Starting phenix.real_space_refine on Mon May 26 10:06:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blk_44658/05_2025/9blk_44658.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blk_44658/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9blk_44658/05_2025/9blk_44658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blk_44658/05_2025/9blk_44658.map" model { file = "/net/cci-nas-00/data/ceres_data/9blk_44658/05_2025/9blk_44658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blk_44658/05_2025/9blk_44658.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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): 2.36s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.78, per 1000 atoms: 0.53 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: 7.31 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 5.46 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: 16.12 Time building geometry restraints manager: 8.55 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: 0.19 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 26.410 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 66.210 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (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 TRP 0.043 0.009 TRP C 460 HIS 0.007 0.002 HIS A1158 PHE 0.040 0.007 PHE A 122 TYR 0.092 0.012 TYR A 844 ARG 0.009 0.001 ARG C 999 Details of bonding type rmsd link_NAG-ASN : bond 0.08141 ( 36) link_NAG-ASN : angle 2.30915 ( 108) link_BETA1-4 : bond 0.06907 ( 9) link_BETA1-4 : angle 4.79149 ( 27) hydrogen bonds : bond 0.17446 ( 1041) hydrogen bonds : angle 8.43842 ( 2994) SS BOND : bond 0.01911 ( 63) SS BOND : angle 2.68191 ( 126) covalent geometry : bond 0.02181 (28659) covalent geometry : angle 1.81566 (39018) *********************** 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 : 2.695 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: 0.3625 time to fit residues: 481.6681 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 : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 0.7980 chunk 266 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 318 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS 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 866 GLN A 888 ASN A 967 GLN A1014 GLN A1059 GLN A1092 ASN B 183 HIS B 239 ASN B 248 HIS 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 183 HIS C 239 ASN C 248 HIS 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: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135645 restraints weight = 35617.453| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.08 r_work: 0.3473 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28767 Z= 0.175 Angle : 0.750 9.284 39279 Z= 0.398 Chirality : 0.050 0.381 4542 Planarity : 0.005 0.056 4968 Dihedral : 7.335 68.649 4749 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.90 % Favored : 98.02 % Rotamer: Outliers : 2.02 % Allowed : 9.11 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 3477 helix: -0.47 (0.18), residues: 762 sheet: 0.17 (0.17), residues: 750 loop : -0.13 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 360 HIS 0.008 0.001 HIS C 215 PHE 0.024 0.002 PHE C 278 TYR 0.034 0.002 TYR B 75 ARG 0.004 0.001 ARG B 681 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 36) link_NAG-ASN : angle 2.73212 ( 108) link_BETA1-4 : bond 0.00684 ( 9) link_BETA1-4 : angle 3.17674 ( 27) hydrogen bonds : bond 0.05513 ( 1041) hydrogen bonds : angle 6.71877 ( 2994) SS BOND : bond 0.00264 ( 63) SS BOND : angle 1.12651 ( 126) covalent geometry : bond 0.00387 (28659) covalent geometry : angle 0.73092 (39018) *********************** 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: 62 poor density : 505 time to evaluate : 2.981 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: 0.7002 (pp) cc_final: 0.6033 (mp) REVERT: A 160 GLU cc_start: 0.7022 (tt0) cc_final: 0.6241 (tm-30) REVERT: A 199 TYR cc_start: 0.6544 (t80) cc_final: 0.6343 (t80) REVERT: A 315 ASN cc_start: 0.6495 (p0) cc_final: 0.6263 (p0) REVERT: A 720 GLN cc_start: 0.6910 (pm20) cc_final: 0.6034 (tt0) REVERT: A 833 ASP cc_start: 0.6669 (p0) cc_final: 0.6354 (t0) REVERT: A 844 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: A 1082 GLU cc_start: 0.6826 (tp30) cc_final: 0.6069 (tp30) REVERT: A 1101 TYR cc_start: 0.8073 (t80) cc_final: 0.7788 (t80) REVERT: A 1206 TYR cc_start: 0.8501 (t80) cc_final: 0.8210 (t80) REVERT: B 160 GLU cc_start: 0.6971 (tt0) cc_final: 0.6243 (tm-30) REVERT: B 199 TYR cc_start: 0.6447 (t80) cc_final: 0.6135 (t80) REVERT: B 246 LEU cc_start: 0.6464 (mt) cc_final: 0.6147 (mp) REVERT: B 283 ILE cc_start: 0.6894 (mt) cc_final: 0.6676 (mt) REVERT: B 371 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.6950 (p0) REVERT: B 833 ASP cc_start: 0.6611 (p0) cc_final: 0.6358 (t0) REVERT: B 1082 GLU cc_start: 0.6752 (tp30) cc_final: 0.6127 (tp30) REVERT: B 1101 TYR cc_start: 0.7963 (t80) cc_final: 0.7655 (t80) REVERT: B 1206 TYR cc_start: 0.8523 (t80) cc_final: 0.8315 (t80) REVERT: C 158 LEU cc_start: 0.6845 (pp) cc_final: 0.5947 (mp) REVERT: C 160 GLU cc_start: 0.7207 (tt0) cc_final: 0.6507 (tm-30) REVERT: C 199 TYR cc_start: 0.6390 (t80) cc_final: 0.6084 (t80) REVERT: C 315 ASN cc_start: 0.6591 (p0) cc_final: 0.6272 (p0) REVERT: C 720 GLN cc_start: 0.7056 (pm20) cc_final: 0.6231 (tt0) REVERT: C 794 VAL cc_start: 0.7380 (t) cc_final: 0.7092 (m) REVERT: C 833 ASP cc_start: 0.6843 (p0) cc_final: 0.6469 (t0) REVERT: C 844 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6793 (m-80) REVERT: C 1082 GLU cc_start: 0.6771 (tp30) cc_final: 0.6072 (tp30) REVERT: C 1101 TYR cc_start: 0.7993 (t80) cc_final: 0.7635 (t80) REVERT: C 1206 TYR cc_start: 0.8387 (t80) cc_final: 0.8147 (t80) outliers start: 62 outliers final: 46 residues processed: 535 average time/residue: 0.3589 time to fit residues: 322.3309 Evaluate side-chains 460 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 411 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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 373 SER Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 454 ARG 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 