Starting phenix.real_space_refine on Mon Aug 25 12:47:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blk_44658/08_2025/9blk_44658.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blk_44658/08_2025/9blk_44658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9blk_44658/08_2025/9blk_44658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blk_44658/08_2025/9blk_44658.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9blk_44658/08_2025/9blk_44658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blk_44658/08_2025/9blk_44658.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 183 5.16 5 C 17832 2.51 5 N 4551 2.21 5 O 5469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28035 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9138 Classifications: {'peptide': 1173} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1122} Chain breaks: 6 Chain: "B" Number of atoms: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9138 Classifications: {'peptide': 1173} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1122} Chain breaks: 6 Chain: "C" Number of atoms: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9138 Classifications: {'peptide': 1173} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1122} Chain breaks: 6 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.66, per 1000 atoms: 0.24 Number of scatterers: 28035 At special positions: 0 Unit cell: (155.088, 150.062, 162.268, 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 183 16.00 O 5469 8.00 N 4551 7.00 C 17832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.06 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.02 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.08 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.04 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.09 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.03 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A 748 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 848 " distance=2.04 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 837 " distance=2.06 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 949 " distance=2.04 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1137 " distance=2.04 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1221 " distance=2.05 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.07 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.02 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.08 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.09 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 748 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 848 " distance=2.04 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 837 " distance=2.05 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 949 " distance=2.04 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1137 " distance=2.04 Simple disulfide: pdb=" SG CYS B1176 " - pdb=" SG CYS B1221 " distance=2.05 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.07 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.04 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.02 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.08 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.04 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.04 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.09 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 683 " distance=2.03 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 748 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 826 " - pdb=" SG CYS C 848 " distance=2.04 Simple disulfide: pdb=" SG CYS C 831 " - pdb=" SG CYS C 837 " distance=2.05 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 949 " distance=2.04 Simple disulfide: pdb=" SG CYS C1126 " - pdb=" SG CYS C1137 " distance=2.04 Simple disulfide: pdb=" SG CYS C1176 " - pdb=" SG CYS C1221 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1401 " - " ASN A 202 " " NAG A1402 " - " ASN A 371 " " NAG A1403 " - " ASN A 449 " " NAG A1404 " - " ASN A 133 " " NAG A1405 " - " ASN A 675 " " NAG A1406 " - " ASN A 695 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A 788 " " NAG A1409 " - " ASN A1194 " " NAG A1410 " - " ASN A1224 " " NAG B1401 " - " ASN B 202 " " NAG B1402 " - " ASN B 371 " " NAG B1403 " - " ASN B 449 " " NAG B1404 " - " ASN B 133 " " NAG B1405 " - " ASN B 675 " " NAG B1406 " - " ASN B 695 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B 788 " " NAG B1409 " - " ASN B1194 " " NAG B1410 " - " ASN B1224 " " NAG C1401 " - " ASN C 202 " " NAG C1402 " - " ASN C 371 " " NAG C1403 " - " ASN C 449 " " NAG C1404 " - " ASN C 133 " " NAG C1405 " - " ASN C 675 " " NAG C1406 " - " ASN C 695 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C 788 " " NAG C1409 " - " ASN C1194 " " NAG C1410 " - " ASN C1224 " " NAG D 1 " - " ASN A 739 " " NAG E 1 " - " ASN A 937 " " NAG F 1 " - " ASN B 739 " " NAG G 1 " - " ASN B 937 " " NAG H 1 " - " ASN C 739 " " NAG I 1 " - " ASN C 937 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6582 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 81 sheets defined 25.3% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 371 through 379 removed outlier: 5.169A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 709 through 711 No H-bonds generated for 'chain 'A' and resid 709 through 711' Processing helix chain 'A' and resid 714 through 715 No H-bonds generated for 'chain 'A' and resid 714 through 715' Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 834 through 839 Processing helix chain 'A' and resid 845 through 875 removed outlier: 3.531A pdb=" N ASP A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 897 through 900 Processing helix chain 'A' and resid 914 through 923 removed outlier: 4.089A pdb=" N LYS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 935 through 938 Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 964 through 978 removed outlier: 3.564A pdb=" N GLY A 970 " --> pdb=" O ASN A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 991 through 1002 Processing helix chain 'A' and resid 1006 through 1012 Processing helix chain 'A' and resid 1013 through 1031 removed outlier: 3.715A pdb=" N ILE A1028 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1058 removed outlier: 4.681A pdb=" N ILE A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A1045 " --> pdb=" O LYS A1041 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1056 " --> pdb=" O ALA A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1079 through 1125 removed outlier: 3.761A pdb=" N ARG A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A1090 " --> pdb=" O GLN A1086 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A1093 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A1096 " --> pdb=" O ASN A1092 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A1111 " --> pdb=" O SER A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1213 No H-bonds generated for 'chain 'A' and resid 1211 through 1213' Processing helix chain 'B' and resid 42 through 46 removed outlier: 4.523A pdb=" N ASN B 45 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 371 through 379 removed outlier: 5.170A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 709 through 711 No H-bonds generated for 'chain 'B' and resid 709 through 711' Processing helix chain 'B' and resid 714 through 715 No H-bonds generated for 'chain 'B' and resid 714 through 715' Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 834 through 839 Processing helix chain 'B' and resid 845 through 875 removed outlier: 3.531A pdb=" N ASP B 849 " --> pdb=" O GLY B 845 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE B 854 " --> pdb=" O ASN B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 897 through 900 Processing helix chain 'B' and resid 914 through 923 removed outlier: 4.090A pdb=" N LYS B 923 " --> pdb=" O LEU B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 934 Processing helix chain 'B' and resid 935 through 938 Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 964 through 978 removed outlier: 3.564A pdb=" N GLY B 970 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 991 through 1002 Processing helix chain 'B' and resid 1006 through 1012 Processing helix chain 'B' and resid 1013 through 1031 removed outlier: 3.716A pdb=" N ILE B1028 " --> pdb=" O ALA B1024 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B1029 " --> pdb=" O LEU B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1058 removed outlier: 4.683A pdb=" N ILE B1042 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B1045 " --> pdb=" O LYS B1041 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B1056 " --> pdb=" O ALA B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1078 Processing helix chain 'B' and resid 1079 through 1125 removed outlier: 3.761A pdb=" N ARG