Starting phenix.real_space_refine on Sun Feb 8 00:46:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q9j_13871/02_2026/7q9j_13871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9j_13871/02_2026/7q9j_13871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q9j_13871/02_2026/7q9j_13871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9j_13871/02_2026/7q9j_13871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q9j_13871/02_2026/7q9j_13871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9j_13871/02_2026/7q9j_13871.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10322 atoms to isotropic. 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 132 5.16 5 C 19240 2.51 5 N 4970 2.21 5 O 5948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30290 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8114 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8094 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 51, 'TRANS': 982} Chain breaks: 7 Chain: "C" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8085 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 7 Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 934 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "E" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 934 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "J" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 934 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.25, per 1000 atoms: 0.24 Number of scatterers: 30290 At special positions: 0 Unit cell: (148.42, 148.42, 227.96, 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 132 16.00 O 5948 8.00 N 4970 7.00 C 19240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=1.80 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 105 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 100 " - pdb=" SG CYS J 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 340 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 279 " " NAG A1304 " - " ASN A 328 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 340 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 279 " " NAG B1305 " - " ASN B 328 " " NAG B1306 " - " ASN B 600 " " NAG B1307 " - " ASN B 613 " " NAG B1308 " - " ASN B 654 " " NAG B1309 " - " ASN B 706 " " NAG B1310 " - " ASN B1071 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 340 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 279 " " NAG C1305 " - " ASN C 328 " " NAG C1306 " - " ASN C 600 " " NAG C1307 " - " ASN C 613 " " NAG C1308 " - " ASN C 654 " " NAG C1309 " - " ASN C 706 " " NAG C1310 " - " ASN C1071 " " NAG C1311 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG M 1 " - " ASN A1095 " " NAG N 1 " - " ASN A1131 " " NAG O 1 " - " ASN B 714 " " NAG P 1 " - " ASN B 798 " " NAG Q 1 " - " ASN B1095 " " NAG R 1 " - " ASN B1131 " " NAG S 1 " - " ASN C 714 " " NAG T 1 " - " ASN C 798 " " NAG U 1 " - " ASN C1095 " " NAG V 1 " - " ASN C1131 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7058 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 67 sheets defined 22.7% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.824A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.271A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.880A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.565A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.605A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.904A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.584A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.257A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 387 removed outlier: 3.869A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.299A pdb=" N ARG B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.749A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN B 761 " --> pdb=" O CYS B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 removed outlier: 3.523A pdb=" N GLY B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.973A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.701A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.575A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.535A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.064A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.243A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.855A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 removed outlier: 4.396A pdb=" N ARG C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 405' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.958A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.592A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 removed outlier: 3.552A pdb=" N GLY C 882 " --> pdb=" O THR C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 888 removed outlier: 4.088A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 910 through 916 removed outlier: 4.023A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.502A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 removed outlier: 3.574A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.551A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1115 No H-bonds generated for 'chain 'C' and resid 1113 through 1115' Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.844A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.547A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.544A pdb=" N GLU F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'K' and resid 26 through 30 Processing helix chain 'K' and resid 78 through 82 removed outlier: 3.547A pdb=" N GLU K 82 " --> pdb=" O ALA K 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.441A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.151A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.578A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.964A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 153 through 162 removed outlier: 7.004A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 313 removed outlier: 6.555A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 325 removed outlier: 5.700A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.604A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'A' and resid 651 through 652 removed outlier: 3.693A pdb=" N GLY A 664 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.806A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 722 " --> pdb=" O PHE A1059 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.806A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 722 " --> pdb=" O PHE A1059 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.461A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.784A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 3.982A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS A1079 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1091 through 1094 removed outlier: 5.176A pdb=" N GLN A1103 " --> pdb=" O GLU A1108 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU A1108 " --> pdb=" O GLN A1103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.579A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 