846 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1112 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 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 255 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 340 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A 369 ASN A 421 ASN A 429 ASN A1092 ASN A1158 HIS B 339 ASN B 369 ASN B 421 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 HIS C 421 ASN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 ASN C1158 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131691 restraints weight = 36463.372| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.15 r_work: 0.3421 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 28767 Z= 0.241 Angle : 0.748 12.151 39279 Z= 0.394 Chirality : 0.052 0.316 4542 Planarity : 0.005 0.059 4968 Dihedral : 6.516 43.865 4749 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.43 % Allowed : 10.15 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3477 helix: -0.53 (0.18), residues: 774 sheet: -0.42 (0.18), residues: 735 loop : -0.49 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 360 HIS 0.007 0.002 HIS B 215 PHE 0.022 0.003 PHE C 384 TYR 0.040 0.003 TYR A 75 ARG 0.006 0.001 ARG B 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 36) link_NAG-ASN : angle 2.38648 ( 108) link_BETA1-4 : bond 0.00616 ( 9) link_BETA1-4 : angle 2.65146 ( 27) hydrogen bonds : bond 0.05312 ( 1041) hydrogen bonds : angle 6.57220 ( 2994) SS BOND : bond 0.00416 ( 63) SS BOND : angle 1.60372 ( 126) covalent geometry : bond 0.00559 (28659) covalent geometry : angle 0.73051 (39018) *********************** 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 543 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 438 time to evaluate : 3.169 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: 0.7207 (pp) cc_final: 0.6222 (mp) REVERT: A 160 GLU cc_start: 0.7220 (tt0) cc_final: 0.6627 (tm-30) REVERT: A 224 TYR cc_start: 0.7596 (m-80) cc_final: 0.7300 (m-80) REVERT: A 371 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7043 (p0) REVERT: A 603 PHE cc_start: 0.5500 (OUTLIER) cc_final: 0.5136 (m-10) REVERT: A 720 GLN cc_start: 0.6972 (pm20) cc_final: 0.6072 (tt0) REVERT: A 833 ASP cc_start: 0.6974 (p0) cc_final: 0.6427 (t0) REVERT: A 844 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: A 1082 GLU cc_start: 0.7016 (tp30) cc_final: 0.6183 (tp30) REVERT: A 1206 TYR cc_start: 0.8578 (t80) cc_final: 0.8328 (t80) REVERT: B 104 PHE cc_start: 0.7474 (t80) cc_final: 0.7264 (t80) REVERT: B 160 GLU cc_start: 0.7204 (tt0) cc_final: 0.6679 (tm-30) REVERT: B 168 MET cc_start: 0.5816 (mmt) cc_final: 0.5408 (mmt) REVERT: B 371 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7217 (p0) REVERT: B 794 VAL cc_start: 0.7689 (t) cc_final: 0.6955 (m) REVERT: B 833 ASP cc_start: 0.6946 (p0) cc_final: 0.6380 (t0) REVERT: B 844 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.7113 (m-80) REVERT: B 925 LYS cc_start: 0.7544 (mmtt) cc_final: 0.6901 (mptt) REVERT: B 1082 GLU cc_start: 0.7042 (tp30) cc_final: 0.6278 (tp30) REVERT: B 1170 ARG cc_start: 0.7505 (ttm110) cc_final: 0.7176 (mtp85) REVERT: B 1206 TYR cc_start: 0.8586 (t80) cc_final: 0.8357 (t80) REVERT: C 158 LEU cc_start: 0.7093 (pp) cc_final: 0.6164 (mp) REVERT: C 160 GLU cc_start: 0.7454 (tt0) cc_final: 0.6795 (tm-30) REVERT: C 371 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.6863 (p0) REVERT: C 454 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6130 (ptp90) REVERT: C 833 ASP cc_start: 0.7067 (p0) cc_final: 0.6528 (t0) REVERT: C 844 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: C 1026 TYR cc_start: 0.7070 (t80) cc_final: 0.6846 (t80) REVERT: C 1028 ILE cc_start: 0.7814 (mt) cc_final: 0.7557 (mm) REVERT: C 1082 GLU cc_start: 0.6891 (tp30) cc_final: 0.6067 (tp30) outliers start: 105 outliers final: 74 residues processed: 501 average time/residue: 0.3441 time to fit residues: 287.5701 Evaluate side-chains 480 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 398 time to evaluate : 3.139 ------------------------------------------------------------------------------- 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 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 371 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 603 PHE 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 899 VAL 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 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 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 129 SER 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 369 ASN 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 881 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 1112 VAL Chi-restraints excluded: chain B residue 1187 SER 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 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 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 453 SER 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 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 1008 ASP Chi-restraints excluded: chain C residue 1012 GLN Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1187 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 60 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 285 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 338 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 369 ASN A 429 ASN A1055 ASN B 215 HIS B 429 ASN C 215 HIS ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.155176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133069 restraints weight = 36416.885| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.13 r_work: 0.3452 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28767 Z= 0.149 Angle : 0.618 10.765 39279 Z= 0.326 Chirality : 0.047 0.297 4542 Planarity : 0.004 0.049 4968 Dihedral : 5.689 32.696 4749 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.61 % Allowed : 11.92 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3477 helix: -0.22 (0.18), residues: 774 sheet: -0.52 (0.18), residues: 717 loop : -0.57 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 360 HIS 0.010 0.001 HIS