B1089 " --> pdb=" O ALA B1085 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B1093 " --> pdb=" O ARG B1089 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B1096 " --> pdb=" O ASN B1092 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B1111 " --> pdb=" O SER B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1213 No H-bonds generated for 'chain 'B' and resid 1211 through 1213' Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 371 through 379 removed outlier: 5.169A pdb=" N SER C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 458 through 463 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 709 through 711 No H-bonds generated for 'chain 'C' and resid 709 through 711' Processing helix chain 'C' and resid 714 through 715 No H-bonds generated for 'chain 'C' and resid 714 through 715' Processing helix chain 'C' and resid 826 through 831 Processing helix chain 'C' and resid 834 through 839 Processing helix chain 'C' and resid 845 through 875 removed outlier: 3.531A pdb=" N ASP C 849 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE C 854 " --> pdb=" O ASN C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 897 through 900 Processing helix chain 'C' and resid 914 through 923 removed outlier: 4.091A pdb=" N LYS C 923 " --> pdb=" O LEU C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 934 Processing helix chain 'C' and resid 935 through 938 Processing helix chain 'C' and resid 946 through 954 Processing helix chain 'C' and resid 964 through 978 removed outlier: 3.564A pdb=" N GLY C 970 " --> pdb=" O ASN C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 991 through 1002 Processing helix chain 'C' and resid 1006 through 1012 Processing helix chain 'C' and resid 1013 through 1031 removed outlier: 3.715A pdb=" N ILE C1028 " --> pdb=" O ALA C1024 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C1029 " --> pdb=" O LEU C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1058 removed outlier: 4.682A pdb=" N ILE C1042 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C1045 " --> pdb=" O LYS C1041 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C1056 " --> pdb=" O ALA C1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1078 Processing helix chain 'C' and resid 1079 through 1125 removed outlier: 3.761A pdb=" N ARG C1089 " --> pdb=" O ALA C1085 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C1090 " --> pdb=" O GLN C1086 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C1093 " --> pdb=" O ARG C1089 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR C1096 " --> pdb=" O ASN C1092 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU C1111 " --> pdb=" O SER C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1213 No H-bonds generated for 'chain 'C' and resid 1211 through 1213' Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 8.230A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 8.230A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 223 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN A 239 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA A 225 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 64 Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 98 removed outlier: 7.795A pdb=" N GLY A 157 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N THR A 204 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 159 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN A 202 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 161 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS A 200 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 163 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 112 Processing sheet with id=AA8, first strand: chain 'A' and resid 174 through 175 removed outlier: 6.417A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 310 through 326 removed outlier: 4.565A pdb=" N GLY A 316 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY A 686 " --> pdb=" O GLY A 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 335 removed outlier: 4.000A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 668 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 366 removed outlier: 3.919A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER A 438 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS A 386 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN A 440 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 384 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 442 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 361 through 366 removed outlier: 3.919A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AB6, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AB7, first strand: chain 'A' and resid 491 through 493 removed outlier: 4.378A pdb=" N CYS A 491 " --> pdb=" O SER A 553 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AB9, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AC1, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AC2, first strand: chain 'A' and resid 738 through 745 removed outlier: 6.417A pdb=" N TYR A 738 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ASN A 778 " --> pdb=" O TYR A 738 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N SER A 740 " --> pdb=" O ASN A 778 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 750 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.068A pdb=" N ASN A 785 " --> pdb=" O LEU B 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 798 through 803 removed outlier: 6.593A pdb=" N ARG A1170 " --> pdb=" O ASN A1192 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN A1192 " --> pdb=" O ARG A1170 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 806 through 808 Processing sheet with id=AC6, first strand: chain 'A' and resid 806 through 808 removed outlier: 5.749A pdb=" N TYR A1161 " --> pdb=" O HIS A1142 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS A1142 " --> pdb=" O TYR A1161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 821 through 824 removed outlier: 3.941A pdb=" N LYS A 821 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 878 through 880 Processing sheet with id=AC9, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AD1, first strand: chain 'A' and resid 1215 through 1218 Processing sheet with id=AD2, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AD3, first strand: chain 'B' and resid 39 through 40 removed outlier: 8.231A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 39 through 40 removed outlier: 8.231A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B 223 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN B 239 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 225 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 61 through 64 Processing sheet with id=AD6, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AD7, first strand: chain 'B' and resid 97 through 98 removed outlier: 7.795A pdb=" N GLY B 157 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR B 204 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 159 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN B 202 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 161 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS B 200 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 163 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 110 through 112 Processing sheet with id=AD9, first strand: chain 'B' and resid 174 through 175 removed outlier: 6.418A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 310 through 326 removed outlier: 4.565A pdb=" N GLY B 316 " --> pdb=" O GLY B 686 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY B 686 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 331 through 335 removed outlier: 4.000A pdb=" N ALA B 331 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B 668 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AE4, first strand: chain 'B' and resid 361 through 366 removed outlier: 3.920A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER B 438 " --> pdb=" O CYS B 386 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS B 386 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN B 440 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE B 384 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR B 442 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 366 removed outlier: 3.920A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AE7, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AE8, first strand: chain 'B' and resid 491 through 493 removed outlier: 4.378A pdb=" N CYS B 491 " --> pdb=" O SER B 553 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AF1, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AF2, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AF3, first strand: chain 'B' and resid 738 through 745 removed outlier: 6.416A