261 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.301A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.961A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.528A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.961A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.344A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.141A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AD1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.500A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.908A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.432A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.038A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD8, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.831A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.643A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.747A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.426A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.287A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.747A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL C 143 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 308 through 313 removed outlier: 6.968A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE6, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.302A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE8, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 3.506A pdb=" N GLU C 651 " --> pdb=" O ILE C 689 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 691 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.845A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1044 through 1049 removed outlier: 6.937A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.432A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.514A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AF7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'F' and resid 9 through 11 removed outlier: 6.478A pdb=" N TRP F 34 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 9 through 11 Processing sheet with id=AG1, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AG2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.463A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 11 through 12 removed outlier: 11.445A pdb=" N TYR H 93 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N TRP H 112 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N CYS H 95 " --> pdb=" O ASP H 110 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG H 97 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR H 108 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR H 99 " --> pdb=" O PHE H 106 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AG6, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.465A pdb=" N TRP E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR E 50 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 11 through 12 removed outlier: 11.468A pdb=" N TYR E 93 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N TRP E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N CYS E 95 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP E 110 " --> pdb=" O CYS E 95 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG E 97 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR E 108 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR E 99 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG9, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.464A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 11 through 12 removed outlier: 11.446A pdb=" N TYR J 93 " --> pdb=" O TRP J 112 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N TRP J 112 " --> pdb=" O TYR J 93 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N CYS J 95 " --> pdb=" O ASP J 110 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASP J 110 " --> pdb=" O CYS J 95 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG J 97 " --> pdb=" O THR J 108 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR J 108 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR J 99 " --> pdb=" O PHE J 106 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.514A pdb=" N TRP K 34 " --> pdb=" O VAL K 46 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 9 through 11 Processing sheet with id=AH4, first strand: chain 'K' and resid 18 through 23 1346 hydrogen bonds defined for protein. 3558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.65 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9628 1.34 - 1.46: 7923 1.46 - 1.59: 13269 1.59 - 1.71: 0 1.71 - 1.83: 162 Bond restraints: 30982 Sorted by residual: bond pdb=" C VAL C 857 " pdb=" N LEU C 858 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.30e+00 bond pdb=" N GLN J 1 " pdb=" CA GLN J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N SER L 1 " pdb=" CA SER L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 30977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 38993 0.95 - 1.90: 2470 1.90 - 2.84: 491 2.84 - 3.79: 192 3.79 - 4.74: 33 Bond angle restraints: 42179 Sorted by residual: angle pdb=" N ILE J 29 " pdb=" CA ILE J 29 " pdb=" C ILE J 29 " ideal model delta sigma weight residual 112.98 109.70 3.28 1.25e+00 6.40e-01 6.89e+00 angle pdb=" N ILE E 29 " pdb=" CA ILE E 29 " pdb=" C ILE E 29 " ideal model delta sigma weight residual 113.00 109.60 3.40 1.30e+00 5.92e-01 6.86e+00 angle pdb=" N ILE H 29 " pdb=" CA ILE H 29 " pdb=" C ILE H 29 " ideal model delta sigma weight residual 112.98 109.72 3.26 1.25e+00 6.40e-01 6.80e+00 angle pdb=" CA GLY C 697 " pdb=" C GLY C 697 " pdb=" O GLY C 697 " ideal model delta sigma weight residual 122.45 120.62 1.83 7.20e-01 1.93e+00 6.44e+00 angle pdb=" N SER J 104 " pdb=" CA SER J 104 " pdb=" C SER J 104 " ideal model delta sigma weight residual 109.25 112.85 -3.60 1.53e+00 4.27e-01 5.53e+00 ... (remaining 42174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 18268 17.46 - 34.92: 650 34.92 - 52.38: 162 52.38 - 69.84: 37 69.84 - 87.30: 11 Dihedral angle restraints: 19128 sinusoidal: 8126 harmonic: 11002 Sorted by residual: dihedral pdb=" CB CYS A1079 " pdb=" SG CYS A1079 " pdb=" SG CYS A1123 " pdb=" CB CYS A1123 " ideal model delta sinusoidal sigma weight residual 93.00 8.93 84.07 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual -86.00 -162.63 76.63 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS C1029 " pdb=" SG CYS C1029 " pdb=" SG CYS C1040 " pdb=" CB CYS C1040 " ideal model delta sinusoidal sigma weight residual -86.00 -157.38 71.38 1 1.00e+01 1.00e-02 6.54e+01 ... (remaining 19125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4572 0.092 - 0.185: 357 0.185 - 0.277: 0 0.277 - 0.370: 0 0.370 - 0.462: 1 Chirality restraints: 4930 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 654 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B1131 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 4927 not shown) Planarity restraints: 5418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 328 " -0.139 2.00e-02 2.50e+03 1.84e-01 4.25e+02 pdb=" CG