C 177 PHE 0.020 0.002 PHE A 278 TYR 0.035 0.002 TYR A 75 ARG 0.003 0.000 ARG A1133 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 36) link_NAG-ASN : angle 2.21266 ( 108) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 2.28113 ( 27) hydrogen bonds : bond 0.04385 ( 1041) hydrogen bonds : angle 6.20671 ( 2994) SS BOND : bond 0.00435 ( 63) SS BOND : angle 1.50895 ( 126) covalent geometry : bond 0.00339 (28659) covalent geometry : angle 0.59975 (39018) *********************** 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 541 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 461 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.5837 (tpp) cc_final: 0.5621 (mmp) REVERT: A 154 LYS cc_start: 0.4537 (mttt) cc_final: 0.2617 (tptm) REVERT: A 158 LEU cc_start: 0.7106 (pp) cc_final: 0.6200 (mp) REVERT: A 160 GLU cc_start: 0.7288 (tt0) cc_final: 0.6612 (tm-30) REVERT: A 166 TYR cc_start: 0.7690 (m-80) cc_final: 0.7202 (m-10) REVERT: A 224 TYR cc_start: 0.7564 (m-80) cc_final: 0.7283 (m-80) REVERT: A 244 MET cc_start: 0.7723 (ptt) cc_final: 0.7266 (mmt) REVERT: A 371 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.6947 (p0) REVERT: A 382 ASP cc_start: 0.6794 (t70) cc_final: 0.6156 (t0) REVERT: A 844 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: A 1082 GLU cc_start: 0.7059 (tp30) cc_final: 0.6257 (tp30) REVERT: A 1170 ARG cc_start: 0.7535 (ttm110) cc_final: 0.7180 (mtp85) REVERT: A 1206 TYR cc_start: 0.8529 (t80) cc_final: 0.8296 (t80) REVERT: B 158 LEU cc_start: 0.6965 (pp) cc_final: 0.5929 (mp) REVERT: B 160 GLU cc_start: 0.7189 (tt0) cc_final: 0.6614 (tm-30) REVERT: B 166 TYR cc_start: 0.7697 (m-80) cc_final: 0.7452 (m-10) REVERT: B 168 MET cc_start: 0.5787 (mmt) cc_final: 0.5418 (mmt) REVERT: B 371 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.7069 (p0) REVERT: B 794 VAL cc_start: 0.7736 (t) cc_final: 0.7079 (m) REVERT: B 844 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.7010 (m-80) REVERT: B 925 LYS cc_start: 0.7460 (mmtt) cc_final: 0.6800 (mptt) REVERT: B 1082 GLU cc_start: 0.6959 (tp30) cc_final: 0.6185 (tp30) REVERT: B 1170 ARG cc_start: 0.7481 (ttm110) cc_final: 0.7142 (mtp85) REVERT: B 1206 TYR cc_start: 0.8524 (t80) cc_final: 0.8297 (t80) REVERT: C 158 LEU cc_start: 0.7019 (pp) cc_final: 0.6099 (mp) REVERT: C 160 GLU cc_start: 0.7312 (tt0) cc_final: 0.6684 (tm-30) REVERT: C 244 MET cc_start: 0.7690 (ptt) cc_final: 0.7365 (mmt) REVERT: C 249 TYR cc_start: 0.6852 (p90) cc_final: 0.6625 (p90) REVERT: C 371 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.6831 (p0) REVERT: C 454 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6086 (ptp90) REVERT: C 455 PHE cc_start: 0.7337 (t80) cc_final: 0.6542 (m-80) REVERT: C 720 GLN cc_start: 0.6950 (pm20) cc_final: 0.6089 (tt0) REVERT: C 844 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.7117 (m-80) outliers start: 80 outliers final: 60 residues processed: 510 average time/residue: 0.3509 time to fit residues: 297.8416 Evaluate side-chains 461 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 394 time to evaluate : 2.823 ------------------------------------------------------------------------------- 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 97 SER 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 195 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 233 VAL 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 815 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 844 TYR 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 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 429 ASN Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 718 THR 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 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 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 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 454 ARG 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 239 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 260 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 ASN B 429 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 = 0.3817 r_free = 0.3817 target = 0.155986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133361 restraints weight = 36263.371| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.16 r_work: 0.3448 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28767 Z= 0.147 Angle : 0.600 10.004 39279 Z= 0.316 Chirality : 0.046 0.262 4542 Planarity : 0.004 0.054 4968 Dihedral : 5.408 33.178 4749 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.87 % Allowed : 13.42 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3477 helix: 0.04 (0.19), residues: 765 sheet: -0.62 (0.18), residues: 702 loop : -0.61 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 360 HIS 0.007 0.001 HIS C 177 PHE 0.022 0.002 PHE A 278 TYR 0.034 0.002 TYR B 75 ARG 0.003 0.000 ARG B1094 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 36) link_NAG-ASN : angle 2.32400 ( 108) link_BETA1-4 : bond 0.00421 ( 9) link_BETA1-4 : angle 1.96107 ( 27) hydrogen bonds : bond 0.04247 ( 1041) hydrogen bonds : angle 6.01996 ( 2994) SS BOND : bond 0.00275 ( 63) SS BOND : angle 1.20913 ( 126) covalent geometry : bond 0.00343 (28659) covalent geometry : angle 0.58339 (39018) *********************** 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 515 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 427 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.5485 (mpt-90) REVERT: A 158 LEU cc_start: 0.7090 (pp) cc_final: 0.6218 (mp) REVERT: A 160 GLU cc_start: 0.7231 (tt0) cc_final: 0.6672 (tm-30) REVERT: A 166 TYR cc_start: 0.7730 (m-80) cc_final: 0.7293 (m-10) REVERT: A 224 TYR cc_start: 0.7546 (m-80) cc_final: 0.7253 (m-80) REVERT: A 244 MET cc_start: 0.7686 (ptt) cc_final: 0.7260 (mmt) REVERT: A 371 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.6984 (p0) REVERT: A 382 ASP cc_start: 0.6715 (t70) cc_final: 0.6123 (t0) REVERT: A 540 ILE cc_start: 0.6895 (mt) cc_final: 0.6501 (pt) REVERT: A 1170 ARG cc_start: 0.7508 (ttm110) cc_final: 0.7173 (mtp85) REVERT: A 1206 TYR cc_start: 0.8527 (t80) cc_final: 0.8313 (t80) REVERT: B 76 