pdb=" N TYR B 738 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN B 778 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N SER B 740 " --> pdb=" O ASN B 778 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR B 756 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 750 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.069A pdb=" N ASN B 785 " --> pdb=" O LEU C 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 798 through 803 removed outlier: 6.592A pdb=" N ARG B1170 " --> pdb=" O ASN B1192 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN B1192 " --> pdb=" O ARG B1170 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 806 through 808 Processing sheet with id=AF7, first strand: chain 'B' and resid 806 through 808 removed outlier: 5.750A pdb=" N TYR B1161 " --> pdb=" O HIS B1142 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N HIS B1142 " --> pdb=" O TYR B1161 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 821 through 824 removed outlier: 3.941A pdb=" N LYS B 821 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 890 through 891 Processing sheet with id=AG1, first strand: chain 'B' and resid 1215 through 1218 Processing sheet with id=AG2, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AG3, first strand: chain 'C' and resid 39 through 40 removed outlier: 8.230A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 39 through 40 removed outlier: 8.230A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 223 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN C 239 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA C 225 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 61 through 64 Processing sheet with id=AG6, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AG7, first strand: chain 'C' and resid 97 through 98 removed outlier: 7.795A pdb=" N GLY C 157 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR C 204 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU C 159 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN C 202 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 161 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS C 200 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 163 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 110 through 112 Processing sheet with id=AG9, first strand: chain 'C' and resid 174 through 175 removed outlier: 6.417A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'C' and resid 310 through 326 removed outlier: 4.566A pdb=" N GLY C 316 " --> pdb=" O GLY C 686 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY C 686 " --> pdb=" O GLY C 316 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 331 through 335 removed outlier: 4.000A pdb=" N ALA C 331 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 668 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AH4, first strand: chain 'C' and resid 361 through 366 removed outlier: 3.919A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 438 " --> pdb=" O CYS C 386 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS C 386 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN C 440 " --> pdb=" O PHE C 384 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 384 " --> pdb=" O GLN C 440 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR C 442 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 361 through 366 removed outlier: 3.919A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AH7, first strand: chain 'C' and resid 484 through 488 Processing sheet with id=AH8, first strand: chain 'C' and resid 491 through 493 removed outlier: 4.379A pdb=" N CYS C 491 " --> pdb=" O SER C 553 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AI1, first strand: chain 'C' and resid 571 through 572 Processing sheet with id=AI2, first strand: chain 'C' and resid 701 through 704 Processing sheet with id=AI3, first strand: chain 'C' and resid 738 through 745 removed outlier: 6.417A pdb=" N TYR C 738 " --> pdb=" O PHE C 776 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN C 778 " --> pdb=" O TYR C 738 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N SER C 740 " --> pdb=" O ASN C 778 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR C 756 " --> pdb=" O VAL C 752 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 750 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 798 through 803 removed outlier: 6.593A pdb=" N ARG C1170 " --> pdb=" O ASN C1192 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN C1192 " --> pdb=" O ARG C1170 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 806 through 808 Processing sheet with id=AI6, first strand: chain 'C' and resid 806 through 808 removed outlier: 5.749A pdb=" N TYR C1161 " --> pdb=" O HIS C1142 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS C1142 " --> pdb=" O TYR C1161 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 821 through 824 removed outlier: 3.941A pdb=" N LYS C 821 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AI9, first strand: chain 'C' and resid 1215 through 1218 1134 hydrogen bonds defined for protein. 2994 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: 8.69 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7369 1.33 - 1.47: 9418 1.47 - 1.61: 11623 1.61 - 1.76: 36 1.76 - 1.90: 213 Bond restraints: 28659 Sorted by residual: bond pdb=" CB HIS B 215 " pdb=" CG HIS B 215 " ideal model delta sigma weight residual 1.497 1.402 0.095 1.40e-02 5.10e+03 4.58e+01 bond pdb=" CB HIS A 215 " pdb=" CG HIS A 215 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.55e+01 bond pdb=" CB HIS C 215 " pdb=" CG HIS C 215 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.54e+01 bond pdb=" CB ILE B 519 " pdb=" CG1 ILE B 519 " ideal model delta sigma weight residual 1.530 1.647 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" CB ILE A 519 " pdb=" CG1 ILE A 519 " ideal model delta sigma weight residual 1.530 1.647 -0.117 2.00e-02 2.50e+03 3.40e+01 ... (remaining 28654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 32043 2.21 - 4.42: 5708 4.42 - 6.63: 1034 6.63 - 8.84: 209 8.84 - 11.05: 24 Bond angle restraints: 39018 Sorted by residual: angle pdb=" C LYS B 473 " pdb=" N PRO B 474 " pdb=" CA PRO B 474 " ideal model delta sigma weight residual 120.31 128.57 -8.26 9.80e-01 1.04e+00 7.10e+01 angle pdb=" C LYS C 473 " pdb=" N PRO C 474 " pdb=" CA PRO C 474 " ideal model delta sigma weight residual 120.31 128.52 -8.21 9.80e-01 1.04e+00 7.02e+01 angle pdb=" C LYS A 473 " pdb=" N PRO A 474 " pdb=" CA PRO A 474 " ideal model delta sigma weight residual 120.31 128.47 -8.16 9.80e-01 1.04e+00 6.94e+01 angle pdb=" C PRO A 34 " pdb=" N PRO A 35 " pdb=" CA PRO A 35 " ideal model delta sigma weight residual 119.84 129.71 -9.87 1.25e+00 6.40e-01 6.24e+01 angle pdb=" C PRO C 34 " pdb=" N PRO C 35 " pdb=" CA PRO C 35 " ideal model delta sigma weight residual 119.84 129.67 -9.83 1.25e+00 6.40e-01 6.19e+01 ... (remaining 39013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 17114 21.18 - 42.36: 362 42.36 - 63.54: 116 63.54 - 84.73: 39 84.73 - 105.91: 21 Dihedral angle restraints: 17652 sinusoidal: 7362 harmonic: 10290 Sorted by residual: dihedral pdb=" CB CYS A 491 " pdb=" SG CYS A 491 " pdb=" SG CYS A 561 " pdb=" CB CYS A 561 " ideal model delta sinusoidal sigma weight residual -86.00 -128.06 42.06 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS B 491 " pdb=" SG CYS B 491 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual -86.00 -128.02 42.02 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS C 491 " pdb=" SG CYS C 491 " pdb=" SG CYS C 561 " pdb=" CB CYS C 561 " ideal model delta sinusoidal sigma weight residual -86.00 -128.01 42.01 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 17649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 3497 0.125 - 0.250: 816 0.250 - 0.375: 168 0.375 - 0.500: 55 0.500 - 0.626: 6 Chirality restraints: 4542 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.38e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.30e+02 ... (remaining 4539 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " 0.084 2.00e-02 2.50e+03 8.68e-02 9.41e+01 pdb=" CG ASN A 709 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " -0.133 2.00e-02 2.50e+03 pdb=" C1 NAG A1407 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " 0.084 2.00e-02 2.50e+03 8.67e-02 9.40e+01 pdb=" CG ASN B 709 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.133 2.00e-02 2.50e+03 pdb=" C1 NAG B1407 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " -0.084 2.00e-02 2.50e+03 8.66e-02 9.37e+01 pdb=" CG ASN C 709 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " 0.133 2.00e-02 2.50e+03 pdb=" C1 NAG C1407 " -0.105 2.00e-02 2.50e+03 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 204 2.57 - 3.16: 22968 3.16 - 3.74: 43502 3.74 - 4.32: 66272 4.32 - 4.90: 104320 Nonbonded interactions: 237266 Sorted by model distance: nonbonded pdb=" OD1 ASP A 351 " pdb=" N LYS A 352 " model vdw 1.992 3.120 nonbonded pdb=" O PRO B 69 " pdb=" OH TYR B 274 " model vdw 2.327 3.040 nonbonded pdb=" O PRO A 69 " pdb=" OH TYR A 274 " model vdw 2.327 3.040 nonbonded pdb=" O PRO C 69 " pdb=" OH TYR C 274 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR B 738 " pdb=" OG1 THR B 771 " model vdw 2.392 3.040 ... (remaining 237261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' 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: 10.