ASN A 328 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A 328 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 328 " 0.318 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 932 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C GLN A 932 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN A 932 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 933 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 949 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C VAL B 949 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL B 949 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN B 950 " 0.009 2.00e-02 2.50e+03 ... (remaining 5415 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 565 2.65 - 3.21: 29055 3.21 - 3.77: 46260 3.77 - 4.34: 65302 4.34 - 4.90: 107114 Nonbonded interactions: 248296 Sorted by model distance: nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.081 3.040 nonbonded pdb=" O PRO B 57 " pdb=" OG SER B 60 " model vdw 2.087 3.040 nonbonded pdb=" O PRO C 57 " pdb=" OG SER C 60 " model vdw 2.090 3.040 nonbonded pdb=" O ASP A1038 " pdb=" OD1 ASP A1038 " model vdw 2.099 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.131 3.040 ... (remaining 248291 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 67 or resid 77 through 246 or resid 259 through \ 824 or resid 852 through 1309)) selection = (chain 'B' and (resid 15 through 67 or resid 77 through 1309)) selection = (chain 'C' and (resid 15 through 824 or resid 852 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.460 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.005 0.232 31090 Z= 0.234 Angle : 0.610 30.399 42452 Z= 0.321 Chirality : 0.044 0.462 4930 Planarity : 0.003 0.038 5374 Dihedral : 9.886 87.303 11917 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.64 % Allowed : 3.46 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3734 helix: 0.78 (0.20), residues: 690 sheet: 0.40 (0.15), residues: 1114 loop : 0.05 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 574 TYR 0.017 0.001 TYR C1064 PHE 0.012 0.001 PHE B 65 TRP 0.007 0.001 TRP A 64 HIS 0.007 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00456 (30982) covalent geometry : angle 0.57264 (42179) SS BOND : bond 0.03258 ( 51) SS BOND : angle 3.26280 ( 102) hydrogen bonds : bond 0.13403 ( 1265) hydrogen bonds : angle 7.45848 ( 3558) link_BETA1-4 : bond 0.00254 ( 13) link_BETA1-4 : angle 1.12304 ( 39) link_NAG-ASN : bond 0.00385 ( 44) link_NAG-ASN : angle 2.48665 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 470 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8828 (tp) cc_final: 0.8610 (tt) REVERT: A 267 LEU cc_start: 0.7948 (mt) cc_final: 0.7664 (mt) REVERT: A 722 GLU cc_start: 0.8034 (tt0) cc_final: 0.7732 (tt0) REVERT: A 760 LEU cc_start: 0.9407 (mt) cc_final: 0.9084 (pp) REVERT: A 866 MET cc_start: 0.8157 (mtt) cc_final: 0.7819 (mmp) REVERT: A 963 LEU cc_start: 0.8901 (mt) cc_final: 0.8614 (tt) REVERT: A 1132 ASN cc_start: 0.7911 (t0) cc_final: 0.7290 (t0) REVERT: B 140 PHE cc_start: 0.7993 (t80) cc_final: 0.7333 (t80) REVERT: B 159 VAL cc_start: 0.9056 (t) cc_final: 0.8682 (m) REVERT: B 201 PHE cc_start: 0.8734 (t80) cc_final: 0.8445 (t80) REVERT: B 223 LEU cc_start: 0.8472 (mp) cc_final: 0.8125 (mp) REVERT: B 297 LYS cc_start: 0.9027 (mttt) cc_final: 0.8708 (ttmt) REVERT: B 559 PHE cc_start: 0.7570 (p90) cc_final: 0.7186 (p90) REVERT: B 562 PHE cc_start: 0.7865 (m-80) cc_final: 0.7624 (m-80) REVERT: B 583 ASP cc_start: 0.8405 (m-30) cc_final: 0.8191 (m-30) REVERT: B 728 MET cc_start: 0.8076 (ptm) cc_final: 0.7685 (ptm) REVERT: B 737 MET cc_start: 0.9228 (ttt) cc_final: 0.8995 (ttt) REVERT: B 785 ILE cc_start: 0.9220 (mm) cc_final: 0.8755 (tt) REVERT: B 977 ILE cc_start: 0.9674 (mt) cc_final: 0.9473 (mm) REVERT: B 981 LEU cc_start: 0.8718 (mt) cc_final: 0.8477 (mp) REVERT: C 118 LEU cc_start: 0.9745 (tp) cc_final: 0.9448 (mt) REVERT: C 157 PHE cc_start: 0.7572 (t80) cc_final: 0.7054 (m-10) REVERT: C 238 PHE cc_start: 0.9334 (p90) cc_final: 0.8999 (p90) REVERT: C 273 LEU cc_start: 0.9206 (tp) cc_final: 0.8795 (mm) REVERT: C 294 SER cc_start: 0.9143 (m) cc_final: 0.8782 (p) REVERT: C 557 LEU cc_start: 0.8556 (mt) cc_final: 0.8304 (mt) REVERT: C 559 PHE cc_start: 0.8268 (p90) cc_final: 0.8033 (p90) REVERT: C 708 SER cc_start: 0.8640 (t) cc_final: 0.8138 (p) REVERT: C 737 MET cc_start: 0.9298 (ttt) cc_final: 0.8895 (ttt) REVERT: C 773 LYS cc_start: 0.9052 (tttt) cc_final: 0.8666 (tppp) REVERT: C 999 GLN cc_start: 0.8449 (tt0) cc_final: 0.8045 (tp40) REVERT: C 1132 ASN cc_start: 0.7703 (t0) cc_final: 0.7316 (t0) REVERT: L 36 GLN cc_start: 0.9158 (tt0) cc_final: 0.8690 (tt0) REVERT: H 32 TYR cc_start: 0.9623 (m-80) cc_final: 0.9395 (m-80) REVERT: E 6 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.6302 (mt0) outliers start: 21 outliers final: 7 residues processed: 488 average time/residue: 0.1945 time to fit residues: 150.9469 Evaluate side-chains 247 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 239 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain E residue 6 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN A 761 ASN A 892 GLN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS C 801 GLN C 904 ASN C 910 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 ASN L 36 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.124284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078590 restraints weight = 108769.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077790 restraints weight = 65368.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077504 restraints weight = 51336.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078190 restraints weight = 48697.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078982 restraints weight = 38996.185| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31090 Z= 0.152 Angle : 0.615 10.353 42452 Z= 0.316 Chirality : 0.045 0.181 4930 Planarity : 0.004 0.038 5374 Dihedral : 6.322 58.698 5284 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.70 % Allowed : 8.13 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3734 helix: 1.38 (0.20), residues: 679 sheet: 0.50 (0.15), residues: 1101 loop : 0.27 (0.15), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.023 0.002 TYR B 448 PHE 0.026 0.002 PHE B 339 TRP 0.010 0.001 TRP B 64 HIS 0.010 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00336 (30982) covalent geometry : angle 0.60220 (42179) SS BOND : bond 0.00290 ( 51) SS BOND : angle 1.61983 ( 102) hydrogen bonds : bond 0.04344 ( 1265) hydrogen bonds : angle 6.00139 ( 3558) link_BETA1-4 : bond 0.00454 ( 13) link_BETA1-4 : angle 1.01183 ( 39) link_NAG-ASN : bond 0.00287 ( 44) link_NAG-ASN : angle 1.88362 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.9347 (t80) cc_final: 0.8843 (t80) REVERT: A 295 GLU cc_start: 0.8595 (tp30) cc_final: 0.7862 (tp30) REVERT: A 722 GLU cc_start: 0.8488 (tt0) cc_final: 0.7823 (tt0) REVERT: A 818 LEU cc_start: 0.9124 (mm) cc_final: 0.8790 (tp) REVERT: A 866 MET cc_start: 0.8465 (mtt) cc_final: 0.7995 (mmp) REVERT: A 947 ASP cc_start: 0.8851 (m-30) cc_final: 0.8365 (t0) REVERT: A 963 LEU cc_start: 0.8914 (mt) cc_final: 0.8567 (tt) REVERT: A 1132 ASN cc_start: 0.7763 (t0) cc_final: 0.7041 (t0) REVERT: B 191 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7911 (mp0) REVERT: B 200 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8650 (t80) REVERT: B 297 LYS cc_start: 0.8977 (mttt) cc_final: 0.8655 (ttmt) REVERT: B 307 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8896 (mtmm) REVERT: B 728 MET cc_start: 0.8178 (ptm) cc_final: 0.7690 (ptm) REVERT: B 785 ILE cc_start: 0.9230 (mm) cc_final: 0.8838 (tt) REVERT: B 981 LEU cc_start: 0.8712 (mt) cc_final: 0.8440 (mp) REVERT: C 106 PHE cc_start: 0.9211 (m-80) cc_final: 0.8694 (m-10) REVERT: C 157 PHE cc_start: 0.7501 (t80) cc_final: 0.7072 (m-10) REVERT: C 238 PHE cc_start: 0.9384 (p90) cc_final: 0.9005 (p90) REVERT: C 273 LEU cc_start: 0.9316 (tp) cc_final: 0.8868 (mm) REVERT: C 557 LEU cc_start: 0.8517 (mt) cc_final: 0.8267 (mt) REVERT: C 559 PHE cc_start: 0.8358 (p90) cc_final: 0.8139 (p90) REVERT: C 689 ILE cc_start: 0.9291 (mt) cc_final: 0.8944 (mm) REVERT: C 707 ASN cc_start: 0.8118 (p0) cc_final: 0.7605 (p0) REVERT: C 772 ASP cc_start: 0.8695 (m-30) cc_final: 0.8476 (t0) REVERT: C 866 MET cc_start: 0.8954 (mtp) cc_final: 0.8750 (mtp) REVERT: C 976 ASP cc_start: 0.9353 (m-30) cc_final: 0.8863 (p0) REVERT: C 981 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8792 (tp) REVERT: C 1104 ARG cc_start: 0.8678 (mtt180) cc_final: 0.8242 (mtt-85) REVERT: C 1132 ASN cc_start: 0.7843 (t0) cc_final: 0.7280 (t0) REVERT: L 68 ASN cc_start: 0.9486 (p0) cc_final: 0.9196 (t0) REVERT: L 104 LYS cc_start: 0.5456 (OUTLIER) cc_final: 0.5228 (mmtm) REVERT: H 32 TYR cc_start: 0.9723 (m-80) cc_final: 0.9521 (m-80) outliers start: 56 outliers final: 21 residues processed: 326 average time/residue: 0.1864 time to fit residues: 99.9266 Evaluate side-chains 239 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 1029 CYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain J residue 32 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 72 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 chunk 255 optimal weight: 20.0000 chunk 271 optimal weight: 0.8980 chunk 213 optimal weight: 0.3980 chunk 307 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 759 GLN A 801 GLN A 892 GLN A 999 GLN ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN C 196 ASN ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 ASN L 26 ASN F 68 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.124291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075766 restraints weight = 110953.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077105 restraints weight = 71946.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.077265 restraints weight = 45274.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077521 restraints weight = 44142.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077985 restraints weight = 39398.189| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31090 Z= 0.141 Angle : 0.576 10.460 42452 Z= 0.293 Chirality : 0.044 0.323 4930 Planarity : 0.003 0.046 5374 Dihedral : 5.639 54.181 5273 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.91 % Allowed : 9.49 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3734 helix: 1.56 (0.20), residues: 685 sheet: 0.57 (0.15), residues: 1077 loop : 0.23 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 53 TYR 0.027 0.001 TYR B 448 PHE 0.030 0.001 PHE B 756 TRP 0.012 0.001 TRP H 34 HIS 0.006 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00313 (30982) covalent geometry : angle 0.56289 (42179) SS BOND : bond 0.00259 ( 51) SS BOND : angle 1.59352 ( 102) hydrogen bonds : bond 0.03996 ( 1265) hydrogen bonds : angle 5.73801 ( 3558) link_BETA1-4 : bond 0.00258 ( 13) link_BETA1-4 : angle 1.04736 ( 39) link_NAG-ASN : bond 0.00247 ( 44) link_NAG-ASN : angle 1.76086 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 235 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.9391 (t80) cc_final: 0.9035 (t80) REVERT: A 295 GLU cc_start: 0.8700 (tp30) cc_final: 0.8037 (tp30) REVERT: A 668 CYS cc_start: 0.5767 (m) cc_final: 0.4138 (m) REVERT: A 722 GLU cc_start: 0.8324 (tt0) cc_final: 0.7799 (tt0) REVERT: A 756 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: A 771 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8704 (mm-40) REVERT: A 818 LEU cc_start: 0.9128 (mm) cc_final: 0.8753 (tp) REVERT: A 866 MET cc_start: 0.8659 (mtt) cc_final: 0.8125 (mmp) REVERT: A 947 ASP cc_start: 0.8863 (m-30) cc_final: 0.8438 (t0) REVERT: A 963 LEU cc_start: 0.8968 (mt) cc_final: 0.8594 (tt) REVERT: A 1132 ASN cc_start: 0.7758 (t0) cc_final: 0.7008 (t0) REVERT: B 191 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7915 (mp0) REVERT: B 297 LYS cc_start: 0.8995 (mttt) cc_final: 0.8648 (ttmt) REVERT: B 307 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8907 (mtmm) REVERT: B 583 ASP cc_start: 0.8997 (m-30) cc_final: 0.8588 (m-30) REVERT: B 728 MET cc_start: 0.8222 (ptm) cc_final: 0.7736 (ptm) REVERT: B 785 ILE cc_start: 0.9239 (mm) cc_final: 0.8803 (tt) REVERT: B 816 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8104 (tt0) REVERT: B 981 LEU cc_start: 0.8660 (mt) cc_final: 0.8447 (mp) REVERT: C 106 PHE cc_start: 0.9245 (m-80) cc_final: 0.8732 (m-10) REVERT: C 157 PHE cc_start: 0.7632 (t80) cc_final: 0.7119 (m-10) REVERT: C 238 PHE cc_start: 0.9423 (p90) cc_final: 0.8929 (p90) REVERT: C 273 LEU cc_start: 0.9358 (tp) cc_final: 0.8869 (mm) REVERT: C 278 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: C 557 LEU cc_start: 0.8546 (mt) cc_final: 0.8312 (mt) REVERT: C 559 PHE cc_start: 0.8476 (p90) cc_final: 0.8217 (p90) REVERT: C 707 ASN cc_start: 0.8264 (p0) cc_final: 0.7795 (p0) REVERT: C 899 MET cc_start: 0.8934 (tpp) cc_final: 0.8691 (tpp) REVERT: C 976 ASP cc_start: 0.9292 (m-30) cc_final: 0.8869 (p0) REVERT: C 981 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8632 (tp) REVERT: C 1132 ASN cc_start: 0.7754 (t0) cc_final: 0.7237 (t0) REVERT: F 53 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6440 (mmp80) outliers start: 63 outliers final: 35 residues processed: 279 average time/residue: 0.1752 time to fit residues: 82.6810 Evaluate side-chains 244 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1029 CYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain J residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 183 optimal weight: 2.9990 chunk 314 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 121 optimal weight: 30.0000 chunk 300 optimal weight: 0.8980 chunk 309 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 5 optimal weight: 30.0000 chunk 272 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN A 999 GLN ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 ASN C 196 ASN C 962 GLN ** H 6 GLN ** 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 = 0.4206 r_free = 0.4206 target = 0.124286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.075703 restraints weight = 109716.