Starting phenix.real_space_refine on Sun Aug 9 22:00:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yze_39691/08_2026/8yze_39691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yze_39691/08_2026/8yze_39691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yze_39691/08_2026/8yze_39691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yze_39691/08_2026/8yze_39691.map" model { file = "/net/cci-nas-00/data/ceres_data/8yze_39691/08_2026/8yze_39691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yze_39691/08_2026/8yze_39691.cif" } resolution = 3.06 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= -0.001 sd= 0.057 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 195 5.16 5 C 24966 2.51 5 N 6456 2.21 5 O 7377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38994 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8128 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 8128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8128 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8128 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "G" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "H" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "I" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 7.65, per 1000 atoms: 0.20 Number of scatterers: 38994 At special positions: 0 Unit cell: (170.17, 160.65, 267.75, 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 195 16.00 O 7377 8.00 N 6456 7.00 C 24966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 167 " distance=2.03 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.03 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Simple disulfide: pdb=" SG CYS I 133 " - pdb=" SG CYS I 141 " distance=2.03 Simple disulfide: pdb=" SG CYS I 344 " - pdb=" SG CYS I 361 " distance=2.03 Simple disulfide: pdb=" SG CYS I 530 " - pdb=" SG CYS I 542 " distance=2.03 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9222 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 54 sheets defined 42.1% alpha, 18.4% 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 removed outlier: 3.627A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.686A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.631A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.513A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.511A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.575A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) 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: 3.563A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 removed outlier: 4.213A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 removed outlier: 4.028A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1160 removed outlier: 3.620A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A1157 " --> pdb=" O ASP A1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.793A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.769A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.522A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.527A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.970A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 755 removed outlier: 4.263A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.680A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.574A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.504A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 4.089A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 removed outlier: 3.888A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1160 removed outlier: 3.674A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B1153 " --> pdb=" O LYS B1149 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B1154 " --> pdb=" O GLU B1150 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B1156 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B1160 " --> pdb=" O PHE B1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.609A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 369' Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.717A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.608A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.542A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 removed outlier: 4.365A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.776A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.577A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.560A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.982A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.910A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1158 removed outlier: 3.637A pdb=" N ASP C1153 " --> pdb=" O LYS C1149 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS C1154 " --> pdb=" O GLU C1150 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR C1155 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE C1156 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C1157 " --> pdb=" O ASP C1153 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.651A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 77 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.514A pdb=" N MET G 82 " --> pdb=" O LEU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 88 Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.615A pdb=" N SER G 106 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL G 107 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 146 through 152 Processing helix chain 'G' and resid 157 through 194 removed outlier: 3.667A pdb=" N ARG G 169 " --> pdb=" O TRP G 165 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLN G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) Proline residue: G 178 - end of helix Processing helix chain 'G' and resid 198 through 205 Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 218 through 252 Proline residue: G 235 - end of helix removed outlier: 4.038A pdb=" N ASN G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 280 removed outlier: 4.126A pdb=" N SER G 280 " --> pdb=" O ASN G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 300 Processing helix chain 'G' and resid 303 through 318 removed outlier: 3.722A pdb=" N VAL G 318 " --> pdb=" O PHE G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 331 Processing helix chain 'G' and resid 365 through 386 Processing helix chain 'G' and resid 387 through 388 No H-bonds generated for 'chain 'G' and resid 387 through 388' Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 398 through 414 removed outlier: 4.583A pdb=" N GLU G 402 " --> pdb=" O GLU G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 431 through 446 removed outlier: 3.543A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 466 Processing helix chain 'G' and resid 469 through 471 No H-bonds generated for 'chain 'G' and resid 469 through 471' Processing helix chain 'G' and resid 472 through 485 Processing helix chain 'G' and resid 499 through 502 Processing helix chain 'G' and resid 503 through 508 Processing helix chain 'G' and resid 512 through 533 removed outlier: 4.050A pdb=" N TYR G 516 " --> pdb=" O PHE G 512 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE G 523 " --> pdb=" O THR G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 559 removed outlier: 3.517A pdb=" N GLY G 551 " --> pdb=" O SER G 547 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 575 removed outlier: 3.710A pdb=" N VAL G 573 " --> pdb=" O ALA G 569 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 599 Proline residue: G 590 - end of helix Processing helix chain 'G' and resid 600 through 602 No H-bonds generated for 'chain 'G' and resid 600 through 602' Processing