal: 5424 harmonic: 8493 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.72 89.72 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 171.05 -78.05 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 151.17 -58.17 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 13914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2184 0.084 - 0.167: 1197 0.167 - 0.251: 223 0.251 - 0.335: 28 0.335 - 0.418: 7 Chirality restraints: 3639 Sorted by residual: chirality pdb=" CA GLU A 773 " pdb=" N GLU A 773 " pdb=" C GLU A 773 " pdb=" CB GLU A 773 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA PRO A 986 " pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CB PRO A 986 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA ASP C 745 " pdb=" N ASP C 745 " pdb=" C ASP C 745 " pdb=" CB ASP C 745 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 3636 not shown) Planarity restraints: 4098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.142 2.00e-02 2.50e+03 8.15e-02 1.66e+02 pdb=" CG TRP C 886 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " 0.111 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.049 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.062 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " 0.119 2.00e-02 2.50e+03 7.25e-02 1.31e+02 pdb=" CG TRP B 886 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " -0.100 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.047 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.101 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 200 " -0.154 2.00e-02 2.50e+03 7.89e-02 1.24e+02 pdb=" CG TYR B 200 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR B 200 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR B 200 " 0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR B 200 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 200 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR B 200 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR B 200 " -0.091 2.00e-02 2.50e+03 ... (remaining 4095 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 11340 3.00 - 3.48: 22163 3.48 - 3.95: 37449 3.95 - 4.43: 41630 4.43 - 4.90: 70630 Nonbonded interactions: 183212 Sorted by model distance: nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.528 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.534 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.549 3.040 nonbonded pdb=" OD1 ASP A 294 " pdb=" OG SER A 297 " model vdw 2.570 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.572 3.040 ... (remaining 183207 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 21.010 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 0.013 0.046 23367 Z= 0.752 Angle : 1.870 8.691 31809 Z= 1.262 Chirality : 0.096 0.418 3639 Planarity : 0.014 0.199 4098 Dihedral : 13.971 88.979 8325 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.38 % Favored : 92.16 % Rotamer: Outliers : 1.68 % Allowed : 4.42 % Favored : 93.90 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 2844 helix: -1.92 (0.16), residues: 651 sheet: -0.15 (0.22), residues: 540 loop : -1.54 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 765 TYR 0.154 0.022 TYR B 200 PHE 0.105 0.013 PHE B 927 TRP 0.142 0.029 TRP C 886 HIS 0.018 0.004 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01256 (23331) covalent geometry : angle 1.86957 (31737) SS BOND : bond 0.01244 ( 36) SS BOND : angle 2.11352 ( 72) hydrogen bonds : bond 0.15955 ( 982) hydrogen bonds : angle 9.00479 ( 2676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 346 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7549 (t80) cc_final: 0.7276 (t80) REVERT: A 353 TRP cc_start: 0.8252 (p-90) cc_final: 0.7520 (p-90) REVERT: A 563 GLN cc_start: 0.4068 (tt0) cc_final: 0.3141 (mm-40) REVERT: A 725 GLU cc_start: 0.8034 (tt0) cc_final: 0.7788 (tt0) REVERT: B 101 ILE cc_start: 0.9077 (mp) cc_final: 0.8777 (tp) REVERT: B 396 TYR cc_start: 0.6943 (m-80) cc_final: 0.6353 (m-80) REVERT: B 737 ASP cc_start: 0.6350 (t0) cc_final: 0.6042 (t0) REVERT: B 976 VAL cc_start: 0.9297 (t) cc_final: 0.8999 (m) REVERT: C 220 PHE cc_start: 0.7989 (t80) cc_final: 0.7736 (t80) REVERT: C 275 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7744 (t80) REVERT: C 318 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8381 (p90) REVERT: C 582 LEU cc_start: 0.8670 (mt) cc_final: 0.8091 (pp) REVERT: C 948 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8970 (mt) outliers start: 43 outliers final: 9 residues processed: 380 average time/residue: 0.1673 time to fit residues: 96.2990 Evaluate side-chains 166 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 317 ASN A 603 ASN A 607 GLN A 804 GLN A 913 GLN C 87 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.115118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088739 restraints weight = 55235.