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077353 restraints weight = 68421.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077313 restraints weight = 40934.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077764 restraints weight = 41681.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077992 restraints weight = 35985.679| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31090 Z= 0.134 Angle : 0.554 10.641 42452 Z= 0.283 Chirality : 0.043 0.192 4930 Planarity : 0.003 0.065 5374 Dihedral : 5.052 48.485 5271 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.06 % Allowed : 10.31 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3734 helix: 1.67 (0.21), residues: 671 sheet: 0.64 (0.15), residues: 1073 loop : 0.22 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 102 TYR 0.022 0.001 TYR A 704 PHE 0.023 0.001 PHE B 559 TRP 0.011 0.001 TRP A 64 HIS 0.005 0.001 HIS C 652 Details of bonding type rmsd covalent geometry : bond 0.00297 (30982) covalent geometry : angle 0.54158 (42179) SS BOND : bond 0.00197 ( 51) SS BOND : angle 1.48846 ( 102) hydrogen bonds : bond 0.03766 ( 1265) hydrogen bonds : angle 5.55994 ( 3558) link_BETA1-4 : bond 0.00296 ( 13) link_BETA1-4 : angle 1.03702 ( 39) link_NAG-ASN : bond 0.00230 ( 44) link_NAG-ASN : angle 1.67902 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.9362 (t80) cc_final: 0.8983 (t80) REVERT: A 295 GLU cc_start: 0.8664 (tp30) cc_final: 0.8031 (tp30) REVERT: A 361 ASP cc_start: 0.9046 (p0) cc_final: 0.8821 (t70) REVERT: A 559 PHE cc_start: 0.8354 (p90) cc_final: 0.8113 (p90) REVERT: A 722 GLU cc_start: 0.8263 (tt0) cc_final: 0.7795 (tt0) REVERT: A 756 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: A 818 LEU cc_start: 0.9086 (mm) cc_final: 0.8721 (tp) REVERT: A 866 MET cc_start: 0.8590 (mtt) cc_final: 0.8075 (mmp) REVERT: A 947 ASP cc_start: 0.8796 (m-30) cc_final: 0.8375 (t0) REVERT: A 1132 ASN cc_start: 0.7703 (t0) cc_final: 0.6979 (t0) REVERT: B 153 MET cc_start: 0.9504 (mmm) cc_final: 0.9285 (mmm) REVERT: B 200 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8364 (t80) REVERT: B 297 LYS cc_start: 0.8975 (mttt) cc_final: 0.8541 (mtpt) REVERT: B 307 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8920 (mtmm) REVERT: B 583 ASP cc_start: 0.8927 (m-30) cc_final: 0.8484 (m-30) REVERT: B 728 MET cc_start: 0.8219 (ptm) cc_final: 0.7935 (ptm) REVERT: B 785 ILE cc_start: 0.9232 (mm) cc_final: 0.8817 (tt) REVERT: B 981 LEU cc_start: 0.8713 (mt) cc_final: 0.8409 (mp) REVERT: B 1048 SER cc_start: 0.8621 (m) cc_final: 0.8084 (p) REVERT: C 106 PHE cc_start: 0.9215 (m-80) cc_final: 0.8778 (m-10) REVERT: C 238 PHE cc_start: 0.9393 (p90) cc_final: 0.8951 (p90) REVERT: C 273 LEU cc_start: 0.9236 (tp) cc_final: 0.8877 (mm) REVERT: C 278 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: C 557 LEU cc_start: 0.8528 (mt) cc_final: 0.8291 (mt) REVERT: C 559 PHE cc_start: 0.8516 (p90) cc_final: 0.8216 (p90) REVERT: C 562 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: C 707 ASN cc_start: 0.8225 (p0) cc_final: 0.7805 (p0) REVERT: C 881 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8595 (m) REVERT: C 981 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8667 (tp) REVERT: C 1132 ASN cc_start: 0.7726 (t0) cc_final: 0.7228 (t0) REVERT: F 53 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7185 (mmp80) outliers start: 68 outliers final: 41 residues processed: 271 average time/residue: 0.1802 time to fit residues: 82.5142 Evaluate side-chains 249 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 1029 CYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 53 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 231 optimal weight: 0.3980 chunk 290 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 333 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 194 optimal weight: 1.9990 chunk 302 optimal weight: 0.0070 chunk 20 optimal weight: 7.9990 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.123707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.075125 restraints weight = 109303.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076222 restraints weight = 68553.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077131 restraints weight = 41189.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077655 restraints weight = 35792.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.077874 restraints weight = 32657.728| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31090 Z= 0.156 Angle : 0.547 10.205 42452 Z= 0.281 Chirality : 0.043 0.168 4930 Planarity : 0.003 0.052 5374 Dihedral : 4.752 41.655 5271 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.06 % Allowed : 11.34 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3734 helix: 1.60 (0.21), residues: 665 sheet: 0.68 (0.16), residues: 1058 loop : 0.19 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1104 TYR 0.019 0.001 TYR C 914 PHE 0.020 0.001 PHE B 559 TRP 0.011 0.001 TRP B 64 HIS 0.005 0.001 HIS C 652 Details of bonding type rmsd covalent geometry : bond 0.00345 (30982) covalent geometry : angle 0.53725 (42179) SS BOND : bond 0.00209 ( 51) SS BOND : angle 1.01002 ( 102) hydrogen bonds : bond 0.03755 ( 1265) hydrogen bonds : angle 5.51761 ( 3558) link_BETA1-4 : bond 0.00261 ( 13) link_BETA1-4 : angle 1.06284 ( 39) link_NAG-ASN : bond 0.00271 ( 44) link_NAG-ASN : angle 1.67271 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 201 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.8689 (tp30) cc_final: 0.8074 (tp30) REVERT: A 559 PHE cc_start: 0.8387 (p90) cc_final: 0.8086 (p90) REVERT: A 722 GLU cc_start: 0.8160 (tt0) cc_final: 0.7904 (tt0) REVERT: A 756 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: A 771 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8798 (mm-40) REVERT: A 818 LEU cc_start: 0.9067 (mm) cc_final: 0.8702 (tp) REVERT: A 866 MET cc_start: 0.8618 (mtt) cc_final: 0.8110 (mmp) REVERT: A 947 ASP cc_start: 0.8745 (m-30) cc_final: 0.8362 (t0) REVERT: A 1132 ASN cc_start: 0.7703 (t0) cc_final: 0.6959 (t0) REVERT: B 200 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8459 (t80) REVERT: B 201 PHE cc_start: 0.8765 (t80) cc_final: 0.8380 (t80) REVERT: B 307 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8955 (mtmm) REVERT: B 448 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8069 (t80) REVERT: B 728 MET cc_start: 0.8252 (ptm) cc_final: 0.7889 (ptm) REVERT: B 785 ILE cc_start: 0.9242 (mm) cc_final: 0.8806 (tt) REVERT: B 981 LEU cc_start: 0.8760 (mt) cc_final: 0.8458 (mp) REVERT: B 1048 SER cc_start: 0.8551 (m) cc_final: 0.8129 (p) REVERT: C 106 PHE cc_start: 0.9191 (m-80) cc_final: 0.8785 (m-10) REVERT: C 153 MET cc_start: 0.8197 (mmm) cc_final: 0.7955 (mmm) REVERT: C 238 PHE cc_start: 0.9339 (p90) cc_final: 0.8932 (p90) REVERT: C 273 LEU cc_start: 0.9250 (tp) cc_final: 0.8878 (mm) REVERT: C 278 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: C 557 LEU cc_start: 0.8512 (mt) cc_final: 0.8242 (mt) REVERT: C 559 PHE cc_start: 0.8528 (p90) cc_final: 0.8237 (p90) REVERT: C 707 ASN