helix chain 'H' and resid 20 through 53 removed outlier: 4.046A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 77 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.584A pdb=" N SER H 106 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL H 107 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 108' Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 155 Processing helix chain 'H' and resid 157 through 194 removed outlier: 3.797A pdb=" N ARG H 169 " --> pdb=" O TRP H 165 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU H 176 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) Proline residue: H 178 - end of helix Processing helix chain 'H' and resid 198 through 205 Processing helix chain 'H' and resid 218 through 252 Proline residue: H 235 - end of helix removed outlier: 3.962A pdb=" N ASN H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 280 removed outlier: 4.216A pdb=" N SER H 280 " --> pdb=" O ASN H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 300 Processing helix chain 'H' and resid 303 through 318 Processing helix chain 'H' and resid 324 through 331 removed outlier: 3.528A pdb=" N TRP H 328 " --> pdb=" O THR H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 386 Processing helix chain 'H' and resid 387 through 388 No H-bonds generated for 'chain 'H' and resid 387 through 388' Processing helix chain 'H' and resid 389 through 393 Processing helix chain 'H' and resid 398 through 414 removed outlier: 4.563A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 431 through 447 Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 469 through 471 No H-bonds generated for 'chain 'H' and resid 469 through 471' Processing helix chain 'H' and resid 472 through 485 Processing helix chain 'H' and resid 498 through 502 Processing helix chain 'H' and resid 503 through 508 Processing helix chain 'H' and resid 512 through 533 removed outlier: 3.735A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE H 523 " --> pdb=" O THR H 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.585A pdb=" N GLY H 551 " --> pdb=" O SER H 547 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 575 removed outlier: 3.708A pdb=" N VAL H 573 " --> pdb=" O ALA H 569 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 599 Proline residue: H 590 - end of helix Processing helix chain 'H' and resid 600 through 602 No H-bonds generated for 'chain 'H' and resid 600 through 602' Processing helix chain 'I' and resid 20 through 53 removed outlier: 4.075A pdb=" N HIS I 34 " --> pdb=" O ASP I 30 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 77 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 90 through 101 Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.907A pdb=" N VAL I 107 " --> pdb=" O GLY I 104 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU I 108 " --> pdb=" O SER I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 129 Processing helix chain 'I' and resid 147 through 155 Processing helix chain 'I' and resid 157 through 194 removed outlier: 3.738A pdb=" N ARG I 169 " --> pdb=" O TRP I 165 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS I 174 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU I 176 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG I 177 " --> pdb=" O GLY I 173 " (cutoff:3.500A) Proline residue: I 178 - end of helix Processing helix chain 'I' and resid 198 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 218 through 252 Proline residue: I 235 - end of helix removed outlier: 3.901A pdb=" N ASN I 250 " --> pdb=" O ALA I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 280 removed outlier: 4.125A pdb=" N SER I 280 " --> pdb=" O ASN I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 300 Processing helix chain 'I' and resid 303 through 318 Processing helix chain 'I' and resid 324 through 331 removed outlier: 3.545A pdb=" N TRP I 328 " --> pdb=" O THR I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 386 removed outlier: 3.531A pdb=" N HIS I 373 " --> pdb=" O PHE I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 388 No H-bonds generated for 'chain 'I' and resid 387 through 388' Processing helix chain 'I' and resid 389 through 393 Processing helix chain 'I' and resid 399 through 414 removed outlier: 3.614A pdb=" N MET I 408 " --> pdb=" O VAL I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 421 Processing helix chain 'I' and resid 431 through 447 Processing helix chain 'I' and resid 448 through 466 removed outlier: 4.452A pdb=" N PHE I 452 " --> pdb=" O GLY I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 471 No H-bonds generated for 'chain 'I' and resid 469 through 471' Processing helix chain 'I' and resid 472 through 485 Processing helix chain 'I' and resid 498 through 502 Processing helix chain 'I' and resid 503 through 508 Processing helix chain 'I' and resid 512 through 533 removed outlier: 3.747A pdb=" N TYR I 516 " --> pdb=" O PHE I 512 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE I 523 " --> pdb=" O THR I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 559 removed outlier: 3.665A pdb=" N GLY I 551 " --> pdb=" O SER I 547 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET I 557 " --> pdb=" O LYS I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 565 through 575 removed outlier: 3.692A pdb=" N VAL I 573 " --> pdb=" O ALA I 569 " (cutoff:3.500A) Processing helix chain 'I' and resid 581 through 599 Proline residue: I 590 - end of helix Processing helix chain 'I' and resid 600 through 602 No H-bonds generated for 'chain 'I' and resid 600 through 602' Processing helix chain 'I' and resid 611 through 615 removed outlier: 4.279A pdb=" N ASP I 615 " --> pdb=" O PRO I 612 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.207A pdb=" N PHE A 47 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 7.942A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68 removed outlier: 3.775A pdb=" N ALA A 95 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 192 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 207 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 204 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 227 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER A 206 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.640A pdb=" N GLY A 109 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 169 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.031A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.372A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 565 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.217A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.358A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.836A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.836A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.574A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.679A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.361A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 59 removed outlier: 7.922A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.640A pdb=" N TYR B 265 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 95 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 92 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 192 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 207 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B 227 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER B 206 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.703A pdb=" N GLY B 109 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B 169 