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091179 restraints weight = 32343.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091194 restraints weight = 20089.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091543 restraints weight = 17665.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091687 restraints weight = 16249.052| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23367 Z= 0.155 Angle : 0.671 8.395 31809 Z= 0.367 Chirality : 0.047 0.209 3639 Planarity : 0.004 0.047 4098 Dihedral : 6.652 59.006 3119 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 1.52 % Allowed : 8.44 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.15), residues: 2844 helix: 0.16 (0.19), residues: 648 sheet: -0.11 (0.19), residues: 711 loop : -1.14 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 403 TYR 0.023 0.002 TYR A 396 PHE 0.023 0.002 PHE A 168 TRP 0.020 0.002 TRP A 104 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00347 (23331) covalent geometry : angle 0.66566 (31737) SS BOND : bond 0.00525 ( 36) SS BOND : angle 1.84653 ( 72) hydrogen bonds : bond 0.04461 ( 982) hydrogen bonds : angle 6.37936 ( 2676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7777 (t80) cc_final: 0.7462 (t80) REVERT: A 104 TRP cc_start: 0.6805 (m-90) cc_final: 0.6381 (m-90) REVERT: A 129 LYS cc_start: 0.8296 (mtmm) cc_final: 0.6457 (mtmm) REVERT: A 133 PHE cc_start: 0.6092 (m-80) cc_final: 0.5752 (m-10) REVERT: A 203 ILE cc_start: 0.8317 (mm) cc_final: 0.8103 (tp) REVERT: A 317 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7769 (p0) REVERT: A 353 TRP cc_start: 0.8145 (p-90) cc_final: 0.7489 (p-90) REVERT: A 563 GLN cc_start: 0.3558 (tt0) cc_final: 0.3113 (mm-40) REVERT: B 306 PHE cc_start: 0.8373 (m-80) cc_final: 0.8097 (m-80) REVERT: B 351 TYR cc_start: 0.8598 (p90) cc_final: 0.8123 (p90) REVERT: B 377 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.7146 (t80) REVERT: B 912 THR cc_start: 0.8038 (t) cc_final: 0.7813 (p) REVERT: B 976 VAL cc_start: 0.9101 (t) cc_final: 0.8767 (m) REVERT: B 1029 MET cc_start: 0.7955 (tpp) cc_final: 0.7712 (tpp) REVERT: C 275 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7815 (t80) REVERT: C 318 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8604 (p90) REVERT: C 619 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7572 (tp30) REVERT: C 784 GLN cc_start: 0.7927 (mt0) cc_final: 0.7502 (mt0) outliers start: 39 outliers final: 16 residues processed: 214 average time/residue: 0.1542 time to fit residues: 52.3038 Evaluate side-chains 153 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 883 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 213 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 762 GLN B 493 GLN B 901 GLN B1002 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.113632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089541 restraints weight = 55123.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088525 restraints weight = 34256.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089283 restraints weight = 30049.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089624 restraints weight = 23335.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089821 restraints weight = 21265.584| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23367 Z= 0.180 Angle : 0.608 10.074 31809 Z= 0.326 Chirality : 0.046 0.170 3639 Planarity : 0.004 0.042 4098 Dihedral : 5.794 53.459 3110 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 1.91 % Allowed : 10.00 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 2844 helix: 0.71 (0.20), residues: 654 sheet: -0.26 (0.18), residues: 732 loop : -0.93 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 214 TYR 0.033 0.002 TYR A 505 PHE 0.020 0.002 PHE A 168 TRP 0.018 0.002 TRP C 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00417 (23331) covalent geometry : angle 0.60655 (31737) SS BOND : bond 0.00369 ( 36) SS BOND : angle 1.16662 ( 72) hydrogen bonds : bond 0.04066 ( 982) hydrogen bonds : angle 5.88694 ( 2676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7494 (t60) cc_final: 0.7258 (t60) REVERT: A 104 TRP cc_start: 0.6972 (m-90) cc_final: 0.6516 (m-90) REVERT: A 129 LYS cc_start: 0.8328 (mtmm) cc_final: 0.7524 (mppt) REVERT: A 353 TRP cc_start: 0.8176 (p-90) cc_final: 0.7618 (p-90) REVERT: A 389 ASP cc_start: 0.7241 (t0) cc_final: 0.6656 (t0) REVERT: A 396 TYR cc_start: 0.8293 (m-80) cc_final: 0.7868 (m-80) REVERT: A 563 GLN cc_start: 0.4013 (tt0) cc_final: 0.3360 (mm-40) REVERT: B 306 PHE cc_start: 0.8538 (m-80) cc_final: 0.8277 (m-80) REVERT: B 351 TYR cc_start: 0.8556 (p90) cc_final: 0.8037 (p90) REVERT: B 912 THR cc_start: 0.8111 (t) cc_final: 0.7911 (p) REVERT: B 976 VAL cc_start: 0.9041 (t) cc_final: 0.8784 (m) REVERT: C 275 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7803 (t80) REVERT: C 619 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7367 (tp30) outliers start: 49 outliers final: 24 residues processed: 201 average time/residue: 0.1488 time to fit residues: 47.7240 Evaluate side-chains 153 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 267 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.0020 chunk 258 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 218 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A 764 ASN B 901 GLN C 115 GLN C 394 ASN C1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.114513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.090483 restraints weight = 54700.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.089471 restraints weight = 35193.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090191 restraints weight = 29812.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090521 restraints weight = 23678.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090707 restraints weight = 21481.937| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23367 Z= 0.137 Angle : 0.564 12.587 31809 Z= 0.299 Chirality : 0.044 0.156 3639 Planarity : 0.004 0.051 4098 Dihedral : 5.272 52.737 3107 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.60 % Allowed : 11.06 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 2844 helix: 0.92 (0.20), residues: 678 sheet: -0.10 (0.19), residues: 678 loop : -0.89 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 214 TYR 0.025 0.001 TYR B 495 PHE 0.021 0.001 PHE A 400 TRP 0.020 0.002 TRP C 436 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00315 (23331) covalent geometry : angle 0.55850 (31737) SS BOND : bond 0.00288 ( 36) SS BOND : angle 1.69769 ( 72) hydrogen bonds : bond 0.03700 ( 982) hydrogen bonds : angle 5.63958 ( 2676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7464 (t60) cc_final: 0.7259 (t60) REVERT: A 92 PHE cc_start: 0.7325 (t80) cc_final: 0.6971 (t80) REVERT: A 389 ASP cc_start: 0.7087 (t0) cc_final: 0.6534 (t0) REVERT: A 563 GLN cc_start: 0.3811 (tt0) cc_final: 0.3432 (mm-40) REVERT: A 568 ASP cc_start: 0.7481 (t0) cc_final: 0.7110 (m-30) REVERT: B 306 PHE cc_start: 0.8584 (m-80) cc_final: 0.8348 (m-80) REVERT: B 351 TYR cc_start: 0.8555 (p90) cc_final: 0.7942 (p90) REVERT: C 275 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7736 (t80) outliers start: 41 outliers final: 26 residues processed: 188 average time/residue: 0.1502 time to fit residues: 45.8875 Evaluate side-chains 151 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 237 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 241 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 901 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.113697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088628 restraints weight = 54741.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088581 restraints weight = 31292.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089271 restraints weight = 27382.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089622 restraints weight = 21849.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089817 restraints weight = 19300.249| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23367 Z= 0.158 Angle : 0.563 16.146 31809 Z= 0.297 Chirality : 0.044 0.165 3639 Planarity : 0.004 0.047 4098 Dihedral : 5.113 52.296 3107 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.11 % Allowed : 11.22 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 2844 helix: 1.11 (0.20), residues: 675 sheet: -0.14 (0.18), residues: 678 loop : -0.83 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 214 TYR 0.018 0.001 TYR B 200 PHE 0.016 0.001 PHE A 400 TRP 0.034 0.002 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00369 (23331) covalent geometry : angle 0.56055 (31737) SS BOND : bond 0.00305 ( 36) SS BOND : angle 1.27318 ( 72) hydrogen bonds : bond 0.03688 ( 982) hydrogen bonds : angle 5.55510 ( 2676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8489 (mtmm) cc_final: 0.7510 (mppt) REVERT: A 389 ASP cc_start: 0.7228 (t0) cc_final: 0.6671 (t0) REVERT: A 563 GLN cc_start: 0.3910 (tt0) cc_final: 0.3355 (mm-40) REVERT: A 740 MET cc_start: 0.8180 (mmm) cc_final: 0.7813 (mmm) REVERT: A 773 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: B 306 PHE cc_start: 0.8547 (m-80) cc_final: 0.8304 (m-80) REVERT: B 351 TYR cc_start: 0.8623 (p90) cc_final: 0.8065 (p90) REVERT: B 377 PHE cc_start: 0.7559 (t80) cc_final: 