cc_start: 0.8296 (p0) cc_final: 0.7862 (p0) REVERT: C 756 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8297 (t80) REVERT: C 772 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8511 (t70) REVERT: C 881 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8647 (m) REVERT: C 931 ILE cc_start: 0.8634 (mm) cc_final: 0.8434 (mm) REVERT: C 1132 ASN cc_start: 0.7737 (t0) cc_final: 0.7232 (t0) REVERT: F 53 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.5564 (mmp80) outliers start: 68 outliers final: 43 residues processed: 253 average time/residue: 0.1809 time to fit residues: 77.7943 Evaluate side-chains 236 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1029 CYS Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 53 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 359 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 358 optimal weight: 9.9990 chunk 349 optimal weight: 20.0000 chunk 149 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 237 optimal weight: 30.0000 chunk 89 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 364 optimal weight: 30.0000 chunk 310 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN A 999 GLN ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 164 ASN C 196 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** 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 = 0.4177 r_free = 0.4177 target = 0.122619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.074854 restraints weight = 109816.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.074807 restraints weight = 73242.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.074620 restraints weight = 51942.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.074954 restraints weight = 48948.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076011 restraints weight = 41619.100| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31090 Z= 0.230 Angle : 0.601 10.080 42452 Z= 0.308 Chirality : 0.044 0.247 4930 Planarity : 0.004 0.044 5374 Dihedral : 4.731 29.763 5271 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.46 % Allowed : 11.64 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3734 helix: 1.39 (0.20), residues: 658 sheet: 0.58 (0.16), residues: 1041 loop : 0.10 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1011 TYR 0.025 0.002 TYR C 914 PHE 0.018 0.002 PHE A1086 TRP 0.016 0.001 TRP C1099 HIS 0.008 0.001 HIS C 652 Details of bonding type rmsd covalent geometry : bond 0.00505 (30982) covalent geometry : angle 0.59042 (42179) SS BOND : bond 0.00518 ( 51) SS BOND : angle 1.07790 ( 102) hydrogen bonds : bond 0.04019 ( 1265) hydrogen bonds : angle 5.66518 ( 3558) link_BETA1-4 : bond 0.00188 ( 13) link_BETA1-4 : angle 1.14741 ( 39) link_NAG-ASN : bond 0.00434 ( 44) link_NAG-ASN : angle 1.85683 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 182 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8316 (mmm) cc_final: 0.8088 (mmm) REVERT: A 201 PHE cc_start: 0.9393 (t80) cc_final: 0.8844 (t80) REVERT: A 295 GLU cc_start: 0.8646 (tp30) cc_final: 0.8031 (tp30) REVERT: A 559 PHE cc_start: 0.8416 (p90) cc_final: 0.8090 (p90) REVERT: A 722 GLU cc_start: 0.8315 (tt0) cc_final: 0.7986 (tt0) REVERT: A 756 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: A 771 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8747 (mm-40) REVERT: A 818 LEU cc_start: 0.9084 (mm) cc_final: 0.8726 (tp) REVERT: A 866 MET cc_start: 0.8575 (mtt) cc_final: 0.8182 (mmp) REVERT: A 947 ASP cc_start: 0.8709 (m-30) cc_final: 0.8366 (t0) REVERT: A 1132 ASN cc_start: 0.7694 (t0) cc_final: 0.6950 (t0) REVERT: B 200 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8508 (t80) REVERT: B 201 PHE cc_start: 0.8890 (t80) cc_final: 0.8432 (t80) REVERT: B 307 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8940 (mtmm) REVERT: B 448 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8204 (t80) REVERT: B 696 LEU cc_start: 0.9078 (mt) cc_final: 0.8814 (mp) REVERT: B 728 MET cc_start: 0.8344 (ptm) cc_final: 0.7990 (ptm) REVERT: B 785 ILE cc_start: 0.9245 (mm) cc_final: 0.8791 (tt) REVERT: B 962 GLN cc_start: 0.9121 (mm110) cc_final: 0.8765 (mp10) REVERT: B 981 LEU cc_start: 0.8798 (mt) cc_final: 0.8524 (mp) REVERT: C 106 PHE cc_start: 0.9215 (m-80) cc_final: 0.8713 (m-10) REVERT: C 153 MET cc_start: 0.8225 (mmm) cc_final: 0.8013 (mmm) REVERT: C 238 PHE cc_start: 0.9357 (p90) cc_final: 0.8974 (p90) REVERT: C 273 LEU cc_start: 0.9219 (tp) cc_final: 0.8893 (mm) REVERT: C 278 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: C 557 LEU cc_start: 0.8594 (mt) cc_final: 0.8192 (mt) REVERT: C 559 PHE cc_start: 0.8601 (p90) cc_final: 0.8258 (p90) REVERT: C 581 ILE cc_start: 0.8112 (mm) cc_final: 0.7395 (tp) REVERT: C 772 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8494 (t70) REVERT: C 931 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8433 (mm) REVERT: C 1132 ASN cc_start: 0.7707 (t0) cc_final: 0.7115 (t0) outliers start: 81 outliers final: 61 residues processed: 248 average time/residue: 0.1717 time to fit residues: 72.4919 Evaluate side-chains 239 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 883 TRP Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1029 CYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 885 PHE Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain J residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 chunk 281 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 305 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 892 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** 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 = 0.4181 r_free = 0.4181 target = 0.122759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074228 restraints weight = 109540.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.075008 restraints weight = 72326.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075381 restraints weight = 44620.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075682 restraints weight = 41642.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076288 restraints weight = 37036.179| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31090 Z= 0.184 Angle : 0.566 11.477 42452 Z= 0.290 Chirality : 0.043 0.189 4930 Planarity : 0.004 0.080 5374 Dihedral : 4.599 28.020 5271 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.46 % Allowed : 11.67 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3734 helix: 1.41 (0.20), residues: 659 sheet: 0.54 (0.16), residues: 1043 loop : 0.12 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 980 TYR 0.020 0.001 TYR C 914 PHE 0.018 0.001 PHE B 559 TRP 0.014 0.001 TRP C1099 HIS 0.006 0.001 HIS C 652 Details of bonding type rmsd covalent geometry : bond 0.00407 (30982) covalent geometry : angle 0.55741 (42179) SS BOND : bond 0.00216 ( 51) SS BOND : angle 0.85036 ( 102) hydrogen bonds : bond 0.03817 ( 1265) hydrogen bonds : angle 5.59042 ( 3558) link_BETA1-4 : bond 0.00207 ( 13) link_BETA1-4 : angle 1.08793 ( 39) link_NAG-ASN : bond 0.00327 ( 44) link_NAG-ASN : angle 1.70955 