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5441 (mpt-90) REVERT: B 154 LYS cc_start: 0.4530 (mttt) cc_final: 0.2634 (tptm) REVERT: B 158 LEU cc_start: 0.6948 (pp) cc_final: 0.5951 (mp) REVERT: B 160 GLU cc_start: 0.7222 (tt0) cc_final: 0.6573 (tm-30) REVERT: B 168 MET cc_start: 0.5836 (mmt) cc_final: 0.5475 (mmt) REVERT: B 283 ILE cc_start: 0.7220 (mt) cc_final: 0.6950 (mm) REVERT: B 371 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.7096 (p0) REVERT: B 382 ASP cc_start: 0.6766 (t70) cc_final: 0.6139 (t0) REVERT: B 794 VAL cc_start: 0.7770 (t) cc_final: 0.7120 (m) REVERT: B 844 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6866 (m-80) REVERT: B 925 LYS cc_start: 0.7460 (mmtt) cc_final: 0.6817 (mptt) REVERT: B 1170 ARG cc_start: 0.7502 (ttm110) cc_final: 0.7161 (mtp85) REVERT: B 1206 TYR cc_start: 0.8485 (t80) cc_final: 0.8273 (t80) REVERT: C 76 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.5251 (mpt-90) REVERT: C 158 LEU cc_start: 0.7022 (pp) cc_final: 0.6123 (mp) REVERT: C 160 GLU cc_start: 0.7289 (tt0) cc_final: 0.6632 (tm-30) REVERT: C 244 MET cc_start: 0.7623 (ptt) cc_final: 0.7327 (mmt) REVERT: C 371 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.6868 (p0) REVERT: C 454 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6163 (ptp90) REVERT: C 455 PHE cc_start: 0.7357 (t80) cc_final: 0.6542 (m-80) REVERT: C 720 GLN cc_start: 0.7021 (pm20) cc_final: 0.6165 (tt0) REVERT: C 844 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: C 1028 ILE cc_start: 0.7912 (mt) cc_final: 0.7685 (mm) REVERT: C 1170 ARG cc_start: 0.7450 (ttm110) cc_final: 0.7153 (mtp85) outliers start: 88 outliers final: 65 residues processed: 486 average time/residue: 0.3516 time to fit residues: 282.3526 Evaluate side-chains 468 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 394 time to evaluate : 2.859 ------------------------------------------------------------------------------- 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 127 ILE 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 590 SER Chi-restraints excluded: chain A residue 817 THR 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 1160 SER 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 332 ASP Chi-restraints excluded: chain B residue 371 ASN 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 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 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 266 VAL Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 590 SER 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 929 VAL Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 1008 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 240 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 235 optimal weight: 0.8980 chunk 190 optimal weight: 9.9990 chunk 91 optimal weight: 0.0980 chunk 298 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 255 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 871 ASN B 426 GLN B 429 ASN B 871 ASN C 426 GLN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132066 restraints weight = 36562.802| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.14 r_work: 0.3443 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28767 Z= 0.172 Angle : 0.623 11.722 39279 Z= 0.329 Chirality : 0.047 0.286 4542 Planarity : 0.004 0.049 4968 Dihedral : 5.403 35.107 4749 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.72 % Allowed : 13.94 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3477 helix: 0.20 (0.19), residues: 738 sheet: -0.63 (0.19), residues: 687 loop : -0.82 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 360 HIS 0.007 0.001 HIS B 177 PHE 0.021 0.002 PHE A 278 TYR 0.036 0.002 TYR B 75 ARG 0.003 0.000 ARG B1094 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 36) link_NAG-ASN : angle 2.23971 ( 108) link_BETA1-4 : bond 0.00372 ( 9) link_BETA1-4 : angle 1.78403 ( 27) hydrogen bonds : bond 0.04334 ( 1041) hydrogen bonds : angle 5.99196 ( 2994) SS BOND : bond 0.00303 ( 63) SS BOND : angle 1.45864 ( 126) covalent geometry : bond 0.00403 (28659) covalent geometry : angle 0.60662 (39018) *********************** 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 521 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 407 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.5521 (mpt-90) REVERT: A 154 LYS cc_start: 0.4566 (mttt) cc_final: 0.2634 (tptm) REVERT: A 158 LEU cc_start: 0.7120 (pp) cc_final: 0.6235 (mp) REVERT: A 160 GLU cc_start: 0.7322 (tt0) cc_final: 0.6670 (tm-30) REVERT: A 166 TYR cc_start: 0.7811 (m-80) cc_final: 0.7326 (m-10) REVERT: A 177 HIS cc_start: 0.6973 (OUTLIER) cc_final: 0.6731 (t-170) REVERT: A 224 TYR cc_start: 0.7576 (m-80) cc_final: 0.7283 (m-80) REVERT: A 244 MET cc_start: 0.7744 (ptt) cc_final: 0.7333 (mmt) REVERT: A 371 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7032 (p0) REVERT: A 382 ASP cc_start: 0.6744 (t70) cc_final: 0.6149 (t0) REVERT: A 720 GLN cc_start: 0.6987 (pm20) cc_final: 0.6148 (tt0) REVERT: A 1170 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7196 (mtp85) REVERT: B 55 ARG cc_start: 0.7098 (mtp85) cc_final: 0.6897 (mtt-85) REVERT: B 76 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5444 (mpt-90) REVERT: B 118 MET cc_start: 0.5197 (mmp) cc_final: 0.4937 (mmp) REVERT: B 158 LEU cc_start: 0.6840 (pp) cc_final: 0.5862 (mp) REVERT: B 160 GLU cc_start: 0.7317 (tt0) cc_final: 0.6624 (tm-30) REVERT: B 283 ILE cc_start: 0.7239 (mt) cc_final: 0.6970 (mm) REVERT: B 371 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7347 (p0) REVERT: B 382 ASP cc_start: 0.6917 (t70) cc_final: 0.6303 (t0) REVERT: B 617 ASP cc_start: 0.7486 (m-30) cc_final: 0.6315 (m-30) REVERT: B 844 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6855 (m-80) REVERT: B 925 LYS cc_start: 0.7506 (mmtt) cc_final: 0.6876 (mptt) REVERT: B 1206 TYR cc_start: 0.8527 (t80) cc_final: 0.8300 (t80) REVERT: C 76 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.5249 (mpt-90) REVERT: C 136 TYR cc_start: 0.6516 (m-80) cc_final: 0.6015 (m-80) REVERT: C 158 LEU cc_start: 0.7014 (pp) cc_final: 0.6098 (mp) REVERT: C 160 GLU cc_start: 0.7338 (tt0) cc_final: 0.6695 (tm-30) REVERT: C 244 MET cc_start: 0.7718 (ptt) cc_final: 0.7392 (mmt) REVERT: C 371 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.6980 (p0) REVERT: C 382 ASP cc_start: 0.6687 (t70) cc_final: 0.6240 (t0) REVERT: C 454 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6248 (ptp90) REVERT: C 720 GLN cc_start: 0.7055 (pm20) cc_final: 0.6203 (tt0) REVERT: C 844 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6969 (m-80) REVERT: C 1170 ARG cc_start: 0.7449 (ttm110) cc_final: 0.7148 (mtp85) outliers start: 114 outliers final: 84 residues processed: 485 average time/residue: 0.3457 time to fit residues: 276.8145 Evaluate side-chains 473 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 379 time to evaluate : 2.735 ------------------------------------------------------------------------------- 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 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 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 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 929 VAL Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 1008 ASP Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 63 PHE 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 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 284 ILE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 371 ASN 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 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 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 249 TYR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 354 VAL 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 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 865 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 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 229 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 291 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.155786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133434 restraints weight = 36276.633| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.14 r_work: 0.3453 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28767 Z= 0.148 Angle : 0.601 10.788 39279 Z= 0.315 Chirality : 0.046 0.282 4542 Planarity : 0.004 0.045 4968 Dihedral : 5.265 35.867 4749 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.30 % Allowed : 14.92 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3477 helix: 0.41 (0.19), residues: 723 sheet: -0.61 (0.19), residues: 687 loop : -0.78 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 360 HIS 0.008 0.001 HIS B 177 PHE 0.022 0.002 PHE B 238 TYR 0.034 0.002 TYR B 75 ARG 0.004 0.000 ARG B1170 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 36) link_NAG-ASN : angle 2.16018 ( 108) link_BETA1-4 : bond 0.00370 ( 9) link_BETA1-4 : angle 1.62833 ( 27) hydrogen bonds : bond 0.04118 ( 1041) hydrogen bonds : angle 5.90660 ( 2994) SS BOND : bond 0.00255 ( 63) SS BOND : angle 1.49708 ( 126) covalent geometry : bond 0.00350 (28659) covalent geometry : angle 0.58483 (39018) *********************** 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 504 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 403 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.5534 (mpt-90) REVERT: A 154 LYS cc_start: 0.4563 (mttt) cc_final: 0.3177 (pttp) REVERT: A 158 LEU cc_start: 0.7050 (pp) cc_final: 0.6236 (mp) REVERT: A 160 GLU cc_start: 0.7487 (tt0) cc_final: 0.6799 (tm-30) REVERT: A 166 TYR cc_start: 0.7751 (m-80) cc_final: 0.7139 (m-10) REVERT: A 177 HIS cc_start: 0.6940 (OUTLIER) cc_final: 0.6626 (t-170) REVERT: A 185 LYS cc_start: 0.5964 (mmtt) cc_final: 0.5256 (mttt) REVERT: A 224 TYR cc_start: 0.7541 (m-80) cc_final: 0.7227 (m-80) REVERT: A 234 THR cc_start: 0.8499 (p) cc_final: 0.8298 (p) REVERT: A 244 MET cc_start: 0.7737 (ptt) cc_final: 0.7342 (mmt) REVERT: A 371 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7003 (p0) REVERT: A 382 ASP cc_start: 0.6757 (t70) cc_final: 0.6198 (t0) REVERT: A 720 GLN cc_start: 0.6909 (pm20) cc_final: 0.6120 (tt0) REVERT: A 1134 ILE cc_start: 0.7859 (mt) cc_final: 0.7622 (tp) REVERT: A 1170 ARG cc_start: 0.7535 (ttm110) cc_final: 0.7157 (mtp85) REVERT: B 55 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6875 (mtt-85) REVERT: B 76 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.5508 (mpt-90) REVERT: B 154 LYS cc_start: 0.4595 (mttt) cc_final: 0.2729 (tptm) REVERT: B 158 LEU cc_start: 0.6735 (pp) cc_final: 0.5917 (mp) REVERT: B 160 GLU cc_start: 0.7458 (tt0) cc_final: 0.6747 (tm-30) REVERT: B 166 TYR cc_start: 0.7734 (m-80) cc_final: 0.7409 (m-10) REVERT: B 234 THR cc_start: 0.8573 (p) cc_final: 0.8357 (p) REVERT: B 244 MET cc_start: 0.7882 (ptt) cc_final: 0.7341 (mmt) REVERT: B 283 ILE cc_start: 0.7263 (mt) cc_final: 0.7001 (mm) REVERT: B 371 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.7305 (p0) REVERT: B 382 ASP cc_start: 0.6873 (t70) cc_final: 0.6301 (t0) REVERT: B 617 ASP cc_start: 0.7332 (m-30) cc_final: 0.6115 (m-30) REVERT: B 844 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: B 925 LYS cc_start: 0.7492 (mmtt) cc_final: 0.6866 (mptt) REVERT: B 1170 ARG cc_start: 0.7566 (ttm110) cc_final: 0.7251 (mtp85) REVERT: B 1206 TYR cc_start: 0.8498 (t80) cc_final: 0.8284 (t80) REVERT: C 76 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.5264 (mpt-90) REVERT: C 136 TYR cc_start: 0.6495 (m-80) cc_final: 0.5988 (m-80) REVERT: C 158 LEU cc_start: 0.6917 (pp) cc_final: 0.6127 (mp) REVERT: C 160 GLU cc_start: 0.7376 (tt0) cc_final: 0.6709 (tm-30) REVERT: C 185 LYS cc_start: 0.5977 (mmtt) cc_final: 0.5266 (mtmt) REVERT: C 244 MET cc_start: 0.7675 (ptt) cc_final: 0.7373 (mmt) REVERT: C 371 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.6922 (p0) REVERT: C 382 ASP cc_start: 0.6638 (t70) cc_final: 0.6227 (t0) REVERT: C 844 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6922 (m-80) REVERT: C 1170 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7112 (mtp85) outliers start: 101 outliers final: 82 residues processed: 470 average time/residue: 0.3498 time to fit residues: 272.1338 Evaluate side-chains 465 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 