0.7347 (t80) REVERT: B 994 ASP cc_start: 0.7993 (t0) cc_final: 0.7633 (t70) REVERT: C 84 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7764 (mp) REVERT: C 275 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7755 (t80) REVERT: C 731 MET cc_start: 0.8873 (ptp) cc_final: 0.8646 (ptp) REVERT: C 1126 CYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7051 (m) outliers start: 54 outliers final: 31 residues processed: 175 average time/residue: 0.1429 time to fit residues: 41.0089 Evaluate side-chains 151 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 114 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.113036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089015 restraints weight = 55059.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087875 restraints weight = 34427.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088635 restraints weight = 30478.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088951 restraints weight = 23837.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089168 restraints weight = 21768.163| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23367 Z= 0.179 Angle : 0.567 12.858 31809 Z= 0.299 Chirality : 0.044 0.198 3639 Planarity : 0.004 0.065 4098 Dihedral : 5.060 52.112 3107 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.15 % Allowed : 11.45 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 2844 helix: 1.16 (0.21), residues: 675 sheet: -0.18 (0.18), residues: 705 loop : -0.78 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 214 TYR 0.018 0.001 TYR C 365 PHE 0.017 0.002 PHE B1089 TRP 0.036 0.002 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00420 (23331) covalent geometry : angle 0.56119 (31737) SS BOND : bond 0.00343 ( 36) SS BOND : angle 1.74759 ( 72) hydrogen bonds : bond 0.03701 ( 982) hydrogen bonds : angle 5.57130 ( 2676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8562 (mtmm) cc_final: 0.7561 (mppt) REVERT: A 347 PHE cc_start: 0.6184 (m-80) cc_final: 0.5810 (m-80) REVERT: A 389 ASP cc_start: 0.7231 (t0) cc_final: 0.6701 (t0) REVERT: A 563 GLN cc_start: 0.4154 (tt0) cc_final: 0.3404 (mm-40) REVERT: A 740 MET cc_start: 0.8200 (mmm) cc_final: 0.7835 (mmm) REVERT: A 773 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: A 873 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: B 326 ILE cc_start: 0.8646 (mm) cc_final: 0.8342 (mm) REVERT: B 351 TYR cc_start: 0.8604 (p90) cc_final: 0.7909 (p90) REVERT: B 377 PHE cc_start: 0.7653 (t80) cc_final: 0.7343 (t80) REVERT: B 994 ASP cc_start: 0.7986 (t0) cc_final: 0.7633 (t70) REVERT: C 731 MET cc_start: 0.8914 (ptp) cc_final: 0.8684 (ptp) REVERT: C 1126 CYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6832 (m) outliers start: 55 outliers final: 38 residues processed: 171 average time/residue: 0.1590 time to fit residues: 43.7198 Evaluate side-chains 152 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 205 optimal weight: 20.0000 chunk 99 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 229 optimal weight: 30.0000 chunk 166 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** 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 = 0.3801 r_free = 0.3801 target = 0.114044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089451 restraints weight = 54508.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089846 restraints weight = 31755.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.090089 restraints weight = 27906.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090513 restraints weight = 22578.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090684 restraints weight = 19545.298| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23367 Z= 0.133 Angle : 0.526 6.883 31809 Z= 0.281 Chirality : 0.043 0.207 3639 Planarity : 0.004 0.055 4098 Dihedral : 4.861 51.429 3107 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.76 % Allowed : 12.00 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 2844 helix: 1.30 (0.21), residues: 678 sheet: -0.19 (0.18), residues: 705 loop : -0.68 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.021 0.001 TYR B 495 PHE 0.029 0.001 PHE C 429 TRP 0.029 0.002 TRP A 353 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00306 (23331) covalent geometry : angle 0.52231 (31737) SS BOND : bond 0.00258 ( 36) SS BOND : angle 1.45466 ( 72) hydrogen bonds : bond 0.03506 ( 982) hydrogen bonds : angle 5.42295 ( 2676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7467 (t60) cc_final: 0.7266 (t60) REVERT: A 129 LYS cc_start: 0.8482 (mtmm) cc_final: 0.7510 (mppt) REVERT: A 347 PHE cc_start: 0.6100 (m-80) cc_final: 0.5803 (m-80) REVERT: A 389 ASP cc_start: 0.7174 (t0) cc_final: 0.6612 (t0) REVERT: A 563 GLN