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 182 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.9352 (t80) cc_final: 0.8805 (t80) REVERT: A 295 GLU cc_start: 0.8713 (tp30) cc_final: 0.8072 (tp30) REVERT: A 559 PHE cc_start: 0.8436 (p90) cc_final: 0.8075 (p90) REVERT: A 722 GLU cc_start: 0.8196 (tt0) cc_final: 0.7947 (tt0) REVERT: A 756 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: A 818 LEU cc_start: 0.9127 (mm) cc_final: 0.8754 (tp) REVERT: A 866 MET cc_start: 0.8681 (mtt) cc_final: 0.8235 (mmp) REVERT: A 947 ASP cc_start: 0.8768 (m-30) cc_final: 0.8392 (t0) REVERT: A 1132 ASN cc_start: 0.7731 (t0) cc_final: 0.6956 (t0) REVERT: B 200 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8501 (t80) REVERT: B 307 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8952 (mtmm) REVERT: B 448 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8152 (t80) REVERT: B 696 LEU cc_start: 0.9104 (mt) cc_final: 0.8858 (mp) REVERT: B 728 MET cc_start: 0.8387 (ptm) cc_final: 0.8039 (ptm) REVERT: B 785 ILE cc_start: 0.9235 (mm) cc_final: 0.8775 (tt) REVERT: B 962 GLN cc_start: 0.9190 (mm110) cc_final: 0.8798 (mp10) REVERT: B 981 LEU cc_start: 0.8792 (mt) cc_final: 0.8511 (mp) REVERT: C 106 PHE cc_start: 0.9188 (m-80) cc_final: 0.8718 (m-10) REVERT: C 153 MET cc_start: 0.8360 (mmm) cc_final: 0.8139 (mmm) REVERT: C 238 PHE cc_start: 0.9340 (p90) cc_final: 0.8973 (p90) REVERT: C 273 LEU cc_start: 0.9282 (tp) cc_final: 0.8941 (mm) REVERT: C 278 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: C 557 LEU cc_start: 0.8496 (mt) cc_final: 0.8230 (mt) REVERT: C 559 PHE cc_start: 0.8527 (p90) cc_final: 0.8239 (p90) REVERT: C 581 ILE cc_start: 0.8360 (mm) cc_final: 0.8102 (mm) REVERT: C 772 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8560 (t70) REVERT: C 881 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8846 (m) REVERT: C 926 SER cc_start: 0.8571 (m) cc_final: 0.8265 (t) REVERT: C 931 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8421 (mm) REVERT: C 1132 ASN cc_start: 0.7686 (t0) cc_final: 0.7119 (t0) outliers start: 81 outliers final: 63 residues processed: 244 average time/residue: 0.1559 time to fit residues: 65.5107 Evaluate side-chains 241 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 170 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 883 TRP Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1029 CYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain J residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 353 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 216 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 142 optimal weight: 30.0000 chunk 199 optimal weight: 0.9990 chunk 362 optimal weight: 50.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 892 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN C 774 ASN F 68 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** 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 = 0.4202 r_free = 0.4202 target = 0.123871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076565 restraints weight = 110344.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076923 restraints weight = 69412.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077268 restraints weight = 43541.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077496 restraints weight = 44978.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.078080 restraints weight = 37140.255| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31090 Z= 0.115 Angle : 0.540 12.595 42452 Z= 0.273 Chirality : 0.043 0.169 4930 Planarity : 0.003 0.046 5374 Dihedral : 4.247 25.643 5271 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.82 % Allowed : 12.70 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3734 helix: 1.51 (0.21), residues: 653 sheet: 0.55 (0.15), residues: 1077 loop : 0.18 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 574 TYR 0.018 0.001 TYR B1064 PHE 0.014 0.001 PHE A 426 TRP 0.011 0.001 TRP B 64 HIS 0.004 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00253 (30982) covalent geometry : angle 0.53309 (42179) SS BOND : bond 0.00150 ( 51) SS BOND : angle 0.72419 ( 102) hydrogen bonds : bond 0.03514 ( 1265) hydrogen bonds : angle 5.40118 ( 3558) link_BETA1-4 : bond 0.00310 ( 13) link_BETA1-4 : angle 1.01765 ( 39) link_NAG-ASN : bond 0.00185 ( 44) link_NAG-ASN : angle 1.48043 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.9382 (t80) cc_final: 0.8867 (t80) REVERT: A 295 GLU cc_start: 0.8653 (tp30) cc_final: 0.8009 (tp30) REVERT: A 559 PHE cc_start: 0.8382 (p90) cc_final: 0.8046 (p90) REVERT: A 722 GLU cc_start: 0.8151 (tt0) cc_final: 0.7860 (tt0) REVERT: A 818 LEU cc_start: 0.9093 (mm) cc_final: 0.8716 (tp) REVERT: A 866 MET cc_start: 0.8599 (mtt) cc_final: 0.8197 (mmp) REVERT: A 947 ASP cc_start: 0.8683 (m-30) cc_final: 0.8364 (t0) REVERT: A 1132 ASN cc_start: 0.7615 (t0) cc_final: 0.6831 (t0) REVERT: B 200 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8446 (t80) REVERT: B 307 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8923 (mtmm) REVERT: B 448 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8167 (t80) REVERT: B 696 LEU cc_start: 0.9103 (mt) cc_final: 0.8851 (mp) REVERT: B 728 MET cc_start: 0.8317 (ptm) cc_final: 0.7996 (ptm) REVERT: B 785 ILE cc_start: 0.9223 (mm) cc_final: 0.8800 (tt) REVERT: B 816 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8036 (tt0) REVERT: B 962 GLN cc_start: 0.9171 (mm110) cc_final: 0.8780 (mp10) REVERT: B 981 LEU cc_start: 0.8804 (mt) cc_final: 0.8487 (mp) REVERT: B 1044 TYR cc_start: 0.8184 (m-10) cc_final: 0.7921 (m-10) REVERT: B 1048 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.7986 (p) REVERT: C 106 PHE cc_start: 0.9222 (m-80) cc_final: 0.8813 (m-10) REVERT: C 238 PHE cc_start: 0.9382 (p90) cc_final: 0.9024 (p90) REVERT: C 241 LEU cc_start: 0.8064 (mt) cc_final: 0.7771 (mp) REVERT: C 273 LEU cc_start: 0.9267 (tp) cc_final: 0.8913 (mm) REVERT: C 278 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: C 557 LEU cc_start: 0.8434 (mt) cc_final: 0.8131 (mt) REVERT: C 559 PHE cc_start: 0.8518 (p90) cc_final: 0.8215 (p90) REVERT: C 581 ILE cc_start: 0.8181 (mm) cc_final: 0.7943 (mm) REVERT: C 719 VAL cc_start: 0.9647 (t) cc_final: 0.9416 (m) REVERT: C 772 ASP cc_start: 0.8833 (t0) cc_final: 0.8490 (t70) REVERT: C 881 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8728 (m) REVERT: C 926 SER cc_start: 0.8503 (m) cc_final: 0.8199 (t) REVERT: C 1132 ASN cc_start: 0.7716 (t0) cc_final: 0.7219 (t0) outliers start: 60 outliers final: 39 residues processed: 245 average time/residue: 0.1628 time to fit residues: 69.2168 Evaluate side-chains 228 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 883 TRP Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1029 CYS Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 53 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 194 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 351 optimal weight: 50.0000 chunk 16 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 305 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 313 optimal weight: 0.0980 chunk 245 optimal weight: 50.0000 chunk 169 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** 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 = 0.4204 r_free = 0.4204 target = 0.123961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076225 restraints weight = 109308.