374 time to evaluate : 2.856 ------------------------------------------------------------------------------- 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 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 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 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 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 354 VAL Chi-restraints excluded: chain B residue 371 ASN 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 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 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 249 TYR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 332 ASP 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 328 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 323 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 665 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN C 426 GLN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 665 ASN C 871 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.153044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130872 restraints weight = 36899.837| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.13 r_work: 0.3425 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 28767 Z= 0.239 Angle : 0.701 12.185 39279 Z= 0.367 Chirality : 0.049 0.287 4542 Planarity : 0.005 0.061 4968 Dihedral : 5.713 40.337 4749 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.62 % Allowed : 15.38 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3477 helix: 0.09 (0.19), residues: 729 sheet: -0.78 (0.19), residues: 714 loop : -0.92 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 360 HIS 0.008 0.002 HIS B 177 PHE 0.022 0.002 PHE B 238 TYR 0.037 0.002 TYR B 75 ARG 0.006 0.000 ARG B1133 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 36) link_NAG-ASN : angle 2.28655 ( 108) link_BETA1-4 : bond 0.00310 ( 9) link_BETA1-4 : angle 1.80839 ( 27) hydrogen bonds : bond 0.04791 ( 1041) hydrogen bonds : angle 6.21166 ( 2994) SS BOND : bond 0.00394 ( 63) SS BOND : angle 1.85188 ( 126) covalent geometry : bond 0.00574 (28659) covalent geometry : angle 0.68360 (39018) *********************** 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 494 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 383 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.5572 (mpt-90) REVERT: A 136 TYR cc_start: 0.6139 (m-80) cc_final: 0.5938 (m-80) REVERT: A 154 LYS cc_start: 0.4668 (mttt) cc_final: 0.3270 (pttp) REVERT: A 158 LEU cc_start: 0.7088 (pp) cc_final: 0.6176 (mt) REVERT: A 160 GLU cc_start: 0.7605 (tt0) cc_final: 0.6909 (tm-30) REVERT: A 166 TYR cc_start: 0.7845 (m-80) cc_final: 0.7340 (m-10) REVERT: A 169 CYS cc_start: 0.5406 (m) cc_final: 0.5164 (m) REVERT: A 177 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6559 (t-170) REVERT: A 185 LYS cc_start: 0.6129 (mmtt) cc_final: 0.5385 (mttt) REVERT: A 224 TYR cc_start: 0.7701 (m-80) cc_final: 0.7406 (m-80) REVERT: A 244 MET cc_start: 0.7883 (ptt) cc_final: 0.7417 (mmt) REVERT: A 325 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.4375 (m-80) REVERT: A 371 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7176 (p0) REVERT: A 382 ASP cc_start: 0.6841 (t70) cc_final: 0.6245 (t0) REVERT: A 720 GLN cc_start: 0.6987 (pm20) cc_final: 0.6163 (tt0) REVERT: A 1170 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7210 (mtp85) REVERT: B 76 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.5541 (mpt-90) REVERT: B 154 LYS cc_start: 0.4617 (mttt) cc_final: 0.2785 (tptm) REVERT: B 158 LEU cc_start: 0.6871 (pp) cc_final: 0.5952 (mp) REVERT: B 160 GLU cc_start: 0.7574 (tt0) cc_final: 0.6848 (tm-30) REVERT: B 166 TYR cc_start: 0.7860 (m-80) cc_final: 0.7481 (m-10) REVERT: B 185 LYS cc_start: 0.5879 (mmtt) cc_final: 0.5171 (mtmt) REVERT: B 371 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7417 (p0) REVERT: B 382 ASP cc_start: 0.6977 (t70) cc_final: 0.6385 (t0) REVERT: B 617 ASP cc_start: 0.7641 (m-30) cc_final: 0.7025 (m-30) REVERT: B 844 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: B 925 LYS cc_start: 0.7591 (mmtt) cc_final: 0.6981 (mptt) REVERT: B 1206 TYR cc_start: 0.8517 (t80) cc_final: 0.8314 (t80) REVERT: C 76 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.5359 (mpt-90) REVERT: C 158 LEU cc_start: 0.7000 (pp) cc_final: 0.6180 (mp) REVERT: C 160 GLU cc_start: 0.7539 (tt0) cc_final: 0.6871 (tm-30) REVERT: C 244 MET cc_start: 0.7819 (ptt) cc_final: 0.7466 (mmt) REVERT: C 332 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7608 (t0) REVERT: C 371 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7018 (p0) REVERT: C 382 ASP cc_start: 0.6801 (t70) cc_final: 0.6314 (t0) REVERT: C 454 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.6215 (ptp90) REVERT: C 720 GLN cc_start: 0.7139 (pm20) cc_final: 0.6229 (tt0) REVERT: C 844 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: C 1170 ARG cc_start: 0.7453 (ttm110) cc_final: 0.7144 (mtp85) outliers start: 111 outliers final: 92 residues processed: 460 average time/residue: 0.3471 time to fit residues: 264.6937 Evaluate side-chains 471 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 367 time to evaluate : 3.050 ------------------------------------------------------------------------------- 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 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 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 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 817 THR Chi-restraints excluded: chain A residue 837 CYS 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 929 VAL Chi-restraints excluded: chain A residue 985 THR 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 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 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 354 VAL Chi-restraints excluded: chain B residue 371 ASN 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 1133 ARG 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 249 TYR 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 332 ASP Chi-restraints excluded: chain C residue 354 