cc_start: 0.4110 (tt0) cc_final: 0.3626 (mm-40) REVERT: A 873 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: B 326 ILE cc_start: 0.8644 (mm) cc_final: 0.8261 (tt) REVERT: B 351 TYR cc_start: 0.8534 (p90) cc_final: 0.8216 (p90) REVERT: B 377 PHE cc_start: 0.7644 (t80) cc_final: 0.7312 (t80) REVERT: B 994 ASP cc_start: 0.7898 (t0) cc_final: 0.7573 (t70) REVERT: C 275 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7708 (t80) REVERT: C 1029 MET cc_start: 0.8378 (tpp) cc_final: 0.7944 (tpp) REVERT: C 1126 CYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6677 (m) outliers start: 45 outliers final: 34 residues processed: 166 average time/residue: 0.1437 time to fit residues: 38.9131 Evaluate side-chains 155 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 198 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 564 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090453 restraints weight = 54369.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090695 restraints weight = 32538.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.091055 restraints weight = 28866.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.091409 restraints weight = 22858.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.091601 restraints weight = 20192.146| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23367 Z= 0.117 Angle : 0.517 8.914 31809 Z= 0.274 Chirality : 0.043 0.194 3639 Planarity : 0.004 0.057 4098 Dihedral : 4.712 50.609 3107 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.80 % Allowed : 12.15 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 2844 helix: 1.49 (0.21), residues: 672 sheet: -0.30 (0.18), residues: 729 loop : -0.56 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.024 0.001 TYR B 495 PHE 0.021 0.001 PHE C 429 TRP 0.040 0.002 TRP A 353 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00266 (23331) covalent geometry : angle 0.51382 (31737) SS BOND : bond 0.00227 ( 36) SS BOND : angle 1.24123 ( 72) hydrogen bonds : bond 0.03435 ( 982) hydrogen bonds : angle 5.31306 ( 2676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7506 (t60) cc_final: 0.7288 (t60) REVERT: A 347 PHE cc_start: 0.6048 (m-80) cc_final: 0.5724 (m-80) REVERT: A 389 ASP cc_start: 0.7103 (t0) cc_final: 0.6566 (t0) REVERT: A 563 GLN cc_start: 0.4119 (tt0) cc_final: 0.3696 (mm-40) REVERT: A 873 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8653 (m-80) REVERT: B 326 ILE cc_start: 0.8639 (mm) cc_final: 0.8281 (tt) REVERT: B 351 TYR cc_start: 0.8530 (p90) cc_final: 0.8174 (p90) REVERT: B 377 PHE cc_start: 0.7627 (t80) cc_final: 0.7327 (t80) REVERT: B 994 ASP cc_start: 0.7847 (t0) cc_final: 0.7632 (t70) REVERT: C 1029 MET cc_start: 0.8320 (tpp) cc_final: 0.7882 (ttm) REVERT: C 1082 CYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4758 (t) REVERT: C 1126 CYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6494 (m) outliers start: 46 outliers final: 36 residues processed: 172 average time/residue: 0.1485 time to fit residues: 41.4725 Evaluate side-chains 159 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 129 optimal weight: 0.0070 chunk 226 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 285 optimal weight: 0.0170 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 955 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.114414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089899 restraints weight = 54908.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090088 restraints weight = 32694.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.090463 restraints weight = 28572.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090802 restraints weight = 23539.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090992 restraints weight = 20566.195| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23367 Z= 0.131 Angle : 0.524 7.000 31809 Z= 0.279 Chirality : 0.043 0.230 3639 Planarity : 0.004 0.051 4098 Dihedral : 4.600 45.834 3105 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 12.35 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2844 helix: 1.53 (0.21), residues: 672 sheet: -0.26 (0.18), residues: 723 loop : -0.55 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 577 TYR 0.016 0.001 TYR B1067 PHE 0.021 0.001 PHE C 429 TRP 0.033 0.002 TRP A 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00303 (23331) covalent geometry : angle 0.52087 (31737) SS BOND : bond 0.00254 ( 36) SS BOND : angle 1.30199 ( 72) hydrogen bonds : bond 0.03441 ( 982) hydrogen bonds : angle 5.30878 ( 2676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6006 (m-80) cc_final: 0.5661 (m-80) REVERT: A 389 ASP cc_start: 0.7114 (t0) cc_final: 0.6544 (t0) REVERT: A 563 GLN cc_start: 