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.010 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 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 : 0.022 0.133 28767 Z= 1.143 Angle : 1.824 11.047 39279 Z= 1.230 Chirality : 0.120 0.626 4542 Planarity : 0.009 0.048 4968 Dihedral : 11.141 105.906 10881 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.10 % Allowed : 0.78 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.13), residues: 3477 helix: -1.27 (0.17), residues: 717 sheet: 0.62 (0.18), residues: 765 loop : 0.14 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 999 TYR 0.092 0.012 TYR A 844 PHE 0.040 0.007 PHE A 122 TRP 0.043 0.009 TRP C 460 HIS 0.007 0.002 HIS A1158 Details of bonding type rmsd covalent geometry : bond 0.02181 (28659) covalent geometry : angle 1.81566 (39018) SS BOND : bond 0.01911 ( 63) SS BOND : angle 2.68191 ( 126) hydrogen bonds : bond 0.17446 ( 1041) hydrogen bonds : angle 8.43842 ( 2994) link_BETA1-4 : bond 0.06907 ( 9) link_BETA1-4 : angle 4.79149 ( 27) link_NAG-ASN : bond 0.08141 ( 36) link_NAG-ASN : angle 2.30915 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 821 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.6648 (t80) cc_final: 0.6284 (t80) REVERT: A 283 ILE cc_start: 0.7310 (mt) cc_final: 0.6946 (mt) REVERT: A 315 ASN cc_start: 0.6537 (p0) cc_final: 0.6139 (p0) REVERT: A 1026 TYR cc_start: 0.7148 (t80) cc_final: 0.6912 (t80) REVERT: A 1082 GLU cc_start: 0.6816 (tp30) cc_final: 0.6071 (tp30) REVERT: A 1101 TYR cc_start: 0.7950 (t80) cc_final: 0.7648 (t80) REVERT: B 199 TYR cc_start: 0.6751 (t80) cc_final: 0.6409 (t80) REVERT: B 283 ILE cc_start: 0.7393 (mt) cc_final: 0.7139 (mm) REVERT: B 315 ASN cc_start: 0.6646 (p0) cc_final: 0.6193 (p0) REVERT: B 1082 GLU cc_start: 0.6682 (tp30) cc_final: 0.6111 (tp30) REVERT: B 1101 TYR cc_start: 0.7914 (t80) cc_final: 0.7597 (t80) REVERT: C 199 TYR cc_start: 0.6721 (t80) cc_final: 0.6260 (t80) REVERT: C 283 ILE cc_start: 0.7250 (mt) cc_final: 0.6958 (mm) REVERT: C 315 ASN cc_start: 0.6475 (p0) cc_final: 0.6115 (p0) REVERT: C 1082 GLU cc_start: 0.6699 (tp30) cc_final: 0.5955 (tp30) REVERT: C 1101 TYR cc_start: 0.7923 (t80) cc_final: 0.7580 (t80) REVERT: C 1206 TYR cc_start: 0.7947 (t80) cc_final: 0.7650 (t80) outliers start: 3 outliers final: 0 residues processed: 824 average time/residue: 0.1800 time to fit residues: 240.2819 Evaluate side-chains 430 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 418 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS A 598 ASN A 606 HIS A 641 GLN A 840 GLN A 866 GLN A 888 ASN A 967 GLN A1014 GLN A1059 GLN A1092 ASN B 183 HIS B 239 ASN B 280 GLN B 418 GLN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS B 598 ASN B 606 HIS B 866 GLN B 888 ASN B 967 GLN B1059 GLN C 239 ASN C 303 GLN C 418 GLN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 HIS C 598 ASN C 606 HIS C 641 GLN ** C 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 866 GLN C 888 ASN C 967 GLN C1059 GLN C1092 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135400 restraints weight = 35805.722| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.09 r_work: 0.3463 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28767 Z= 0.181 Angle : 0.748 9.113 39279 Z= 0.398 Chirality : 0.050 0.403 4542 Planarity : 0.005 0.055 4968 Dihedral : 7.314 68.764 4749 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.87 % Favored : 98.04 % Rotamer: Outliers : 2.19 % Allowed : 9.11 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.13), residues: 3477 helix: -0.45 (0.18), residues: 762 sheet: 0.18 (0.17), residues: 750 loop : -0.11 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 681 TYR 0.035 0.002 TYR B 75 PHE 0.023 0.002 PHE C 278 TRP 0.017 0.002 TRP A 360 HIS 0.008 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00388 (28659) covalent geometry : angle 0.72713 (39018) SS BOND : bond 0.00677 ( 63) SS BOND : angle 1.12612 ( 126) hydrogen bonds : bond 0.05563 ( 1041) hydrogen bonds : angle 6.72262 ( 2994) link_BETA1-4 : bond 0.00580 ( 9) link_BETA1-4 : angle 3.15584 ( 27) link_NAG-ASN : bond 0.01201 ( 36) link_NAG-ASN : angle 2.87018 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 500 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7011 (pp) cc_final: 0.6044 (mp) REVERT: A 160 GLU cc_start: 0.6968 (tt0) cc_final: 0.6191 (tm-30) REVERT: A 199 TYR cc_start: 0.6548 (t80) cc_final: 0.6340 (t80) REVERT: A 315 ASN cc_start: 0.6508 (p0) cc_final: 0.6279 (p0) REVERT: A 720 GLN cc_start: 0.6916 (pm20) cc_final: 0.6030 (tt0) REVERT: A 833 ASP cc_start: 0.6669 (p0) cc_final: 0.6353 (t0) REVERT: A 844 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6862 (m-80) REVERT: A 1082 GLU cc_start: 0.6882 (tp30) cc_final: 0.6134 (tp30) REVERT: A 1101 TYR cc_start: 0.8080 (t80) cc_final: 0.7784 (t80) REVERT: A 1206 TYR cc_start: 0.8497 (t80) cc_final: 0.8213 (t80) REVERT: B 160 GLU cc_start: 0.6940 (tt0) cc_final: 0.6209 (tm-30) REVERT: B 199 TYR cc_start: 0.6457 (t80) cc_final: 0.6141 (t80) REVERT: B 246 LEU cc_start: 0.6512 (mt) cc_final: 0.6204 (mp) REVERT: B 283 ILE cc_start: 0.6905 (mt) cc_final: 0.6681 (mt) REVERT: B 315 ASN cc_start: 0.6472 (p0) cc_final: 0.6181 (p0) REVERT: B 371 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.6985 (p0) REVERT: B 833 ASP cc_start: 0.6614 (p0) cc_final: 0.6234 (t0) REVERT: B 1082 GLU cc_start: 0.6768 (tp30) cc_final: 0.6134 (tp30) REVERT: B 1101 TYR cc_start: 0.7962 (t80) cc_final: 0.7644 (t80) REVERT: B 1206 TYR cc_start: 0.8538 (t80) cc_final: 0.8314 (t80) REVERT: C 158 LEU cc_start: 0.6849 (pp) cc_final: 0.5950 (mp) REVERT: C 160 GLU cc_start: 0.7217 (tt0) cc_final: 0.6522 (tm-30) REVERT: C 199 TYR cc_start: 0.6397 (t80) cc_final: 0.6082 (t80) REVERT: C 315 ASN cc_start: 0.6571 (p0) cc_final: 0.6258 (p0) REVERT: C 720 GLN cc_start: 0.7015 (pm20) cc_final: 0.6196 (tt0) REVERT: C 794 VAL cc_start: 0.7386 (t) cc_final: 0.7103 (m) REVERT: C 833 ASP cc_start: 0.6837 (p0) cc_final: 0.6463 (t0) REVERT: C 844 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: C 1082 GLU cc_start: 0.6793 (tp30) cc_final: 0.6089 (tp30) REVERT: C 1101 TYR cc_start: 0.8004 (t80) cc_final: 0.7634 (t80) REVERT: C 1206 TYR cc_start: 0.8383 (t80) cc_final: 0.8139 (t80) outliers start: 67 outliers final: 47 residues processed: 530 average time/residue: 0.1560 time to fit residues: 138.9696 Evaluate side-chains 460 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 410 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 844 TYR Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 1012 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1187 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 239 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 333 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 346 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 421 ASN A 429 ASN A1092 ASN A1158 HIS B 239 ASN B 369 ASN B 421 ASN B 429 ASN B1158 HIS C 183 HIS C 421 ASN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 ASN C1158 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134352 restraints weight = 36530.671| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.18 r_work: 0.3459 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28767 Z= 0.173 Angle : 0.671 11.461 39279 Z= 0.355 Chirality : 0.049 0.328 4542 Planarity : 0.004 0.052 4968 Dihedral : 6.249 46.185 4749 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.78 % Allowed : 10.25 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.13), residues: 3477 helix: -0.26 (0.18), residues: 765 sheet: -0.25 (0.17), residues: 774 loop : -0.26 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.036 0.002 TYR A 75 PHE 0.021 0.002 PHE C 238 TRP 0.021 0.002 TRP A 360 HIS 0.007 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00396 (28659) covalent geometry : angle 0.65455 (39018) SS BOND : bond 0.00381 ( 63) SS BOND : angle 1.36793 ( 126) hydrogen bonds : bond 0.04848 ( 1041) hydrogen bonds : angle 6.31933 ( 2994) link_BETA1-4 : bond 0.00580 ( 9) link_BETA1-4 : angle 2.61265 ( 27) link_NAG-ASN : bond 0.00557 ( 36) link_NAG-ASN : angle 2.25065 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 459 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7156 (pp) cc_final: 0.6188 (mp) REVERT: A 160 GLU