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.031A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.358A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE B 565 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.123A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.171A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.271A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.815A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.815A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.577A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.483A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.777A pdb=" N VAL C 51 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 67 through 68 removed outlier: 3.768A pdb=" N ALA C 95 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 192 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS C 207 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL C 227 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N SER C 206 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.731A pdb=" N GLY C 109 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE C 169 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.075A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.129A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.935A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.342A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.826A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.826A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.611A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.497A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 131 through 134 removed outlier: 5.655A pdb=" N GLU G 140 " --> pdb=" O ASN G 134 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 262 through 263 removed outlier: 5.770A pdb=" N LEU G 262 " --> pdb=" O VAL G 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'G' and resid 347 through 352 removed outlier: 6.052A pdb=" N ASP G 355 " --> pdb=" O LEU G 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 131 through 134 removed outlier: 5.695A pdb=" N GLU H 140 " --> pdb=" O ASN H 134 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 262 through 263 removed outlier: 5.794A pdb=" N LEU H 262 " --> pdb=" O VAL H 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 347 through 352 removed outlier: 3.536A pdb=" N LEU H 359 " --> pdb=" O THR H 347 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP H 355 " --> pdb=" O LEU H 351 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 131 through 134 removed outlier: 5.752A pdb=" N GLU I 140 " --> pdb=" O ASN I 134 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 262 through 263 removed outlier: 5.843A pdb=" N LEU I 262 " --> pdb=" O VAL I 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'I' and resid 347 through 352 removed outlier: 5.951A pdb=" N ASP I 355 " --> pdb=" O LEU I 351 " (cutoff:3.500A) 1766 hydrogen bonds defined for protein. 4965 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: 8.50 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7327 1.33 - 1.45: 10528 1.45 - 1.57: 21856 1.57 - 1.69: 0 1.69 - 1.81: 282 Bond restraints: 39993 Sorted by residual: bond pdb=" C ILE C 896 " pdb=" N PRO C 897 " ideal model delta sigma weight residual 1.331 1.380 -0.049 1.31e-02 5.83e+03 1.42e+01 bond pdb=" C ILE A 896 " pdb=" N PRO A 897 " ideal model delta sigma weight residual 1.331 1.380 -0.049 1.31e-02 5.83e+03 1.42e+01 bond pdb=" C CYS A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.333 1.376 -0.043 1.17e-02 7.31e+03 1.35e+01 bond pdb=" N ASP A 985 " pdb=" CA ASP A 985 " ideal model delta sigma weight residual 1.462 1.434 0.028 8.50e-03 1.38e+04 1.05e+01 bond pdb=" N THR B 333 " pdb=" CA THR B 333 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.25e-02 6.40e+03 1.01e+01 ... (remaining 39988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 53966 2.68 - 5.37: 380 5.37 - 8.05: 28 8.05 - 10.73: 10 10.73 - 13.42: 6 Bond angle restraints: 54390 Sorted by residual: angle pdb=" N THR B 333 " pdb=" CA THR B 333 " pdb=" C THR B 333 " ideal model delta sigma weight residual 110.36 123.78 -13.42 1.55e+00 4.16e-01 7.49e+01 angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.11 122.76 -11.65 1.59e+00 3.96e-01 5.36e+01 angle pdb=" N LEU A 335 " pdb=" CA LEU A 335 " pdb=" C LEU A 335 " ideal model delta sigma weight residual 110.41 118.18 -7.77 1.23e+00 6.61e-01 3.99e+01 angle pdb=" C ILE A 896 " pdb=" N PRO A 897 " pdb=" CA PRO A 897 " ideal model delta sigma weight residual 119.85 113.66 6.19 1.01e+00 9.80e-01 3.75e+01 angle pdb=" C THR C 531 " pdb=" CA THR C 531 " pdb=" CB THR C 531 " ideal model delta sigma weight residual 116.53 107.76 8.77 1.47e+00 4.63e-01 3.56e+01 ... (remaining 54385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 22938 17.39 - 34.77: 645 34.77 - 52.16: 118 52.16 - 69.55: 27 69.55 - 86.94: 5 Dihedral angle restraints: 23733 sinusoidal: 9417 harmonic: 14316 Sorted by residual: dihedral pdb=" N SER C 530 " pdb=" C SER C 530 " pdb=" CA SER C 530 " pdb=" CB SER C 530 " ideal model delta harmonic sigma weight residual 122.80 132.83 -10.03 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" N LYS A 529 " pdb=" C LYS A 529 " pdb=" CA LYS A 529 " pdb=" CB LYS A 529 " ideal model delta harmonic sigma weight residual 122.80 132.60 -9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C LEU B 984 " pdb=" N LEU B 984 " pdb=" CA LEU B 984 " pdb=" CB LEU B 984 " ideal model delta harmonic sigma weight residual -122.60 -132.22 9.62 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 23730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 5765 0.102 - 0.205: 188 0.205 - 0.307: 15 0.307 - 0.409: 4 0.409 - 0.511: 4 Chirality restraints: 5976 Sorted by residual: chirality pdb=" CG LEU B 984 " pdb=" CB LEU B 984 " pdb=" CD1 LEU B 984 " pdb=" CD2 LEU B 984 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA LEU B 984 " pdb=" N LEU B 984 " pdb=" C LEU B 984 " pdb=" CB LEU B 984 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CG LEU A 984 " pdb=" CB LEU A 984 " pdb=" CD1 LEU A 984 " pdb=" CD2 LEU A 984 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.46 2.00e-01 2.50e+01 5.40e+00 ... (remaining 5973 not shown) Planarity restraints: 7026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 329 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C PHE C 329 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE C 329 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO C 330 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 224 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 225 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO A 330 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.032 5.00e-02 4.00e+02 ... (remaining 7023 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3646 2.74 - 3.28: 37255 3.28 - 3.82: 63069 3.82 - 4.36: 72841 4.36 - 4.90: 129188 Nonbonded interactions: 305999 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR B 500 " pdb=" OH TYR H 41 " model vdw 2.253 3.040 nonbonded pdb=" O VAL A 608 " pdb=" OH TYR A 636 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR C 500 " pdb=" OH TYR I 41 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR G 41 " model vdw 2.267 3.040 ... (remaining 305994 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.430 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 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 : 0.003 0.049 40035 Z= 0.179 Angle : 0.595 13.417 54474 Z= 0.368 Chirality : 0.044 0.511 5976 Planarity : 0.004 0.064 7026 Dihedral : 8.314 86.937 14385 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.19 % Favored : 97.66 % Rotamer: Outliers : 2.43 % Allowed : 3.84 % Favored : 93.73 % 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 (0.11), residues: 4839 helix: 0.44 (0.12), residues: 1776 sheet: 0.25 (0.19), residues: 576 loop : -1.59 (0.11), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1019 TYR 0.019 0.001 TYR G 385 PHE 0.021 0.001 PHE C 371 TRP 0.007 0.001 TRP A 633 HIS 0.002 0.000 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.18 (39993) covalent geometry : angle 0.59500 / 0.37 (54390) SS BOND : bond 0.00124 / 0.09 ( 42) SS BOND : angle 0.66061 / 0.45 ( 84) hydrogen bonds : bond 0.17621 / 11.55 ( 1751) hydrogen bonds : angle 6.38856 / 4.42 ( 4965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 511 time to evaluate : 1.047 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 TYR cc_start: 0.6631 (t80) cc_final: 0.6351 (t80) REVERT: B 365 TYR cc_start: 0.8889 (m-80) cc_final: 0.8434 (m-10) REVERT: B 629 LEU cc_start: 0.7374 (tp) cc_final: 0.6970 (tp) REVERT: G 249 MET cc_start: 0.2776 (mtp) cc_final: 0.2237 (ttm) REVERT: G 548 THR cc_start: 0.5710 (p) cc_final: 0.5470 (t) REVERT: H 62 MET cc_start: 0.8258 (ttp) cc_final: 0.7661 (tpt) REVERT: H 359 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7084 (mt) REVERT: I 81 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7003 (pp30) REVERT: I 82 MET cc_start: 0.3082 (mtp) cc_final: 0.2256 (tmm) REVERT: I 174 LYS cc_start: 0.4927 (mtpp) cc_final: 0.4671 (tmtt) REVERT: I 383 MET cc_start: 0.5680 (mtp) cc_final: 0.4196 (ptm) outliers start: 105 outliers final: 19 residues processed: 597 average time/residue: 0.2267 time to fit residues: 219.9902 Evaluate side-chains 276 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain H residue 365 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 470 optimal weight: 50.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN A 197 ASN A 321 GLN A 493 GLN A 628 GLN A 677 GLN A 787 GLN A 804 GLN A 872 GLN A 901 GLN A 935 GLN A 957 GLN A1002 GLN A1071 GLN A1125 ASN B 65 ASN B 174 GLN B 197 ASN B 321 GLN B 360 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 677 GLN B 804 GLN B 872 GLN B 901 GLN B 914 ASN B 955 ASN B 965 GLN B1010 GLN B1011 GLN B1071 GLN B1125 ASN B1142 GLN C 174 GLN C 321 GLN C 394 ASN C 493 GLN C 580 GLN C 628 GLN C 677 GLN C 804 GLN C 872 GLN C 901 GLN C 913 GLN C 914 ASN C 935 GLN C 955 ASN C 965 GLN C1002 GLN C1010 GLN C1011 GLN C1071 GLN C1125 ASN C1142 GLN G 60 GLN G 210 ASN G 378 HIS G 417 HIS H 60 GLN H 64 ASN H 98 GLN H 210 ASN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 508 ASN ** H 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 578 ASN I 340 GLN I 378 HIS I 508 ASN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 578 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.156226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.103641 restraints weight = 156169.928| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 5.29 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 40035 Z= 0.216 Angle : 0.640 11.940 54474 Z= 0.328 Chirality : 0.045 0.181 5976 Planarity : 0.005 0.068 7026 Dihedral : 4.238 50.830 5274 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 2.15 % Allowed : 7.52 % Favored : 90.32 % 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: 0.03 (0.12), residues: 4839 helix: 1.33 (0.12), residues: 1815 sheet: 0.27 (0.18), residues: 735 loop : -1.15 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 983 TYR 0.023 0.002 TYR I 385 PHE 0.025 0.002 PHE I 285 TRP 0.028 0.002 TRP G 473 HIS 0.010 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (39993) covalent geometry : angle 0.63781 / 0.33 (54390) SS BOND : bond 0.00910 / 0.58 ( 42) SS BOND : angle 1.42123 / 0.95 ( 84) hydrogen bonds : bond 0.05214 / 3.33 ( 1751) hydrogen bonds : angle 4.81671 / 3.33 ( 4965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 252 time to evaluate : 1.212 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 TYR cc_start: 0.8374 (t80) cc_final: 0.8170 (t80) REVERT: B 90 ASP cc_start: 0.9454 (m-30) cc_final: 0.9140 (t0) REVERT: B 375 PHE cc_start: 0.6679 (m-80) cc_final: 0.6451 (m-80) REVERT: B 453 TYR cc_start: 0.8105 (p90) cc_final: 0.7485 (p90) REVERT: C 90 ASP cc_start: 0.9029 (t0) cc_final: 0.8636 (t0) REVERT: C 171 TYR cc_start: 0.6934 (m-80) cc_final: 0.6347 (t80) REVERT: G 192 ARG cc_start: 0.7377 (ptp-110) cc_final: 0.7130 (tpm170) REVERT: G 249 MET cc_start: 0.1838 (mtp) cc_final: 0.1472 (ttm) REVERT: G 270 MET cc_start: 0.1044 (mpp) cc_final: 0.0814 (mpp) REVERT: G 323 MET cc_start: 0.1652 (mmt) cc_final: 0.0836 (mmt) REVERT: G 332 MET cc_start: -0.0428 (ppp) cc_final: -0.0836 (ppp) REVERT: G 359 LEU cc_start: -0.2954 (OUTLIER) cc_final: -0.3546 (tt) REVERT: G 455 MET cc_start: 0.0942 (tmm) cc_final: 0.0509 (tmm) REVERT: G 579 MET cc_start: 0.0173 (mtt) cc_final: -0.1644 (ptp) REVERT: H 270 MET cc_start: 0.8200 (mmm) cc_final: 0.7809 (mmm) REVERT: H 505 HIS cc_start: 0.9089 (m-70) cc_final: 0.8834 (m-70) REVERT: H 512 PHE cc_start: 0.8675 (m-80) cc_final: 0.8357 (m-80) REVERT: I 78 THR cc_start: 0.7105 (OUTLIER) cc_final: 0.6832 (p) REVERT: I 82 MET cc_start: 0.3009 (mtp) cc_final: 0.2350 (tmm) REVERT: I 297 MET cc_start: -0.0546 (OUTLIER) cc_final: -0.1068 (mtt) REVERT: I 323 MET cc_start: -0.1883 (mmt) cc_final: -0.3158 (mmm) REVERT: I 360 MET cc_start: 0.5919 (tpt) cc_final: 0.5333 (ptm) REVERT: I 383 MET cc_start: 0.6291 (mtp) cc_final: 0.5434 (ptm) outliers start: 93 outliers final: 49 residues processed: 333 average time/residue: 0.2253 time to fit residues: 125.1780 Evaluate side-chains 255 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 573 VAL Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain I residue 297 MET Chi-restraints excluded: chain I residue 505 HIS Chi-restraints excluded: chain I residue 548 THR Chi-restraints excluded: chain I residue 574 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 140 optimal weight: 0.3980 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 318 optimal weight: 50.0000 chunk 143 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.1894 > 50:) chunk 184 optimal weight: 8.9990 chunk 346 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN A 613 GLN B 414 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 935 GLN C 65 ASN C 343 ASN C 613 GLN G 340 GLN H 98 GLN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.153566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100332 restraints weight = 146043.362| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 6.19 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 40035 Z= 0.179 Angle : 0.562 11.885 54474 Z= 0.287 Chirality : 0.043 0.199 5976 Planarity : 0.004 0.057 7026 Dihedral : 4.032 42.240 5267 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 2.01 % Allowed : 8.33 % Favored : 89.65 % 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: 0.38 (0.12), residues: 4839 helix: 1.71 (0.12), residues: 1791 sheet: 0.34 (0.19), residues: 735 loop : -0.96 (0.13), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.023 0.001 TYR G 385 PHE 0.026 0.002 PHE H 504 TRP 0.020 0.001 TRP C 452 HIS 0.010 0.001 HIS H 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (39993) covalent geometry : angle 0.55992 / 0.29 (54390) SS BOND : bond 0.00217 / 0.12 ( 42) SS BOND : angle 1.43804 / 0.85 ( 84) hydrogen bonds : bond 0.04970 / 3.19 ( 1751) hydrogen bonds : angle 4.68531 / 3.21 ( 4965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 213 time to evaluate : 1.500 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: 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: symmetry clash revert: symmetry clash REVERT: A 636 TYR cc_start: 0.8296 (t80) cc_final: 0.8074 (t80) REVERT: A 1141 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8499 (tm) REVERT: B 329 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: B 365 TYR cc_start: 0.8914 (m-10) cc_final: 0.8697 (m-10) REVERT: B 374 PHE cc_start: 0.8747 (m-80) cc_final: 0.8298 (t80) REVERT: B 434 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8496 (tp) REVERT: B 453 TYR cc_start: 0.8248 (p90) cc_final: 0.7381 (p90) REVERT: B 869 MET cc_start: 0.9051 (mtt) cc_final: 0.8739 (mtt) REVERT: C 90 ASP cc_start: 0.8822 (t0) cc_final: 0.8287 (t0) REVERT: C 171 TYR cc_start: 0.6880 (m-80) cc_final: 0.6248 (t80) REVERT: C 201 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8445 (t80) REVERT: C 237 ARG cc_start: 0.8279 (mtp85) cc_final: 0.7765 (mtm-85) REVERT: C 375 PHE cc_start: 0.6480 (m-10) cc_final: 0.6229 (m-10) REVERT: G 74 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7795 (pptt) REVERT: G 83 TYR cc_start: 0.4960 (m-80) cc_final: 0.4339 (m-80) REVERT: G 249 MET cc_start: 0.1914 (mtp) cc_final: 0.1474 (ttm) REVERT: G 323 MET cc_start: 0.1275 (mmt) cc_final: 0.0404 (mmt) REVERT: G 332 MET cc_start: -0.0018 (ppp) cc_final: -0.0318 (ppp) REVERT: G 359 LEU cc_start: -0.2675 (OUTLIER) cc_final: -0.2883 (tt) REVERT: G 455 MET cc_start: 0.1385 (tmm) cc_final: 0.0979 (tmm) REVERT: H 249 MET cc_start: 0.3482 (mmm) cc_final: 0.3118 (mmm) REVERT: H 270 MET cc_start: 0.8076 (mmm) cc_final: 0.7758 (mmm) REVERT: H 512 PHE cc_start: 0.8650 (m-80) cc_final: 0.8047 (m-80) REVERT: H 518 ARG cc_start: 0.8671 (ptp-170) cc_final: 0.8437 (ptp-110) REVERT: I 78 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.6881 (p) REVERT: I 82 MET cc_start: 0.3431 (mtp) cc_final: 0.2639 (tmm) REVERT: I 155 SER cc_start: 0.2926 (OUTLIER) cc_final: 0.2385 (m) REVERT: I 156 LEU cc_start: 0.4720 (OUTLIER) cc_final: 0.4462 (mm) REVERT: I 323 MET cc_start: -0.2079 (mmt) cc_final: -0.2476 (tpp) REVERT: I 360 MET cc_start: 0.6336 (tpt) cc_final: 0.5795 (ptm) REVERT: I 455 MET cc_start: 0.3333 (ppp) cc_final: 0.1853 (ptt) REVERT: I 480 MET cc_start: -0.0830 (ptt) cc_final: -0.1051 (ptt) outliers start: 87 outliers final: 51 residues processed: 293 average time/residue: 0.2434 time to fit residues: 119.0714 Evaluate side-chains 256 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 573 VAL Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 398 GLU Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 505 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 142 optimal weight: 8.9990 chunk 397 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 317 optimal weight: 0.9980 chunk 232 optimal weight: 50.0000 chunk 229 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 330 optimal weight: 30.0000 chunk 37 optimal weight: 30.0000 chunk 422 optimal weight: 0.6980 chunk 337 optimal weight: 50.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN G 540 HIS H 64 ASN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 524 GLN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.151535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097604 restraints weight = 146714.598| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 5.95 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 40035 Z= 0.179 Angle : 0.555 9.674 54474 Z= 0.283 Chirality : 0.042 0.179 5976 Planarity : 0.004 0.055 7026 Dihedral : 4.063 43.404 5262 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.80 % Rotamer: Outliers : 2.22 % Allowed : 8.73 % Favored : 89.05 % 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: 0.52 (0.12), residues: 4839 helix: 1.80 (0.12), residues: 1815 sheet: 0.40 (0.19), residues: 732 loop : -0.88 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 983 TYR 0.019 0.001 TYR G 385 PHE 0.019 0.001 PHE B 464 TRP 0.027 0.001 TRP G 461 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (39993) covalent geometry : angle 0.55280 / 0.28 (54390) SS BOND : bond 0.00319 / 0.18 ( 42) SS BOND : angle 1.25093 / 0.83 ( 84) hydrogen bonds : bond 0.04889 / 3.16 ( 1751) hydrogen bonds : angle 4.58648 / 3.14 ( 4965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 203 time to evaluate : 1.257 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: 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 816 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.7956 (p) REVERT: A 1141 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8553 (tm) REVERT: B 329 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: B 417 ASN cc_start: 0.8658 (t0) cc_final: 0.8431 (t0) REVERT: C 169 PHE cc_start: 0.7501 (m-80) cc_final: 0.7202 (m-80) REVERT: C 171 TYR cc_start: 0.7192 (m-80) cc_final: 0.6493 (t80) REVERT: C 201 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.8570 (t80) REVERT: C 237 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7925 (mtm-85) REVERT: G 74 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7852 (pptt) REVERT: G 249 MET cc_start: 0.1821 (mtp) cc_final: 0.1437 (ttm) REVERT: G 323 MET cc_start: 0.1519 (mmt) cc_final: 0.0809 (mmt) REVERT: G 332 MET cc_start: 0.0368 (ppp) cc_final: -0.0028 (ppp) REVERT: G 480 MET cc_start: 0.4330 (ttp) cc_final: 0.3109 (mmt) REVERT: G 579 MET cc_start: -0.0093 (mtt) cc_final: -0.0766 (mmm) REVERT: H 69 TRP cc_start: 0.9000 (t-100) cc_final: 0.8711 (t60) REVERT: H 249 MET cc_start: 0.4144 (mmm) cc_final: 0.3793 (mmm) REVERT: H 373 HIS cc_start: 0.9351 (OUTLIER) cc_final: 0.8948 (m-70) REVERT: H 376 MET cc_start: 0.6735 (ttm) cc_final: 0.6507 (ttm) REVERT: H 512 PHE cc_start: 0.8672 (m-80) cc_final: 0.7997 (m-80) REVERT: I 62 MET cc_start: 0.2515 (mmm) cc_final: 0.2028 (tmm) REVERT: I 78 THR cc_start: 0.7137 (OUTLIER) cc_final: 0.6861 (p) REVERT: I 82 MET cc_start: 0.3383 (mtp) cc_final: 0.2658 (tmm) REVERT: I 155 SER cc_start: 0.3042 (OUTLIER) cc_final: 0.2705 (m) REVERT: I 156 LEU cc_start: 0.4870 (OUTLIER) cc_final: 0.4628 (mm) REVERT: I 323 MET cc_start: -0.2442 (mmt) cc_final: -0.3345 (mmm) REVERT: I 360 MET cc_start: 0.6221 (tpt) cc_final: 0.5638 (ptm) REVERT: I 383 MET cc_start: 0.5383 (mtm) cc_final: 0.4727 (mpp) REVERT: I 455 MET cc_start: 0.2988 (ppp) cc_final: 0.0472 (ttp) outliers start: 96 outliers final: 61 residues processed: 291 average time/residue: 0.2228 time to fit residues: 107.9206 Evaluate side-chains 253 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 373 HIS Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain H residue 398 GLU Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain H residue 555 PHE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 505 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 166 optimal weight: 2.9990 chunk 350 optimal weight: 50.0000 chunk 168 optimal weight: 2.9990 chunk 372 optimal weight: 6.9990 chunk 357 optimal weight: 0.4980 chunk 86 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 427 optimal weight: 5.9990 chunk 328 optimal weight: 40.