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 629 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 759 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 0.0370 chunk 350 optimal weight: 4.9990 chunk 267 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 337 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 282 optimal weight: 0.0270 chunk 124 optimal weight: 0.1980 chunk 229 optimal weight: 0.9980 chunk 323 optimal weight: 0.1980 chunk 154 optimal weight: 0.5980 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS C 426 GLN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.158108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135924 restraints weight = 36126.899| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.14 r_work: 0.3489 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28767 Z= 0.116 Angle : 0.600 10.187 39279 Z= 0.313 Chirality : 0.045 0.287 4542 Planarity : 0.004 0.042 4968 Dihedral : 5.186 37.651 4749 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.89 % Allowed : 17.40 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3477 helix: 0.49 (0.19), residues: 741 sheet: -0.75 (0.19), residues: 726 loop : -0.81 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 360 HIS 0.008 0.001 HIS B 177 PHE 0.028 0.002 PHE B 238 TYR 0.031 0.002 TYR B 75 ARG 0.007 0.000 ARG B1133 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 36) link_NAG-ASN : angle 2.10316 ( 108) link_BETA1-4 : bond 0.00425 ( 9) link_BETA1-4 : angle 1.40229 ( 27) hydrogen bonds : bond 0.03779 ( 1041) hydrogen bonds : angle 5.80129 ( 2994) SS BOND : bond 0.00319 ( 63) SS BOND : angle 1.65277 ( 126) covalent geometry : bond 0.00260 (28659) covalent geometry : angle 0.58349 (39018) *********************** 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 489 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 431 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.5457 (mpt-90) REVERT: A 136 TYR cc_start: 0.5949 (m-80) cc_final: 0.5741 (m-80) REVERT: A 154 LYS cc_start: 0.4611 (mttt) cc_final: 0.3245 (pttp) REVERT: A 158 LEU cc_start: 0.6886 (pp) cc_final: 0.6121 (mt) REVERT: A 160 GLU cc_start: 0.7606 (tt0) cc_final: 0.6830 (tm-30) REVERT: A 166 TYR cc_start: 0.7760 (m-80) cc_final: 0.7314 (m-10) REVERT: A 169 CYS cc_start: 0.5141 (m) cc_final: 0.4825 (m) REVERT: A 177 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.6438 (t-170) REVERT: A 185 LYS cc_start: 0.5975 (mmtt) cc_final: 0.5260 (mttt) REVERT: A 224 TYR cc_start: 0.7504 (m-80) cc_final: 0.7193 (m-80) REVERT: A 234 THR cc_start: 0.8367 (p) cc_final: 0.8152 (p) REVERT: A 244 MET cc_start: 0.7589 (ptt) cc_final: 0.7263 (mmt) REVERT: A 371 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.7041 (p0) REVERT: A 382 ASP cc_start: 0.6534 (t70) cc_final: 0.6101 (t0) REVERT: A 617 ASP cc_start: 0.6906 (m-30) cc_final: 0.5949 (m-30) REVERT: A 720 GLN cc_start: 0.6878 (pm20) cc_final: 0.6084 (tt0) REVERT: B 76 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.5394 (mpt-90) REVERT: B 158 LEU cc_start: 0.6679 (pp) cc_final: 0.5904 (mp) REVERT: B 160 GLU cc_start: 0.7555 (tt0) cc_final: 0.6822 (tm-30) REVERT: B 166 TYR cc_start: 0.7731 (m-80) cc_final: 0.7320 (m-10) REVERT: B 234 THR cc_start: 0.8525 (p) cc_final: 0.8303 (p) REVERT: B 244 MET cc_start: 0.7820 (ptt) cc_final: 0.7398 (mmt) REVERT: B 283 ILE cc_start: 0.7243 (mt) cc_final: 0.7021 (mm) REVERT: B 295 MET cc_start: 0.6823 (tpt) cc_final: 0.6562 (tpt) REVERT: B 371 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7159 (p0) REVERT: B 382 ASP cc_start: 0.6793 (t70) cc_final: 0.6306 (t0) REVERT: B 617 ASP cc_start: 0.7295 (m-30) cc_final: 0.6297 (m-30) REVERT: B 634 ASP cc_start: 0.6902 (t0) cc_final: 0.6656 (t0) REVERT: B 844 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: B 925 LYS cc_start: 0.7490 (mmtt) cc_final: 0.6628 (tmtt) REVERT: B 1170 ARG cc_start: 0.7536 (ttm110) cc_final: 0.7238 (mtp85) REVERT: B 1206 TYR cc_start: 0.8407 (t80) cc_final: 0.8196 (t80) REVERT: C 76 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5200 (mpt-90) REVERT: C 158 LEU cc_start: 0.6833 (pp) cc_final: 0.6041 (mt) REVERT: C 160 GLU cc_start: 0.7457 (tt0) cc_final: 0.6759 (tm-30) REVERT: C 234 THR cc_start: 0.8535 (p) cc_final: 0.8295 (p) REVERT: C 332 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7625 (t0) REVERT: C 371 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6791 (p0) REVERT: C 382 ASP cc_start: 0.6582 (t70) cc_final: 0.6242 (t0) REVERT: C 844 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: C 1170 ARG cc_start: 0.7443 (ttm110) cc_final: 0.7126 (mtp85) REVERT: C 1199 TYR cc_start: 0.7424 (t80) cc_final: 0.7067 (t80) outliers start: 58 outliers final: 43 residues processed: 473 average time/residue: 0.3372 time to fit residues: 265.8729 Evaluate side-chains 436 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 383 time to evaluate : 2.966 ------------------------------------------------------------------------------- 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 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 837 CYS Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 41 VAL 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 195 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 371 ASN 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 911 SER Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 1008 ASP 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 112 VAL 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 249 TYR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 332 ASP 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 844 TYR Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 947 LEU 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 198 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 306 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 715 ASN A 859 ASN B 369 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129278 restraints weight = 37070.485| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.09 r_work: 0.3416 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.160 28767 Z= 0.336 Angle : 0.850 13.795 