cc_start: 0.7207 (tt0) cc_final: 0.6548 (tm-30) REVERT: A 224 TYR cc_start: 0.7436 (m-80) cc_final: 0.7079 (m-80) REVERT: A 371 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.6906 (p0) REVERT: A 720 GLN cc_start: 0.6878 (pm20) cc_final: 0.6035 (tt0) REVERT: A 833 ASP cc_start: 0.6877 (p0) cc_final: 0.6360 (t0) REVERT: A 844 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: A 1082 GLU cc_start: 0.7024 (tp30) cc_final: 0.6288 (tp30) REVERT: A 1101 TYR cc_start: 0.7874 (t80) cc_final: 0.7663 (t80) REVERT: A 1206 TYR cc_start: 0.8540 (t80) cc_final: 0.8252 (t80) REVERT: B 104 PHE cc_start: 0.7260 (t80) cc_final: 0.6802 (t80) REVERT: B 160 GLU cc_start: 0.7162 (tt0) cc_final: 0.6524 (tm-30) REVERT: B 371 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7105 (p0) REVERT: B 794 VAL cc_start: 0.7588 (t) cc_final: 0.6785 (m) REVERT: B 833 ASP cc_start: 0.6816 (p0) cc_final: 0.6345 (t0) REVERT: B 844 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: B 925 LYS cc_start: 0.7471 (mmtt) cc_final: 0.6815 (mptt) REVERT: B 1082 GLU cc_start: 0.6853 (tp30) cc_final: 0.6207 (tp30) REVERT: B 1101 TYR cc_start: 0.7861 (t80) cc_final: 0.7649 (t80) REVERT: B 1170 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7154 (mtp85) REVERT: B 1206 TYR cc_start: 0.8581 (t80) cc_final: 0.8355 (t80) REVERT: C 158 LEU cc_start: 0.6960 (pp) cc_final: 0.6067 (mp) REVERT: C 160 GLU cc_start: 0.7359 (tt0) cc_final: 0.6713 (tm-30) REVERT: C 249 TYR cc_start: 0.6964 (p90) cc_final: 0.6682 (p90) REVERT: C 371 ASN cc_start: 0.7369 (OUTLIER) cc_final: 0.6804 (p0) REVERT: C 454 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.6213 (ptp90) REVERT: C 794 VAL cc_start: 0.7635 (t) cc_final: 0.7428 (m) REVERT: C 833 ASP cc_start: 0.7041 (p0) cc_final: 0.6485 (t0) REVERT: C 844 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: C 1026 TYR cc_start: 0.7029 (t80) cc_final: 0.6813 (t80) REVERT: C 1082 GLU cc_start: 0.6889 (tp30) cc_final: 0.6158 (tp30) REVERT: C 1101 TYR cc_start: 0.7935 (t80) cc_final: 0.7670 (t80) outliers start: 85 outliers final: 60 residues processed: 507 average time/residue: 0.1426 time to fit residues: 121.5016 Evaluate side-chains 475 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 408 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 844 TYR Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 1217 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 1008 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 108 optimal weight: 0.1980 chunk 345 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 329 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 106 optimal weight: 0.3980 chunk 209 optimal weight: 0.0370 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN B 215 HIS B 339 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133063 restraints weight = 36348.301| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.16 r_work: 0.3447 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28767 Z= 0.173 Angle : 0.640 10.065 39279 Z= 0.337 Chirality : 0.048 0.297 4542 Planarity : 0.004 0.052 4968 Dihedral : 5.638 30.709 4749 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.81 % Allowed : 11.85 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.14), residues: 3477 helix: -0.18 (0.18), residues: 774 sheet: -0.42 (0.18), residues: 702 loop : -0.50 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 687 TYR 0.037 0.002 TYR C 75 PHE 0.019 0.002 PHE A 278 TRP 0.024 0.002 TRP C 360 HIS 0.011 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00405 (28659) covalent geometry : angle 0.62343 (39018) SS BOND : bond 0.00513 ( 63) SS BOND : angle 1.45396 ( 126) hydrogen bonds : bond 0.04515 ( 1041) hydrogen bonds : angle 6.16593 ( 2994) link_BETA1-4 : bond 0.00461 ( 9) link_BETA1-4 : angle 2.32567 ( 27) link_NAG-ASN : bond 0.00431 ( 36) link_NAG-ASN : angle 2.20280 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 436 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7125 (pp) cc_final: 0.6216 (mp) REVERT: A 160 GLU cc_start: 0.7260 (tt0) cc_final: 0.6653 (tm-30) REVERT: A 166 TYR cc_start: 0.7692 (m-80) cc_final: 0.7214 (m-10) REVERT: A 224 TYR cc_start: 0.7533 (m-80) cc_final: 0.7248 (m-80) REVERT: A 371 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.6985 (p0) REVERT: A 720 GLN cc_start: 0.6882 (pm20) cc_final: 0.6011 (tt0) REVERT: A 844 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: A 1082 GLU cc_start: 0.7072 (tp30) cc_final: 0.6296 (tp30) REVERT: A 1170 ARG cc_start: 0.7540 (ttm110) cc_final: 0.7176 (mtp85) REVERT: A 1206 TYR cc_start: 0.8558 (t80) cc_final: 0.8334 (t80) REVERT: B 160 GLU cc_start: 0.7130 (tt0) cc_final: 0.6583 (tm-30) REVERT: B 371 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.7170 (p0) REVERT: B 794 VAL cc_start: 0.7687 (t) cc_final: 0.6947 (m) REVERT: B 833 ASP cc_start: 0.7016 (p0) cc_final: 0.6344 (t0) REVERT: B 844 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: B 925 LYS cc_start: 0.7478 (mmtt) cc_final: 0.6828 (mptt) REVERT: B 1082 GLU cc_start: 0.6921 (tp30) cc_final: 0.6245 (tp30) REVERT: B 1170 ARG cc_start: 0.7476 (ttm110) cc_final: 0.7152 (mtp85) REVERT: B 1206 TYR cc_start: 0.8535 (t80) cc_final: 0.8300 (t80) REVERT: C 158 LEU cc_start: 0.7003 (pp) cc_final: 0.6083 (mp) REVERT: C 160 GLU cc_start: 0.7262 (tt0) cc_final: 0.6636 (tm-30) REVERT: C 249 TYR cc_start: 0.6855 (p90) cc_final: 0.6641 (p90) REVERT: C 371 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.6910 (p0) REVERT: C 455 PHE cc_start: 0.7334 (t80) cc_final: 0.6570 (m-80) REVERT: C 720 GLN cc_start: 0.6939 (pm20) cc_final: 0.6095 (tt0) REVERT: C 844 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: C 1028 ILE cc_start: 0.7831 (mt) cc_final: 0.7607 (mm) REVERT: C 1082 GLU cc_start: 0.6916 (tp30) cc_final: 0.6139 (tp30) outliers start: 86 outliers final: 60 residues processed: 490 average time/residue: 0.1618 time to fit residues: 133.1107 Evaluate side-chains 466 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 400 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 844 TYR Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 718 THR Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 1008 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 135 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 280 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN B 871 ASN C 215 HIS ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 665 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131761 restraints weight = 36489.593| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.15 r_work: 0.3435 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28767 Z= 0.198 Angle : 0.658 8.675 39279 Z= 0.346 Chirality : 0.049 0.373 4542 Planarity : 0.005 0.062 4968 Dihedral : 5.698 33.940 4749 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.66 % Allowed : 12.80 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.14), residues: 3477 helix: 0.07 (0.19), residues: 738 sheet: -0.62 (0.19), residues: 660 loop : -0.73 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.038 0.002 TYR B 75 PHE 0.022 0.002 PHE B 278 TRP 0.030 0.002 TRP B 360 HIS 0.010 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00467 (28659) covalent geometry : angle 0.64135 (39018) SS BOND : bond 0.00409 ( 63) SS BOND : angle 1.36783 ( 126) hydrogen bonds : bond 0.04604 ( 1041) hydrogen bonds : angle 6.19781 ( 2994) link_BETA1-4 : bond 0.00402 ( 9) link_BETA1-4 : angle 1.96562 ( 27) link_NAG-ASN : bond 0.00742 ( 36) link_NAG-ASN : angle 2.36216 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 428 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.6905 (t) cc_final: 0.6637 (m) REVERT: A 55 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6898 (mtt180) REVERT: A 76 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5580 (mpt-90) REVERT: A 154 LYS cc_start: 0.4561 (mttt) cc_final: 0.2654 (tptm) REVERT: A 158 LEU cc_start: 0.7138 (pp) cc_final: 0.6235 (mp) REVERT: A 160 GLU cc_start: 0.7311 (tt0) cc_final: 0.6715 (tm-30) REVERT: A 224 TYR cc_start: 0.7619 (m-80) cc_final: 0.7372 (m-80) REVERT: A 244 MET cc_start: 0.7741 (ptt) cc_final: 0.7335 (mmt) REVERT: A 371 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7069 (p0) REVERT: A 382 ASP cc_start: 0.6783 (t70) cc_final: 0.6175 (t0) REVERT: A 540 ILE cc_start: 0.6850 (mt) cc_final: 0.6424 (pt) REVERT: A 1170 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7216 (mtp85) REVERT: B 55 ARG cc_start: 0.7064 (mtp85) cc_final: 0.6819 (mtt-85) REVERT: B 76 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.5508 (mpt-90) REVERT: B 158 LEU cc_start: 0.6867 (pp) cc_final: 0.5893 (mp) REVERT: B 160 GLU cc_start: 0.7244 (tt0) cc_final: 0.6633 (tm-30) REVERT: B 283 ILE cc_start: 0.7321 (mt) cc_final: 0.7075 (mm) REVERT: B 371 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7320 (p0) REVERT: B 382 ASP cc_start: 0.6864 (t70) cc_final: 0.6237 (t0) REVERT: B 794 VAL cc_start: 0.7792 (t) cc_final: 0.7165 (m) REVERT: B 844 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: B 925 LYS cc_start: 0.7537 (mmtt) cc_final: 0.6914 (mptt) REVERT: B 1170 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7183 (mtp85) REVERT: B 1206 TYR cc_start: 0.8549 (t80) cc_final: 0.8313 (t80) REVERT: C 22 THR cc_start: 0.6932 (t) cc_final: 0.6671 (m) REVERT: C 50 TYR cc_start: 0.7765 (p90) cc_final: 0.7425 (p90) REVERT: C 76 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5308 (mpt-90) REVERT: C 158 LEU cc_start: 0.7057 (pp) cc_final: 0.6125 (mp) REVERT: C 160 GLU cc_start: 0.7339 (tt0) cc_final: 0.6721 (tm-30) REVERT: C 244 MET cc_start: 0.7669 (ptt) cc_final: 0.7398 (mmt) REVERT: C 371 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.7012 (p0) REVERT: C 455 PHE cc_start: 0.7441 (t80) cc_final: 0.6589 (m-80) REVERT: C 720 GLN cc_start: 0.6969 (pm20) cc_final: 0.6111 (tt0) REVERT: C 844 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.7001 (m-80) REVERT: C 1170 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7140 (mtp85) outliers start: 112 outliers final: 79 residues processed: 507 average time/residue: 0.1604 time to fit residues: 135.1258 Evaluate side-chains 468 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 381 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 844 TYR Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1187 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 147 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN A 871 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 871 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.152954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130776 restraints weight = 36803.759| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.14 r_work: 0.3422 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 28767 Z= 0.227 Angle : 0.689 13.072 39279 Z= 0.362 Chirality : 0.049 0.285 4542 Planarity : 0.005 0.066 4968 Dihedral : 5.821 38.366 4749 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.18 % Allowed : 13.91 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3477 helix: 0.10 (0.19), residues: 705 sheet: -0.76 (0.19), residues: 684 loop : -0.93 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1133 TYR 0.042 0.002 TYR B 75 PHE 0.022 0.002 PHE A 278 TRP 0.033 0.002 TRP C 360 HIS 0.010 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00539 (28659) covalent geometry : angle 0.67039 (39018) SS BOND : bond 0.00384 ( 63) SS BOND : angle 1.84527 ( 126) hydrogen bonds : bond 0.04802 ( 1041) hydrogen bonds : angle 6.27414 ( 2994) link_BETA1-4 : bond 0.00366 ( 9) link_BETA1-4 : angle 1.87759 ( 27) link_NAG-ASN : bond 0.00437 ( 36) link_NAG-ASN : angle 2.33784 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 404 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.5548 (mpt-90) REVERT: A 154 LYS cc_start: 0.4615 (mttt) cc_final: 0.2742 (tptm) REVERT: A 158 LEU cc_start: 0.7114 (pp) cc_final: 0.6185 (mt) REVERT: A 160 GLU cc_start: 0.7466 (tt0) cc_final: 0.6763 (tm-30) REVERT: A 177 HIS cc_start: 0.6985 (t-170) cc_final: 0.6690 (t-170) REVERT: A 185 LYS cc_start: 0.6083 (mmtt) cc_final: 0.5301 (mttt) REVERT: A 224 TYR cc_start: 0.7675 (m-80) cc_final: 0.7430 (m-80) REVERT: A 244 MET cc_start: 0.7816 (ptt) cc_final: 0.7377 (mmt) REVERT: A 325 TYR cc_start: 0.6463 (OUTLIER) cc_final: 0.4381 (m-80) REVERT: A 371 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7134 (p0) REVERT: A 382 ASP cc_start: 0.6820 (t70) cc_final: 0.6205 (t0) REVERT: A 603 PHE cc_start: 0.5457 (OUTLIER) cc_final: 0.5098 (m-10) REVERT: A 720 GLN cc_start: 0.7014 (pm20) cc_final: 0.6138 (tt0) REVERT: A 1030 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.6100 (mt-10) REVERT: A 1170 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7216 (mtp85) REVERT: B 76 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.5548 (mpt-90) REVERT: B 118 MET cc_start: 0.5203 (mmp) cc_final: 0.4909 (mmp) REVERT: B 158 LEU cc_start: 0.6905 (pp) cc_final: 0.5945 (mp) REVERT: B 160 GLU cc_start: 0.7444 (tt0) cc_final: 0.6720 (tm-30) REVERT: B 185 LYS cc_start: 0.5917 (mmtt) cc_final: 0.5178 (mtmt) REVERT: B 187 LEU cc_start: 0.7741 (tp) cc_final: 0.7500 (tp) REVERT: B 325 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.4293 (m-80) REVERT: B 382 ASP cc_start: 0.6980 (t70) cc_final: 0.6379 (t0) REVERT: B 794 VAL cc_start: 0.7859 (t) cc_final: 0.7293 (m) REVERT: B 844 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: B 925 LYS cc_start: 0.7552 (mmtt) cc_final: 0.6945 (mptt) REVERT: B 1170 ARG cc_start: 0.7577 (ttm110) cc_final: 0.7213 (mtp85) REVERT: B 1206 TYR cc_start: 0.8540 (t80) cc_final: 0.8324 (t80) REVERT: C 76 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5365 (mpt-90) REVERT: C 158 LEU cc_start: 0.7029 (pp) cc_final: 0.6203 (mp) REVERT: C 160 GLU cc_start: 0.7414 (tt0) cc_final: 0.6751 (tm-30) REVERT: C 185 LYS cc_start: 0.5990 (mmtt) cc_final: 0.5210 (mtmt) REVERT: C 244 MET cc_start: 0.7799 (ptt) cc_final: 0.7438 (mmt) REVERT: C 371 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7134 (p0) REVERT: C 382 ASP cc_start: 0.6752 (t70) cc_final: 0.6298 (t0) REVERT: C 720 GLN cc_start: 0.7019 (pm20) cc_final: 0.6147 (tt0) REVERT: C 844 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: C 1170 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7152 (mtp85) outliers start: 128 outliers final: 96 residues processed: 495 average time/residue: 0.1639 time to fit residues: 134.7944 Evaluate side-chains 476 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 369 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 844 TYR Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1008 ASP Chi-restraints excluded: chain C residue 1187 SER Chi-restraints excluded: chain C residue 1215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 188 optimal weight: 0.8980 chunk 311 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 201 optimal weight: 0.4980 chunk 221 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN ** C 429 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 = 0.3820 r_free = 0.3820 target = 0.156171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134002 restraints weight = 36308.181| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.15 r_work: 0.3466 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28767 Z= 0.131 Angle : 0.598 12.104 39279 Z= 0.313 Chirality : 0.046 0.267 4542 Planarity : 0.004 0.051 4968 Dihedral : 5.385 37.949 4749 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.55 % Allowed : 16.03 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3477 helix: 0.33 (0.19), residues: 726 sheet: -0.79 (0.18), residues: 738 loop : -0.83 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1094 TYR 0.036 0.002 TYR B 75 PHE 0.023 0.002 PHE C 278 TRP 0.022 0.002 TRP C 360 HIS 0.008 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00302 (28659) covalent geometry : angle 0.57981 (39018) SS BOND : bond 0.00239 ( 63) SS BOND : angle 1.68005 ( 126) hydrogen bonds : bond 0.04014 ( 1041) hydrogen bonds : angle 5.94642 ( 2994) link_BETA1-4 : bond 0.00361 ( 9) link_BETA1-4 : angle 1.53895 ( 27) link_NAG-ASN : bond 0.00413 ( 36) link_NAG-ASN : angle 2.16847 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 417 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.5493 (mpt-90) REVERT: A 154 LYS cc_start: 0.4565 (mttt) cc_final: 0.3219 (pttp) REVERT: A 158 LEU cc_start: 0.7034 (pp) cc_final: 0.6152 (mt) REVERT: A 160 GLU cc_start: 0.7553 (tt0) cc_final: 0.6816 (tm-30) REVERT: A 166 TYR cc_start: 0.7755 (m-80) cc_final: 0.7148 (m-10) REVERT: A 177 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6432 (t-170) REVERT: A 185 LYS cc_start: 0.6002 (mmtt) cc_final: 0.5263 (mttt) REVERT: A 224 TYR cc_start: 0.7561 (m-80) cc_final: 0.7282 (m-80) REVERT: A 244 MET cc_start: 0.7642 (ptt) cc_final: 0.7313 (mmt) REVERT: A 371 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7005 (p0) REVERT: A 382 ASP cc_start: 0.6674 (t70) cc_final: 0.6137 (t0) REVERT: A 389 ILE cc_start: 0.5983 (tt) cc_final: 0.5680 (tt) REVERT: A 658 LEU cc_start: 0.7087 (mp) cc_final: 0.6678 (mt) REVERT: A 720 GLN cc_start: 0.7009 (pm20) cc_final: 0.6165 (tt0) REVERT: A 1170 ARG cc_start: 0.7568 (ttm110) cc_final: 0.7176 (mtp85) REVERT: B 76 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.5472 (mpt-90) REVERT: B 158 LEU cc_start: 0.6707 (pp) cc_final: 0.5902 (mp) REVERT: B 160 GLU cc_start: 0.7446 (tt0) cc_final: 0.6763 (tm-30) REVERT: B 166 TYR cc_start: 0.7703 (m-80) cc_final: 0.7379 (m-10) REVERT: B 244 MET cc_start: 0.7828 (ptt) cc_final: 0.7394 (mmt) REVERT: B 283 ILE cc_start: 0.7360 (mt) cc_final: 0.7106 (mm) REVERT: B 285 PHE cc_start: 0.7268 (p90) cc_final: 0.7032 (p90) REVERT: B 382 ASP cc_start: 0.6847 (t70) cc_final: 0.6303 (t0) REVERT: B 617 ASP cc_start: 0.7243 (m-30) cc_final: 0.6444 (m-30) REVERT: B 634 ASP cc_start: 0.6886 (t0) cc_final: 0.6684 (t0) REVERT: B 844 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6955 (m-80) REVERT: B 925 LYS cc_start: 0.7507 (mmtt) cc_final: 0.6871 (mptt) REVERT: C 57 TYR cc_start: 0.7291 (m-80) cc_final: 0.7046 (m-80) REVERT: C 76 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.5243 (mpt-90) REVERT: C 158 LEU cc_start: 0.6903 (pp) cc_final: 0.6132 (mp) REVERT: C 160 GLU cc_start: 0.7465 (tt0) cc_final: 0.6740 (tm-30) REVERT: C 185 LYS cc_start: 0.6080 (mmtt) cc_final: 0.5281 (mtmt) REVERT: C 234 THR cc_start: 0.8507 (p) cc_final: 0.8301 (p) REVERT: C 244 MET cc_start: 0.7601 (ptt) cc_final: 0.7395 (mmt) REVERT: C 371 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.6974 (p0) REVERT: C 382 ASP cc_start: 0.6650 (t70) cc_final: 0.6112 (t0) REVERT: C 720 GLN cc_start: 0.7058 (pm20) cc_final: 0.6186 (tt0) REVERT: C 844 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6973 (m-80) REVERT: C 1170 ARG cc_start: 0.7459 (ttm110) cc_final: 0.7110 (mtp85) outliers start: 78 outliers final: 61 residues processed: 469 average time/residue: 0.1627 time to fit residues: 126.1772 Evaluate side-chains 450 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 381 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 837 CYS Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 844 TYR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 1008 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 162 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1012 GLN C 426 GLN ** C 429 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 = 0.3792 r_free = 0.3792 target = 0.153583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131351 restraints weight = 36792.181| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.14 r_work: 0.3435 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 28767 Z= 0.214 Angle : 0.685 11.468 39279 Z= 0.356 Chirality : 0.049 0.263 4542 Planarity : 0.005 0.061 4968 Dihedral : 5.694 41.112 4749 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.26 % Allowed : 16.36 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.14), residues: 3477 helix: 0.01 (0.19), residues: 747 sheet: -0.79 (0.19), residues: 720 loop : -0.97 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1133 TYR 0.036 0.002 TYR C 75 PHE 0.022 0.002 PHE A 238 TRP 0.033 0.002 TRP C 360 HIS 0.009 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00512 (28659) covalent geometry : angle 0.66568 (39018) SS BOND : bond 0.00572 ( 63) SS BOND : angle 1.99848 ( 126) hydrogen bonds : bond 0.04604 ( 1041) hydrogen bonds : angle 6.17098 ( 2994) link_BETA1-4 : bond 0.00344 ( 9) link_BETA1-4 : angle 1.70286 ( 27) link_NAG-ASN : bond 0.00411 ( 36) link_NAG-ASN : angle 2.22422 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 386 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5565 (mpt-90) REVERT: A 154 LYS cc_start: 0.4613 (mttt) cc_final: 0.2776 (tptm) REVERT: A 158 LEU cc_start: 0.7080 (pp) cc_final: 0.6149 (mt) REVERT: A 160 GLU cc_start: 0.7659 (tt0) cc_final: 0.6939 (tm-30) REVERT: A 169 CYS cc_start: 0.5270 (m) cc_final: 0.4998 (m) REVERT: A 177 HIS cc_start: 0.6705 (OUTLIER) cc_final: 0.6345 (t-170) REVERT: A 185 LYS cc_start: 0.6142 (mmtt) cc_final: 0.5370 (mttt) REVERT: A 224 TYR cc_start: 0.7675 (m-80) cc_final: 0.7418 (m-80) REVERT: A 244 MET cc_start: 0.7800 (ptt) cc_final: 0.7427 (mmt) REVERT: A 371 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7229 (p0) REVERT: A 382 ASP cc_start: 0.6787 (t70) cc_final: 0.6190 (t0) REVERT: A 720 GLN cc_start: 0.6937 (pm20) cc_final: 0.6089 (tt0) REVERT: A 1129 SER cc_start: 0.7370 (t) cc_final: 0.7076 (m) REVERT: A 1170 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7192 (mtp85) REVERT: B 76 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5509 (mpt-90) REVERT: B 154 LYS cc_start: 0.4649 (mttt) cc_final: 0.2794 (tptm) REVERT: B 158 LEU cc_start: 0.6858 (pp) cc_final: 0.5942 (mp) REVERT: B 160 GLU cc_start: 0.7584 (tt0) cc_final: 0.6821 (tm-30) REVERT: B 166 TYR cc_start: 0.7792 (m-80) cc_final: 0.7409 (m-10) REVERT: B 185 LYS cc_start: 0.5942 (mmtt) cc_final: 0.5200 (mtmt) REVERT: B 244 MET cc_start: 0.7963 (ptt) cc_final: 0.7487 (mmt) REVERT: B 285 PHE cc_start: 0.7350 (p90) cc_final: 0.6972 (p90) REVERT: B 382 ASP cc_start: 0.6940 (t70) cc_final: 0.6381 (t0) REVERT: B 617 ASP cc_start: 0.7480 (m-30) cc_final: 0.7000 (m-30) REVERT: B 844 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: B 925 LYS cc_start: 0.7565 (mmtt) cc_final: 0.6957 (mptt) REVERT: B 1129 SER cc_start: 0.7399 (t) cc_final: 0.7141 (m) REVERT: B 1133 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7863 (ttm170) REVERT: B 1170 ARG cc_start: 0.7609 (ttm110) cc_final: 0.7272 (mtp85) REVERT: C 50 TYR cc_start: 0.7807 (p90) cc_final: 0.7452 (p90) REVERT: C 76 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.5325 (mpt-90) REVERT: C 158 LEU cc_start: 0.6987 (pp) cc_final: 0.6124 (mt) REVERT: C 160 GLU cc_start: 0.7567 (tt0) cc_final: 0.6851 (tm-30) REVERT: C 185 LYS cc_start: 0.6196 (mmtt) cc_final: 0.5357 (mtmt) REVERT: C 244 MET cc_start: 0.7754 (ptt) cc_final: 0.7469 (mmt) REVERT: C 371 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7127 (p0) REVERT: C 382 ASP cc_start: 0.6732 (t70) cc_final: 0.6296 (t0) REVERT: C 720 GLN cc_start: 0.7054 (pm20) cc_final: 0.6185 (tt0) REVERT: C 844 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: C 1170 ARG cc_start: 0.7463 (ttm110) cc_final: 0.7124 (mtp85) outliers start: 100 outliers final: 78 residues processed: 455 average time/residue: 0.1616 time to fit residues: 122.2665 Evaluate side-chains 452 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 366 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 837 CYS Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 844 TYR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 1008 ASP Chi-restraints excluded: chain C residue 1012 GLN Chi-restraints excluded: chain C residue 1215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 226 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 198 optimal weight: 0.8980 chunk 339 optimal weight: 6.9990 chunk 345 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 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 = 0.3803 r_free = 0.3803 target = 0.154539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132446 restraints weight = 36655.308| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.12 r_work: 0.3449 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 28767 Z= 0.182 Angle : 0.666 12.279 39279 Z= 0.345 Chirality : 0.048 0.256 4542 Planarity : 0.005 0.055 4968 Dihedral : 5.643 41.898 4749 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.10 % Allowed : 17.04 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.14), residues: 3477 helix: 0.02 (0.19), residues: 753 sheet: -0.80 (0.19), residues: 717 loop : -1.00 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 336 TYR 0.036 0.002 TYR B 75 PHE 0.033 0.002 PHE B 238 TRP 0.036 0.002 TRP C 360 HIS 0.009 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00434 (28659) covalent geometry : angle 0.64534 (39018) SS BOND : bond 0.00445 ( 63) SS BOND : angle 2.12180 ( 126) hydrogen bonds : bond 0.04377 ( 1041) hydrogen bonds : angle 6.10946 ( 2994) link_BETA1-4 : bond 0.00367 ( 9) link_BETA1-4 : angle 1.63753 ( 27) link_NAG-ASN : bond 0.00378 ( 36) link_NAG-ASN : angle 2.18169 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 377 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5509 (mpt-90) REVERT: A 154 LYS cc_start: 0.4763 (mttt) cc_final: 0.3440 (pttp) REVERT: A 158 LEU cc_start: 0.7031 (pp) cc_final: 0.6149 (mt) REVERT: A 160 GLU cc_start: 0.7733 (tt0) cc_final: 0.6966 (tm-30) REVERT: A 166 TYR cc_start: 0.7794 (m-80) cc_final: 0.7307 (m-10) REVERT: A 177 HIS cc_start: 0.6721 (OUTLIER) cc_final: 0.6385 (t-170) REVERT: A 185 LYS cc_start: 0.6104 (mmtt) cc_final: 0.5367 (mttt) REVERT: A 224 TYR cc_start: 0.7647 (m-80) cc_final: 0.7383 (m-80) REVERT: A 244 MET cc_start: 0.7742 (ptt) cc_final: 0.7381 (mmt) REVERT: A 371 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7147 (p0) REVERT: A 382 ASP cc_start: 0.6733 (t70) cc_final: 0.6189 (t0) REVERT: A 617 ASP cc_start: 0.7371 (m-30) cc_final: 0.6957 (m-30) REVERT: A 658 LEU cc_start: 0.7071 (mp) cc_final: 0.6710 (mt) REVERT: A 720 GLN cc_start: 0.6934 (pm20) cc_final: 0.6091 (tt0) REVERT: A 1170 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7226 (mtp85) REVERT: B 76 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.5536 (mpt-90) REVERT: B 154 LYS cc_start: 0.4688 (mttt) cc_final: 0.2900 (tptm) REVERT: B 158 LEU cc_start: 0.6856 (pp) cc_final: 