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 117 GLN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 599 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 = 0.4440 r_free = 0.4440 target = 0.146753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.093398 restraints weight = 156923.141| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.35 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40035 Z= 0.149 Angle : 0.532 9.018 54474 Z= 0.269 Chirality : 0.042 0.241 5976 Planarity : 0.004 0.066 7026 Dihedral : 4.012 42.331 5262 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 2.25 % Allowed : 9.35 % Favored : 88.40 % 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: 0.65 (0.12), residues: 4839 helix: 1.94 (0.12), residues: 1794 sheet: 0.47 (0.19), residues: 717 loop : -0.81 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 518 TYR 0.020 0.001 TYR G 183 PHE 0.016 0.001 PHE G 315 TRP 0.027 0.001 TRP C 452 HIS 0.007 0.001 HIS H 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (39993) covalent geometry : angle 0.53117 / 0.27 (54390) SS BOND : bond 0.00227 / 0.13 ( 42) SS BOND : angle 1.05656 / 0.67 ( 84) hydrogen bonds : bond 0.04603 / 2.98 ( 1751) hydrogen bonds : angle 4.49989 / 3.08 ( 4965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 195 time to evaluate : 1.492 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: 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 816 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.7933 (p) REVERT: A 1141 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8837 (tm) REVERT: B 329 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 334 ASN cc_start: 0.2618 (OUTLIER) cc_final: 0.2243 (t0) REVERT: B 423 TYR cc_start: 0.7518 (t80) cc_final: 0.7173 (t80) REVERT: B 869 MET cc_start: 0.9129 (mtt) cc_final: 0.8822 (mtt) REVERT: C 113 ASP cc_start: 0.8453 (t0) cc_final: 0.7945 (p0) REVERT: C 169 PHE cc_start: 0.7082 (m-80) cc_final: 0.6839 (m-80) REVERT: C 171 TYR cc_start: 0.7184 (m-80) cc_final: 0.6782 (t80) REVERT: C 201 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8619 (t80) REVERT: C 375 PHE cc_start: 0.6545 (m-80) cc_final: 0.6025 (m-80) REVERT: G 74 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7860 (pptt) REVERT: G 152 MET cc_start: -0.3299 (mmt) cc_final: -0.4000 (mmt) REVERT: G 249 MET cc_start: 0.1785 (mtp) cc_final: 0.1431 (ttm) REVERT: G 323 MET cc_start: 0.1091 (mmt) cc_final: 0.0243 (mmt) REVERT: G 376 MET cc_start: 0.5262 (ttt) cc_final: 0.4985 (ptm) REVERT: G 455 MET cc_start: 0.0911 (tmm) cc_final: 0.0074 (tmm) REVERT: G 579 MET cc_start: 0.0125 (mtt) cc_final: -0.0738 (mmm) REVERT: H 373 HIS cc_start: 0.9202 (OUTLIER) cc_final: 0.8694 (m-70) REVERT: H 376 MET cc_start: 0.6712 (ttm) cc_final: 0.6406 (ttm) REVERT: H 512 PHE cc_start: 0.8542 (m-80) cc_final: 0.7922 (m-80) REVERT: I 78 THR cc_start: 0.7141 (OUTLIER) cc_final: 0.6933 (p) REVERT: I 82 MET cc_start: 0.3230 (mtp) cc_final: 0.2580 (tmm) REVERT: I 155 SER cc_start: 0.3220 (OUTLIER) cc_final: 0.3008 (m) REVERT: I 156 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4958 (mm) REVERT: I 360 MET cc_start: 0.6009 (tpt) cc_final: 0.5373 (ptm) REVERT: I 383 MET cc_start: 0.5855 (mtm) cc_final: 0.5340 (mpp) REVERT: I 455 MET cc_start: 0.2670 (ppp) cc_final: 0.1360 (ptt) REVERT: I 527 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6194 (tp30) outliers start: 97 outliers final: 61 residues processed: 282 average time/residue: 0.2376 time to fit residues: 112.6069 Evaluate side-chains 243 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 373 HIS Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain H residue 398 GLU Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 505 HIS Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 505 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 18 optimal weight: 3.9990 chunk 230 optimal weight: 0.4980 chunk 232 optimal weight: 50.0000 chunk 367 optimal weight: 50.0000 chunk 475 optimal weight: 50.0000 chunk 75 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 452 optimal weight: 40.0000 chunk 316 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 HIS H 540 HIS ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 599 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 = 0.4442 r_free = 0.4442 target = 0.151694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099370 restraints weight = 155217.817| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 5.73 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40035 Z= 0.145 Angle : 0.532 12.200 54474 Z= 0.268 Chirality : 0.042 0.209 5976 Planarity : 0.004 0.052 7026 Dihedral : 4.019 43.466 5262 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.90 % Rotamer: Outliers : 2.08 % Allowed : 9.81 % Favored : 88.10 % 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: 0.71 (0.12), residues: 4839 helix: 1.92 (0.12), residues: 1806 sheet: 0.54 (0.19), residues: 714 loop : -0.72 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.021 0.001 TYR B 453 PHE 0.016 0.001 PHE B 464 TRP 0.020 0.001 TRP G 461 HIS 0.005 0.001 HIS H 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (39993) covalent geometry : angle 0.53063 / 0.27 (54390) SS BOND : bond 0.00259 / 0.15 ( 42) SS BOND : angle 1.07704 / 0.68 ( 84) hydrogen bonds : bond 0.04578 / 2.96 ( 1751) hydrogen bonds : angle 4.47884 / 3.06 ( 4965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 180 time to evaluate : 1.378 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: 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 816 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 906 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8681 (m-10) REVERT: A 1141 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8581 (tm) REVERT: B 329 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: B 453 TYR cc_start: 0.8547 (p90) cc_final: 0.8197 (p90) REVERT: C 171 TYR cc_start: 0.7506 (m-80) cc_final: 0.6655 (t80) REVERT: C 201 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8749 (t80) REVERT: G 74 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7865 (pptt) REVERT: G 249 MET cc_start: 0.1804 (mtp) cc_final: 0.1416 (ttm) REVERT: G 323 MET cc_start: 0.1379 (mmt) cc_final: -0.0198 (mmp) REVERT: G 376 MET cc_start: 0.5417 (ttt) cc_final: 0.5123 (ptm) REVERT: G 579 MET cc_start: 0.0243 (mtt) cc_final: -0.0490 (mmm) REVERT: H 37 GLU cc_start: 0.7835 (mt-10) cc_final: 0.6732 (tp30) REVERT: H 82 MET cc_start: -0.0213 (mpp) cc_final: -0.0512 (mtm) REVERT: H 249 MET cc_start: 0.3957 (mmm) cc_final: 0.3617 (mmm) REVERT: H 373 HIS cc_start: 0.9368 (OUTLIER) cc_final: 0.9031 (m-70) REVERT: H 512 PHE cc_start: 0.8457 (m-80) cc_final: 0.7928 (m-80) REVERT: I 62 MET cc_start: 0.2308 (mmm) cc_final: 0.1826 (tmm) REVERT: I 78 THR cc_start: 0.7209 (OUTLIER) cc_final: 0.6935 (p) REVERT: I 82 MET cc_start: 0.3295 (mtp) cc_final: 0.2618 (tmm) REVERT: I 155 SER cc_start: 0.2967 (OUTLIER) cc_final: 0.2721 (m) REVERT: I 156 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.5157 (mm) REVERT: I 360 MET cc_start: 0.6063 (tpt) cc_final: 0.5496 (ptm) REVERT: I 383 MET cc_start: 0.6177 (mtm) cc_final: 0.5789 (mpp) REVERT: I 455 MET cc_start: 0.3269 (ppp) cc_final: 0.2048 (ptt) outliers start: 90 outliers final: 63 residues processed: 259 average time/residue: 0.2291 time to fit residues: 100.0789 Evaluate side-chains 245 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 173 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 373 HIS Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 505 HIS Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 505 HIS Chi-restraints excluded: chain I residue 574 VAL Chi-restraints excluded: chain I residue 592 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 429 optimal weight: 30.0000 chunk 207 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 384 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 408 optimal weight: 0.0370 chunk 427 optimal weight: 6.9990 chunk 237 optimal weight: 50.0000 chunk 334 optimal weight: 50.0000 chunk 158 optimal weight: 0.9980 chunk 230 optimal weight: 8.9990 overall best weight: 3.