0.4155 (tt0) cc_final: 0.3634 (mm-40) REVERT: A 873 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: B 326 ILE cc_start: 0.8624 (mm) cc_final: 0.8272 (tt) REVERT: B 351 TYR cc_start: 0.8542 (p90) cc_final: 0.8167 (p90) REVERT: B 377 PHE cc_start: 0.7702 (t80) cc_final: 0.7377 (t80) REVERT: B 994 ASP cc_start: 0.7868 (t0) cc_final: 0.7660 (t70) REVERT: C 1029 MET cc_start: 0.8300 (tpp) cc_final: 0.7856 (ttm) REVERT: C 1082 CYS cc_start: 0.5107 (OUTLIER) cc_final: 0.4778 (t) REVERT: C 1126 CYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6500 (m) outliers start: 47 outliers final: 41 residues processed: 161 average time/residue: 0.1540 time to fit residues: 39.7159 Evaluate side-chains 163 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 210 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 285 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN B 115 GLN B1135 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.110405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086616 restraints weight = 55033.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084945 restraints weight = 37343.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085844 restraints weight = 32569.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086159 restraints weight = 25358.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086339 restraints weight = 23193.585| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 23367 Z= 0.332 Angle : 0.683 9.712 31809 Z= 0.360 Chirality : 0.048 0.297 3639 Planarity : 0.005 0.050 4098 Dihedral : 5.205 46.902 3105 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.72 % Allowed : 12.58 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 2844 helix: 0.87 (0.20), residues: 681 sheet: -0.42 (0.18), residues: 714 loop : -0.76 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 577 TYR 0.030 0.002 TYR A 505 PHE 0.034 0.002 PHE B1089 TRP 0.037 0.003 TRP C 436 HIS 0.007 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00778 (23331) covalent geometry : angle 0.67800 (31737) SS BOND : bond 0.00541 ( 36) SS BOND : angle 1.78024 ( 72) hydrogen bonds : bond 0.04261 ( 982) hydrogen bonds : angle 5.87493 ( 2676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7563 (mppt) REVERT: A 347 PHE cc_start: 0.6174 (m-80) cc_final: 0.5642 (m-80) REVERT: A 389 ASP cc_start: 0.7266 (t0) cc_final: 0.6795 (t0) REVERT: A 563 GLN cc_start: 0.4320 (tt0) cc_final: 0.3453 (mm-40) REVERT: A 740 MET cc_start: 0.8083 (mmm) cc_final: 0.7655 (mmm) REVERT: B 115 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7823 (tp-100) REVERT: B 326 ILE cc_start: 0.8691 (mm) cc_final: 0.8446 (mm) REVERT: B 351 TYR cc_start: 0.8587 (p90) cc_final: 0.8224 (p90) REVERT: B 994 ASP cc_start: 0.8079 (t0) cc_final: 0.7849 (t70) REVERT: C 577 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7763 (mmm-85) REVERT: C 1029 MET cc_start: 0.8674 (tpp) cc_final: 0.8082 (ttm) REVERT: C 1126 CYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6900 (m) outliers start: 44 outliers final: 36 residues processed: 154 average time/residue: 0.1620 time to fit residues: 40.1612 Evaluate side-chains 146 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 43 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** C 394 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 = 0.3762 r_free = 0.3762 target = 0.111583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087144 restraints weight = 54920.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086900 restraints weight = 33400.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087563 restraints weight = 30180.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087923 restraints weight = 22607.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088105 restraints weight = 20450.092| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 23367 Z= 0.208 Angle : 0.608 9.818 31809 Z= 0.322 Chirality : 0.045 0.271 3639 Planarity : 0.004 0.065 4098 Dihedral : 5.080 47.085 3105 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.68 % Allowed : 12.74 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 2844 helix: 0.98 (0.20), residues: 681 sheet: -0.44 (0.18), residues: 738 loop : -0.75 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 237 TYR 0.024 0.002 TYR C 365 PHE 0.025 0.002 PHE B 377 TRP 0.035 0.002 TRP C 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00486 (23331) covalent geometry : angle 0.60182 (31737) SS BOND : bond 0.00446 ( 36) SS BOND : angle 1.90633 ( 72) hydrogen bonds : bond 0.03919 ( 982) hydrogen bonds : angle 5.75678 ( 2676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.42 seconds wall clock time: 56 minutes 13.65 seconds (3373.65 seconds total)