0.5919 (mp) REVERT: B 160 GLU cc_start: 0.7641 (tt0) cc_final: 0.6880 (tm-30) REVERT: B 166 TYR cc_start: 0.7796 (m-80) cc_final: 0.7351 (m-10) REVERT: B 169 CYS cc_start: 0.5440 (m) cc_final: 0.5201 (m) REVERT: B 185 LYS cc_start: 0.6014 (mmtt) cc_final: 0.5295 (mtmt) REVERT: B 244 MET cc_start: 0.7943 (ptt) cc_final: 0.7489 (mmt) REVERT: B 285 PHE cc_start: 0.7292 (p90) cc_final: 0.6965 (p90) REVERT: B 378 PHE cc_start: 0.6855 (m-10) cc_final: 0.6603 (m-80) REVERT: B 382 ASP cc_start: 0.6916 (t70) cc_final: 0.6359 (t0) REVERT: B 617 ASP cc_start: 0.7427 (m-30) cc_final: 0.6946 (m-30) REVERT: B 844 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: B 925 LYS cc_start: 0.7559 (mmtt) cc_final: 0.6950 (mptt) REVERT: B 1129 SER cc_start: 0.7379 (t) cc_final: 0.7116 (m) REVERT: B 1133 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7801 (ttm170) REVERT: C 50 TYR cc_start: 0.7740 (p90) cc_final: 0.7424 (p90) REVERT: C 76 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.5314 (mpt-90) REVERT: C 158 LEU cc_start: 0.6968 (pp) cc_final: 0.6124 (mt) REVERT: C 160 GLU cc_start: 0.7589 (tt0) cc_final: 0.6850 (tm-30) REVERT: C 185 LYS cc_start: 0.6136 (mmtt) cc_final: 0.5386 (mtmt) REVERT: C 234 THR cc_start: 0.8624 (p) cc_final: 0.8382 (p) REVERT: C 244 MET cc_start: 0.7702 (ptt) cc_final: 0.7470 (mmt) REVERT: C 371 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7091 (p0) REVERT: C 382 ASP cc_start: 0.6724 (t70) cc_final: 0.6285 (t0) REVERT: C 462 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8174 (mttm) REVERT: C 720 GLN cc_start: 0.7052 (pm20) cc_final: 0.6180 (tt0) REVERT: C 844 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: C 1170 ARG cc_start: 0.7483 (ttm110) cc_final: 0.7138 (mtp85) outliers start: 95 outliers final: 82 residues processed: 444 average time/residue: 0.1618 time to fit residues: 119.5323 Evaluate side-chains 457 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 367 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 837 CYS Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 844 TYR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 325 TYR Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 1008 ASP Chi-restraints excluded: chain C residue 1215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 188 optimal weight: 0.0070 chunk 241 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 268 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 ASN ** C 429 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 = 0.3833 r_free = 0.3833 target = 0.157289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135035 restraints weight = 36428.220| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.15 r_work: 0.3479 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 28767 Z= 0.127 Angle : 0.605 13.267 39279 Z= 0.313 Chirality : 0.046 0.258 4542 Planarity : 0.004 0.042 4968 Dihedral : 5.270 39.779 4749 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.38 % Allowed : 17.86 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.14), residues: 3477 helix: 0.30 (0.19), residues: 762 sheet: -0.83 (0.19), residues: 738 loop : -0.89 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1094 TYR 0.030 0.002 TYR B 75 PHE 0.029 0.002 PHE B 238 TRP 0.039 0.002 TRP C 360 HIS 0.009 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00300 (28659) covalent geometry : angle 0.58536 (39018) SS BOND : bond 0.00359 ( 63) SS BOND : angle 1.98166 ( 126) hydrogen bonds : bond 0.03852 ( 1041) hydrogen bonds : angle 5.86575 ( 2994) link_BETA1-4 : bond 0.00417 ( 9) link_BETA1-4 : angle 1.41832 ( 27) link_NAG-ASN : bond 0.00389 ( 36) link_NAG-ASN : angle 2.05977 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 408 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 CYS cc_start: 0.4624 (OUTLIER) cc_final: 0.3181 (p) REVERT: A 57 TYR cc_start: 0.7216 (m-80) cc_final: 0.7014 (m-80) REVERT: A 76 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.5423 (mpt-90) REVERT: A 154 LYS cc_start: 0.4725 (mttt) cc_final: 0.2906 (tptm) REVERT: A 158 LEU cc_start: 0.6882 (pp) cc_final: 0.6111 (mt) REVERT: A 160 GLU cc_start: 0.7762 (tt0) cc_final: 0.6987 (tm-30) REVERT: A 166 TYR cc_start: 0.7783 (m-80) cc_final: 0.7359 (m-10) REVERT: A 177 HIS cc_start: 0.6654 (OUTLIER) cc_final: 0.6342 (t-170) REVERT: A 185 LYS cc_start: 0.6127 (mmtt) cc_final: 0.5376 (mttt) REVERT: A 224 TYR cc_start: 0.7570 (m-80) cc_final: 0.7304 (m-80) REVERT: A 234 THR cc_start: 0.8471 (p) cc_final: 0.8199 (p) REVERT: A 244 MET cc_start: 0.7576 (ptt) cc_final: 0.7310 (mmt) REVERT: A 371 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7120 (p0) REVERT: A 382 ASP cc_start: 0.6550 (t70) cc_final: 0.6110 (t0) REVERT: A 389 ILE cc_start: 0.5920 (tt) cc_final: 0.5649 (tt) REVERT: A 617 ASP cc_start: 0.7100 (m-30) cc_final: 0.6350 (m-30) REVERT: A 658 LEU cc_start: 0.7010 (mp) cc_final: 0.6652 (mt) REVERT: A 720 GLN cc_start: 0.6911 (pm20) cc_final: 0.6105 (tt0) REVERT: B 76 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.5404 (mpt-90) REVERT: B 154 LYS cc_start: 0.4673 (mttt) cc_final: 0.2898 (tptm) REVERT: B 158 LEU cc_start: 0.6639 (pp) cc_final: 0.5899 (mp) REVERT: B 160 GLU cc_start: 0.7654 (tt0) cc_final: 0.6859 (tm-30) REVERT: B 166 TYR cc_start: 0.7724 (m-80) cc_final: 0.7309 (m-10) REVERT: B 169 CYS cc_start: 0.5423 (m) cc_final: 0.5107 (m) REVERT: B 234 THR cc_start: 0.8535 (p) cc_final: 0.8305 (p) REVERT: B 244 MET cc_start: 0.7869 (ptt) cc_final: 0.7472 (mmt) REVERT: B 283 ILE cc_start: 0.7289 (mt) cc_final: 0.7066 (mm) REVERT: B 378 PHE cc_start: 0.6754 (m-10) cc_final: 0.6537 (m-80) REVERT: B 382 ASP cc_start: 0.6746 (t70) cc_final: 0.6272 (t0) REVERT: B 617 ASP cc_start: 0.7266 (m-30) cc_final: 0.6751 (m-30) REVERT: B 844 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6805 (m-80) REVERT: B 925 LYS cc_start: 0.7505 (mmtt) cc_final: 0.6634 (tmtt) REVERT: B 1129 SER cc_start: 0.7318 (t) cc_final: 0.7051 (m) REVERT: C 76 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5238 (mpt-90) REVERT: C 158 LEU cc_start: 0.6867 (pp) cc_final: 0.6085 (mt) REVERT: C 160 GLU cc_start: 0.7538 (tt0) cc_final: 0.6786 (tm-30) REVERT: C 169 CYS cc_start: 0.5601 (m) cc_final: 0.5382 (m) REVERT: C 185 LYS cc_start: 0.6007 (mmtt) cc_final: 0.5315 (mttt) REVERT: C 234 THR cc_start: 0.8491 (p) cc_final: 0.8267 (p) REVERT: C 371 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7020 (p0) REVERT: C 382 ASP cc_start: 0.6664 (t70) cc_final: 0.6190 (t0) REVERT: C 389 ILE cc_start: 0.6074 (tt) cc_final: 0.5669 (tt) REVERT: C 462 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8161 (mttm) REVERT: C 720 GLN cc_start: 0.7034 (pm20) cc_final: 0.6147 (tt0) REVERT: C 844 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: C 1170 ARG cc_start: 0.7429 (ttm110) cc_final: 0.7094 (mtp85) outliers start: 73 outliers final: 62 residues processed: 455 average time/residue: 0.1656 time to fit residues: 125.6819 Evaluate side-chains 452 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 381 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 837 CYS Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 844 TYR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1187 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 1008 ASP Chi-restraints excluded: chain C residue 1215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 241 optimal weight: 0.7980 chunk 317 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 278 optimal weight: 0.0770 chunk 261 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 chunk 176 optimal weight: 0.0970 chunk 95 optimal weight: 9.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134368 restraints weight = 36451.002| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.13 r_work: 0.3471 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 28767 Z= 0.153 Angle : 0.630 11.211 39279 Z= 0.326 Chirality : 0.047 0.255 4542 Planarity : 0.004 0.046 4968 Dihedral : 5.323 39.489 4749 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.64 % Allowed : 17.83 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.14), residues: 3477 helix: 0.29 (0.19), residues: 768 sheet: -0.72 (0.19), residues: 717 loop : -0.96 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.031 0.002 TYR A 75 PHE 0.031 0.002 PHE B 238 TRP 0.037 0.002 TRP C 360 HIS 0.009 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00369 (28659) covalent geometry : angle 0.60985 (39018) SS BOND : bond 0.00447 ( 63) SS BOND : angle 2.12368 ( 126) hydrogen bonds : bond 0.04023 ( 1041) hydrogen bonds : angle 5.87693 ( 2994) link_BETA1-4 : bond 0.00424 ( 9) link_BETA1-4 : angle 1.49752 ( 27) link_NAG-ASN : bond 0.00380 ( 36) link_NAG-ASN : angle 2.05698 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6672.90 seconds wall clock time: 115 minutes 26.21 seconds (6926.21 seconds total)