39279 Z= 0.440 Chirality : 0.054 0.314 4542 Planarity : 0.006 0.072 4968 Dihedral : 6.254 44.517 4749 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.71 % Allowed : 17.47 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3477 helix: -0.16 (0.18), residues: 726 sheet: -0.92 (0.19), residues: 747 loop : -1.18 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 360 HIS 0.009 0.002 HIS B 177 PHE 0.037 0.003 PHE B 238 TYR 0.040 0.003 TYR C 75 ARG 0.012 0.001 ARG B1133 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 36) link_NAG-ASN : angle 2.42584 ( 108) link_BETA1-4 : bond 0.00361 ( 9) link_BETA1-4 : angle 1.89422 ( 27) hydrogen bonds : bond 0.05499 ( 1041) hydrogen bonds : angle 6.56423 ( 2994) SS BOND : bond 0.00723 ( 63) SS BOND : angle 2.76490 ( 126) covalent geometry : bond 0.00813 (28659) covalent geometry : angle 0.82721 (39018) ********************** 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 470 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 387 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5627 (mpt-90) REVERT: A 154 LYS cc_start: 0.4880 (mttt) cc_final: 0.3527 (pttp) REVERT: A 158 LEU cc_start: 0.7126 (pp) cc_final: 0.6164 (mt) REVERT: A 160 GLU cc_start: 0.7763 (tt0) cc_final: 0.7046 (tm-30) REVERT: A 166 TYR cc_start: 0.7924 (m-80) cc_final: 0.7535 (m-10) REVERT: A 177 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6606 (t-170) REVERT: A 185 LYS cc_start: 0.6066 (mmtt) cc_final: 0.5327 (mttt) REVERT: A 224 TYR cc_start: 0.7725 (m-80) cc_final: 0.7426 (m-80) REVERT: A 244 MET cc_start: 0.7946 (ptt) cc_final: 0.7484 (mmt) REVERT: A 371 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7289 (p0) REVERT: A 378 PHE cc_start: 0.6929 (m-10) cc_final: 0.6678 (m-80) REVERT: A 382 ASP cc_start: 0.6906 (t70) cc_final: 0.6368 (t0) REVERT: A 603 PHE cc_start: 0.5709 (OUTLIER) cc_final: 0.5083 (m-80) REVERT: A 720 GLN cc_start: 0.7005 (pm20) cc_final: 0.6192 (tt0) REVERT: A 1170 ARG cc_start: 0.7601 (ttm110) cc_final: 0.7232 (mtp85) REVERT: B 76 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.5635 (mpt-90) REVERT: B 154 LYS cc_start: 0.4748 (mttt) cc_final: 0.2980 (tptm) REVERT: B 158 LEU cc_start: 0.6970 (pp) cc_final: 0.6057 (mp) REVERT: B 160 GLU cc_start: 0.7800 (tt0) cc_final: 0.7045 (tm-30) REVERT: B 185 LYS cc_start: 0.5910 (mmtt) cc_final: 0.5175 (mtmt) REVERT: B 382 ASP cc_start: 0.6996 (t70) cc_final: 0.6461 (t0) REVERT: B 844 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: B 925 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7002 (mptt) REVERT: B 1129 SER cc_start: 0.7549 (t) cc_final: 0.7330 (m) REVERT: C 76 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.5407 (mpt-90) REVERT: C 158 LEU cc_start: 0.7036 (pp) cc_final: 0.6190 (mt) REVERT: C 160 GLU cc_start: 0.7676 (tt0) cc_final: 0.6940 (tm-30) REVERT: C 169 CYS cc_start: 0.5845 (m) cc_final: 0.5634 (m) REVERT: C 185 LYS cc_start: 0.6313 (mmtt) cc_final: 0.5477 (mtmt) REVERT: C 332 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7635 (t0) REVERT: C 371 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7278 (p0) REVERT: C 382 ASP cc_start: 0.6810 (t70) cc_final: 0.6261 (t0) REVERT: C 844 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: C 1170 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7166 (mtp85) outliers start: 83 outliers final: 62 residues processed: 444 average time/residue: 0.3517 time to fit residues: 258.8611 Evaluate side-chains 437 residues out of total 3063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 365 time to evaluate : 2.727 ------------------------------------------------------------------------------- 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 126 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 161 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 332 ASP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 632 ASN Chi-restraints excluded: chain A residue 638 ILE 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 947 LEU 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 A residue 1198 MET Chi-restraints excluded: chain B residue 21 CYS 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 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 369 ASN Chi-restraints excluded: chain B residue 398 CYS 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 1008 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 112 VAL 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 332 ASP Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 759 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 173 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 305 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 245 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN ** C1086 GLN ** 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 = 0.3770 r_free = 0.3770 target = 0.151361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129792 restraints weight = 37096.143| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.07 r_work: 0.3422 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.589 28767 Z= 0.324 Angle : 1.050 59.199 39279 Z= 0.571 Chirality : 0.055 1.195 4542 Planarity : 0.006 0.073 4968 Dihedral : 6.295 53.730 4749 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 2.55 % Allowed : 18.25 % Favored : 79.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3477 helix: -0.19 (0.18), residues: 726 sheet: -0.92 (0.19), residues: 717 loop : -1.25 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 360 HIS 0.008 0.002 HIS B 177 PHE 0.032 0.003 PHE B 238 TYR 0.039 0.003 TYR C 75 ARG 0.013 0.001 ARG B1133 Details of bonding type rmsd link_NAG-ASN : bond 0.00813 ( 36) link_NAG-ASN : angle 2.79986 ( 108) link_BETA1-4 : bond 0.00269 ( 9) link_BETA1-4 : angle 1.86278 ( 27) hydrogen bonds : bond 0.05340 ( 1041) hydrogen bonds : angle 6.54234 ( 2994) SS BOND : bond 0.01509 ( 63) SS BOND : angle 5.14161 ( 126) covalent geometry : bond 0.00826 (28659) covalent geometry : angle 1.00021 (39018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14501.82 seconds wall clock time: 252 minutes 42.28 seconds (15162.28 seconds total)