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN G 535 HIS H 64 ASN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 373 HIS ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.148821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090663 restraints weight = 146446.302| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.64 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 40035 Z= 0.214 Angle : 0.595 11.644 54474 Z= 0.302 Chirality : 0.043 0.259 5976 Planarity : 0.004 0.067 7026 Dihedral : 4.282 44.293 5262 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 2.27 % Allowed : 10.02 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.12), residues: 4839 helix: 1.73 (0.12), residues: 1842 sheet: 0.52 (0.19), residues: 708 loop : -0.76 (0.13), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 983 TYR 0.021 0.001 TYR B 365 PHE 0.023 0.001 PHE G 369 TRP 0.036 0.001 TRP G 461 HIS 0.012 0.001 HIS H 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (39993) covalent geometry : angle 0.59299 / 0.30 (54390) SS BOND : bond 0.00358 / 0.18 ( 42) SS BOND : angle 1.25438 / 0.80 ( 84) hydrogen bonds : bond 0.05326 / 3.46 ( 1751) hydrogen bonds : angle 4.67308 / 3.20 ( 4965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 173 time to evaluate : 1.523 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 SER cc_start: 0.8293 (OUTLIER) cc_final: 0.7844 (p) REVERT: A 906 PHE cc_start: 0.9513 (OUTLIER) cc_final: 0.9114 (m-10) REVERT: A 1141 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8835 (tm) REVERT: C 201 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8700 (t80) REVERT: C 375 PHE cc_start: 0.6733 (m-80) cc_final: 0.6293 (m-80) REVERT: G 74 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7972 (pptt) REVERT: G 152 MET cc_start: -0.3892 (mtt) cc_final: -0.4722 (tpp) REVERT: G 234 LYS cc_start: 0.4739 (tptt) cc_final: 0.4344 (tmtt) REVERT: G 249 MET cc_start: 0.1575 (mtp) cc_final: 0.1215 (ttm) REVERT: G 270 MET cc_start: 0.1694 (mpp) cc_final: 0.0687 (mpp) REVERT: G 323 MET cc_start: 0.1266 (mmt) cc_final: 0.0108 (mmp) REVERT: G 455 MET cc_start: 0.0955 (tmm) cc_final: 0.0444 (tmm) REVERT: G 579 MET cc_start: 0.0910 (mtt) cc_final: 0.0169 (mmm) REVERT: H 373 HIS cc_start: 0.9244 (OUTLIER) cc_final: 0.8889 (m-70) REVERT: H 376 MET cc_start: 0.7169 (ttm) cc_final: 0.6945 (ttm) REVERT: H 512 PHE cc_start: 0.8503 (m-80) cc_final: 0.8140 (m-80) REVERT: H 529 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7569 (pp) REVERT: I 62 MET cc_start: 0.2831 (mmm) cc_final: 0.2530 (tmm) REVERT: I 78 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6897 (p) REVERT: I 82 MET cc_start: 0.3097 (mtp) cc_final: 0.2433 (tmm) REVERT: I 155 SER cc_start: 0.3279 (OUTLIER) cc_final: 0.3008 (m) REVERT: I 156 LEU cc_start: 0.5605 (OUTLIER) cc_final: 0.5381 (mm) REVERT: I 360 MET cc_start: 0.6065 (tpt) cc_final: 0.5523 (ptm) REVERT: I 383 MET cc_start: 0.5900 (mtm) cc_final: 0.5576 (mpp) REVERT: I 480 MET cc_start: -0.0241 (ptt) cc_final: -0.0791 (tmm) outliers start: 98 outliers final: 62 residues processed: 259 average time/residue: 0.2152 time to fit residues: 94.5124 Evaluate side-chains 234 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 163 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 34 HIS Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 373 HIS Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 505 HIS Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 505 HIS Chi-restraints excluded: chain I residue 518 ARG Chi-restraints excluded: chain I residue 592 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 96 optimal weight: 0.5980 chunk 268 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 279 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 34 optimal weight: 40.0000 chunk 240 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 GLN B 343 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 598 GLN ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.145456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.092393 restraints weight = 157702.955| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.23 r_work: 0.2936 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 40035 Z= 0.111 Angle : 0.525 10.801 54474 Z= 0.263 Chirality : 0.041 0.255 5976 Planarity : 0.004 0.050 7026 Dihedral : 4.040 42.971 5262 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 1.62 % Allowed : 10.95 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4839 helix: 1.99 (0.12), residues: 1806 sheet: 0.58 (0.19), residues: 705 loop : -0.63 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.036 0.001 TYR G 510 PHE 0.028 0.001 PHE B 169 TRP 0.030 0.001 TRP G 461 HIS 0.006 0.001 HIS H 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (39993) covalent geometry : angle 0.52409 / 0.26 (54390) SS BOND : bond 0.00245 / 0.15 ( 42) SS BOND : angle 0.89320 / 0.60 ( 84) hydrogen bonds : bond 0.04311 / 2.79 ( 1751) hydrogen bonds : angle 4.43893 / 3.04 ( 4965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 1.511 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.7951 (p) REVERT: A 906 PHE cc_start: 0.9534 (OUTLIER) cc_final: 0.9208 (m-10) REVERT: B 25 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5830 (tp) REVERT: C 171 TYR cc_start: 0.7494 (m-80) cc_final: 0.7013 (t80) REVERT: C 375 PHE cc_start: 0.5448 (m-80) cc_final: 0.5240 (m-80) REVERT: G 74 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8073 (pptt) REVERT: G 152 MET cc_start: -0.2697 (mtt) cc_final: -0.4170 (tpp) REVERT: G 249 MET cc_start: 0.1363 (mtp) cc_final: 0.1136 (ttm) REVERT: G 270 MET cc_start: 0.2688 (mpp) cc_final: 0.1431 (mpp) REVERT: G 323 MET cc_start: 0.4874 (mmt) cc_final: 0.4515 (mmt) REVERT: G 579 MET cc_start: 0.4351 (mtt) cc_final: 0.3488 (mmm) REVERT: H 62 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7158 (mpp) REVERT: H 249 MET cc_start: 0.4289 (mmm) cc_final: 0.3961 (mmm) REVERT: H 373 HIS cc_start: 0.9318 (OUTLIER) cc_final: 0.9014 (m-70) REVERT: H 376 MET cc_start: 0.7045 (ttm) cc_final: 0.6807 (ttm) REVERT: H 512 PHE cc_start: 0.8368 (m-80) cc_final: 0.8048 (m-80) REVERT: I 62 MET cc_start: 0.2446 (mmm) cc_final: 0.2129 (tmm) REVERT: I 78 THR cc_start: 0.7087 (OUTLIER) cc_final: 0.6783 (p) REVERT: I 82 MET cc_start: 0.2894 (mtp) cc_final: 0.2428 (tmm) REVERT: I 360 MET cc_start: 0.5396 (tpt) cc_final: 0.4701 (ptm) REVERT: I 383 MET cc_start: 0.6044 (mtm) cc_final: 0.5817 (mpp) REVERT: I 408 MET cc_start: 0.2641 (mtt) cc_final: 0.2318 (ttm) REVERT: I 455 MET cc_start: 0.3014 (ppp) cc_final: 0.2075 (ptt) REVERT: I 480 MET cc_start: 0.1009 (ptt) cc_final: 0.0683 (ptt) REVERT: I 594 TRP cc_start: 0.0287 (t60) cc_final: -0.0058 (t60) outliers start: 70 outliers final: 49 residues processed: 235 average time/residue: 0.2409 time to fit residues: 94.5642 Evaluate side-chains 220 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 165 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 34 HIS Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 573 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 373 HIS Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 505 HIS Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 505 HIS Chi-restraints excluded: chain I residue 518 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 130 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 407 optimal weight: 5.9990 chunk 378 optimal weight: 0.7980 chunk 404 optimal weight: 8.9990 chunk 482 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 397 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 599 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 = 0.4419 r_free = 0.4419 target = 0.148862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093244 restraints weight = 147663.346| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 5.60 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40035 Z= 0.177 Angle : 0.566 10.534 54474 Z= 0.286 Chirality : 0.043 0.245 5976 Planarity : 0.004 0.048 7026 Dihedral : 4.150 42.591 5260 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 1.69 % Allowed : 10.90 % Favored : 87.41 % 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: 0.81 (0.12), residues: 4839 helix: 1.97 (0.12), residues: 1812 sheet: 0.55 (0.19), residues: 708 loop : -0.63 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.019 0.001 TYR G 510 PHE 0.020 0.001 PHE H 40 TRP 0.030 0.001 TRP G 461 HIS 0.007 0.001 HIS H 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (39993) covalent geometry : angle 0.56478 / 0.29 (54390) SS BOND : bond 0.00305 / 0.17 ( 42) SS BOND : angle 1.11157 / 0.72 ( 84) hydrogen bonds : bond 0.04915 / 3.18 ( 1751) hydrogen bonds : angle 4.56057 / 3.12 ( 4965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 167 time to evaluate : 1.468 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.7888 (p) REVERT: A 906 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8969 (m-10) REVERT: C 375 PHE cc_start: 0.6046 (m-80) cc_final: 0.5694 (m-80) REVERT: G 74 LYS cc_start: 0.8273 (mmmt) cc_final: 0.7976 (pptt) REVERT: G 249 MET cc_start: 0.1516 (mtp) cc_final: 0.1182 (ttm) REVERT: G 376 MET cc_start: 0.4651 (ppp) cc_final: 0.4277 (tpt) REVERT: G 579 MET cc_start: 0.0357 (mtt) cc_final: -0.0156 (mmm) REVERT: H 62 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7634 (mpp) REVERT: H 249 MET cc_start: 0.4217 (mmm) cc_final: 0.3914 (mmm) REVERT: H 376 MET cc_start: 0.7126 (ttm) cc_final: 0.6911 (ttm) REVERT: H 512 PHE cc_start: 0.8197 (m-80) cc_final: 0.7941 (m-80) REVERT: I 62 MET cc_start: 0.2749 (mmm) cc_final: 0.2414 (tmm) REVERT: I 78 THR cc_start: 0.7470 (OUTLIER) cc_final: 0.7202 (p) REVERT: I 82 MET cc_start: 0.3152 (mtp) cc_final: 0.2538 (tmm) REVERT: I 360 MET cc_start: 0.5757 (tpt) cc_final: 0.5112 (ptm) REVERT: I 383 MET cc_start: 0.5934 (mtm) cc_final: 0.5636 (mpp) REVERT: I 408 MET cc_start: 0.3592 (mtt) cc_final: 0.3174 (ttm) REVERT: I 455 MET cc_start: 0.2935 (ppp) cc_final: 0.1658 (ptt) REVERT: I 480 MET cc_start: -0.0440 (ptt) cc_final: -0.0658 (ptt) REVERT: I 594 TRP cc_start: -0.1042 (t60) cc_final: -0.1356 (t60) outliers start: 73 outliers final: 55 residues processed: 229 average time/residue: 0.2114 time to fit residues: 82.1318 Evaluate side-chains 220 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 34 HIS Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 573 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 505 HIS Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 505 HIS Chi-restraints excluded: chain I residue 518 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 26 optimal weight: 40.0000 chunk 230 optimal weight: 0.5980 chunk 458 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 424 optimal weight: 5.9990 chunk 444 optimal weight: 0.6980 chunk 482 optimal weight: 9.9990 chunk 395 optimal weight: 0.8980 chunk 348 optimal weight: 20.0000 chunk 443 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 599 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 = 0.4429 r_free = 0.4429 target = 0.149139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.093537 restraints weight = 148684.693| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 5.62 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40035 Z= 0.128 Angle : 0.546 11.313 54474 Z= 0.273 Chirality : 0.042 0.249 5976 Planarity : 0.004 0.049 7026 Dihedral : 4.067 42.808 5260 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 1.57 % Allowed : 10.97 % Favored : 87.45 % 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: 0.85 (0.12), residues: 4839 helix: 1.99 (0.12), residues: 1809 sheet: 0.59 (0.19), residues: 702 loop : -0.58 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 983 TYR 0.030 0.001 TYR C 171 PHE 0.029 0.001 PHE B 169 TRP 0.028 0.001 TRP G 461 HIS 0.011 0.001 HIS I 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (39993) covalent geometry : angle 0.54525 / 0.27 (54390) SS BOND : bond 0.00263 / 0.15 ( 42) SS BOND : angle 0.91632 / 0.61 ( 84) hydrogen bonds : bond 0.04462 / 2.88 ( 1751) hydrogen bonds : angle 4.46755 / 3.06 ( 4965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 166 time to evaluate : 1.181 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7771 (p) REVERT: A 906 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.9065 (m-10) REVERT: G 74 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7972 (pptt) REVERT: G 152 MET cc_start: -0.3574 (mtt) cc_final: -0.5018 (tpp) REVERT: G 249 MET cc_start: 0.1527 (mtp) cc_final: 0.1196 (ttm) REVERT: G 579 MET cc_start: 0.0298 (mtt) cc_final: -0.0171 (mmm) REVERT: H 62 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7757 (mpp) REVERT: H 249 MET cc_start: 0.4205 (mmm) cc_final: 0.3911 (mmm) REVERT: H 325 GLN cc_start: 0.8801 (pm20) cc_final: 0.8534 (pm20) REVERT: H 455 MET cc_start: 0.8707 (ppp) cc_final: 0.8208 (tpt) REVERT: H 474 MET cc_start: 0.9150 (ttt) cc_final: 0.7867 (ttt) REVERT: H 477 TRP cc_start: 0.9317 (t-100) cc_final: 0.8770 (t60) REVERT: H 480 MET cc_start: 0.3519 (mmt) cc_final: 0.2909 (mmt) REVERT: I 62 MET cc_start: 0.3191 (mmm) cc_final: 0.2942 (tmm) REVERT: I 78 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.7077 (p) REVERT: I 82 MET cc_start: 0.3114 (mtp) cc_final: 0.2509 (tmm) REVERT: I 152 MET cc_start: 0.1229 (ptt) cc_final: -0.1652 (mmt) REVERT: I 360 MET cc_start: 0.5953 (tpt) cc_final: 0.5340 (ptm) REVERT: I 383 MET cc_start: 0.5931 (mtm) cc_final: 0.5639 (mpp) REVERT: I 408 MET cc_start: 0.3640 (mtt) cc_final: 0.3175 (ttm) REVERT: I 455 MET cc_start: 0.2896 (ppp) cc_final: 0.1528 (ptt) outliers start: 68 outliers final: 55 residues processed: 227 average time/residue: 0.2226 time to fit residues: 84.0790 Evaluate side-chains 221 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain G residue 34 HIS Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 573 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 394 ASN Chi-restraints excluded: chain H residue 505 HIS Chi-restraints excluded: chain H residue 510 TYR Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 505 HIS Chi-restraints excluded: chain I residue 518 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 250 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 478 optimal weight: 40.0000 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN A1135 ASN B 343 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.149344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.095222 restraints weight = 145393.919| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 5.99 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 40035 Z= 0.168 Angle : 0.573 11.383 54474 Z= 0.289 Chirality : 0.043 0.240 5976 Planarity : 0.004 0.049 7026 Dihedral : 4.118 42.252 5259 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.53 % Allowed : 11.11 % Favored : 87.36 % 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: 0.80 (0.12), residues: 4839 helix: 1.93 (0.12), residues: 1812 sheet: 0.59 (0.19), residues: 708 loop : -0.61 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 983 TYR 0.018 0.001 TYR G 385 PHE 0.027 0.001 PHE C 169 TRP 0.029 0.001 TRP G 461 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (39993) covalent geometry : angle 0.57149 / 0.29 (54390) SS BOND : bond 0.00304 / 0.17 ( 42) SS BOND : angle 1.06178 / 0.68 ( 84) hydrogen bonds : bond 0.04873 / 3.15 ( 1751) hydrogen bonds : angle 4.55813 / 3.11 ( 4965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14344.55 seconds wall clock time: 244 minutes 36.16 seconds (14676.16 seconds total)