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076772 restraints weight = 69607.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077622 restraints weight = 42604.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078232 restraints weight = 37113.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078442 restraints weight = 33176.777| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31090 Z= 0.105 Angle : 0.545 16.618 42452 Z= 0.273 Chirality : 0.043 0.312 4930 Planarity : 0.003 0.048 5374 Dihedral : 4.045 24.162 5271 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.36 % Allowed : 13.25 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3734 helix: 1.55 (0.21), residues: 636 sheet: 0.63 (0.15), residues: 1073 loop : 0.18 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 574 TYR 0.017 0.001 TYR C 200 PHE 0.024 0.001 PHE C 272 TRP 0.012 0.001 TRP B 64 HIS 0.007 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00230 (30982) covalent geometry : angle 0.53820 (42179) SS BOND : bond 0.00148 ( 51) SS BOND : angle 0.90831 ( 102) hydrogen bonds : bond 0.03424 ( 1265) hydrogen bonds : angle 5.33849 ( 3558) link_BETA1-4 : bond 0.00313 ( 13) link_BETA1-4 : angle 1.03717 ( 39) link_NAG-ASN : bond 0.00178 ( 44) link_NAG-ASN : angle 1.43780 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.9344 (t80) cc_final: 0.8835 (t80) REVERT: A 295 GLU cc_start: 0.8646 (tp30) cc_final: 0.7993 (tp30) REVERT: A 559 PHE cc_start: 0.8360 (p90) cc_final: 0.7985 (p90) REVERT: A 722 GLU cc_start: 0.8150 (tt0) cc_final: 0.7863 (tt0) REVERT: A 772 ASP cc_start: 0.8325 (m-30) cc_final: 0.7776 (m-30) REVERT: A 818 LEU cc_start: 0.9073 (mm) cc_final: 0.8700 (tp) REVERT: A 866 MET cc_start: 0.8618 (mtt) cc_final: 0.8219 (mmp) REVERT: A 947 ASP cc_start: 0.8671 (m-30) cc_final: 0.8367 (t0) REVERT: A 1132 ASN cc_start: 0.7562 (t0) cc_final: 0.6783 (t0) REVERT: B 200 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8433 (t80) REVERT: B 307 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8899 (mtmm) REVERT: B 448 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8199 (t80) REVERT: B 696 LEU cc_start: 0.9090 (mt) cc_final: 0.8860 (mp) REVERT: B 728 MET cc_start: 0.8331 (ptm) cc_final: 0.8114 (ptm) REVERT: B 785 ILE cc_start: 0.9215 (mm) cc_final: 0.8809 (tt) REVERT: B 981 LEU cc_start: 0.8797 (mt) cc_final: 0.8490 (mp) REVERT: B 1026 MET cc_start: 0.8730 (tpp) cc_final: 0.8467 (tpp) REVERT: B 1044 TYR cc_start: 0.8178 (m-10) cc_final: 0.7950 (m-10) REVERT: B 1048 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7956 (p) REVERT: C 106 PHE cc_start: 0.9208 (m-80) cc_final: 0.8820 (m-10) REVERT: C 238 PHE cc_start: 0.9334 (p90) cc_final: 0.8987 (p90) REVERT: C 241 LEU cc_start: 0.8052 (mt) cc_final: 0.7724 (mp) REVERT: C 273 LEU cc_start: 0.9235 (tp) cc_final: 0.8899 (mm) REVERT: C 278 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: C 557 LEU cc_start: 0.8447 (mt) cc_final: 0.8149 (mt) REVERT: C 559 PHE cc_start: 0.8535 (p90) cc_final: 0.8230 (p90) REVERT: C 581 ILE cc_start: 0.8157 (mm) cc_final: 0.7920 (mm) REVERT: C 719 VAL cc_start: 0.9657 (t) cc_final: 0.9437 (m) REVERT: C 772 ASP cc_start: 0.8778 (t0) cc_final: 0.8485 (t70) REVERT: C 881 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8682 (m) REVERT: C 926 SER cc_start: 0.8504 (m) cc_final: 0.8201 (t) REVERT: C 1132 ASN cc_start: 0.7702 (t0) cc_final: 0.7196 (t0) outliers start: 45 outliers final: 36 residues processed: 235 average time/residue: 0.1715 time to fit residues: 69.7637 Evaluate side-chains 223 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 883 TRP Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1029 CYS Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain F residue 48 TYR Chi-restraints excluded: chain F residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 42 optimal weight: 0.6980 chunk 167 optimal weight: 0.1980 chunk 52 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 290 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.124007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075848 restraints weight = 109985.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077152 restraints weight = 71117.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.077165 restraints weight = 44123.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077496 restraints weight = 45091.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.078046 restraints weight = 37373.334| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.313 31090 Z= 0.172 Angle : 0.693 59.200 42452 Z= 0.371 Chirality : 0.045 0.691 4930 Planarity : 0.004 0.054 5374 Dihedral : 4.041 24.130 5271 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.33 % Allowed : 13.71 % Favored : 84.96 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3734 helix: 1.54 (0.21), residues: 636 sheet: 0.64 (0.15), residues: 1073 loop : 0.18 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.000 ARG F 76 TYR 0.028 0.001 TYR K 85 PHE 0.025 0.001 PHE C 272 TRP 0.012 0.001 TRP B 64 HIS 0.006 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00407 (30982) covalent geometry : angle 0.68818 (42179) SS BOND : bond 0.00174 ( 51) SS BOND : angle 0.85478 ( 102) hydrogen bonds : bond 0.03453 ( 1265) hydrogen bonds : angle 5.33640 ( 3558) link_BETA1-4 : bond 0.00266 ( 13) link_BETA1-4 : angle 1.02146 ( 39) link_NAG-ASN : bond 0.00176 ( 44) link_NAG-ASN : angle 1.44437 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.9348 (t80) cc_final: 0.8841 (t80) REVERT: A 295 GLU cc_start: 0.8633 (tp30) cc_final: 0.7974 (tp30) REVERT: A 559 PHE cc_start: 0.8368 (p90) cc_final: 0.7994 (p90) REVERT: A 722 GLU cc_start: 0.8153 (tt0) cc_final: 0.7895 (tt0) REVERT: A 772 ASP cc_start: 0.8299 (m-30) cc_final: 0.7746 (m-30) REVERT: A 818 LEU cc_start: 0.9085 (mm) cc_final: 0.8714 (tp) REVERT: A 866 MET cc_start: 0.8608 (mtt) cc_final: 0.8226 (mmp) REVERT: A 947 ASP cc_start: 0.8667 (m-30) cc_final: 0.8364 (t0) REVERT: A 1132 ASN cc_start: 0.7585 (t0) cc_final: 0.6793 (t0) REVERT: B 86 PHE cc_start: 0.9254 (t80) cc_final: 0.8396 (t80) REVERT: B 200 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8429 (t80) REVERT: B 307 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8886 (mtmm) REVERT: B 448 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8142 (t80) REVERT: B 728 MET cc_start: 0.8323 (ptm) cc_final: 0.8104 (ptm) REVERT: B 785 ILE cc_start: 0.9209 (mm) cc_final: 0.8801 (tt) REVERT: B 981 LEU cc_start: 0.8816 (mt) cc_final: 0.8503 (mp) REVERT: B 1026 MET cc_start: 0.8747 (tpp) cc_final: 0.8483 (tpp) REVERT: B 1044 TYR cc_start: 0.8216 (m-10) cc_final: 0.7968 (m-10) REVERT: B 1048 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7906 (p) REVERT: C 106 PHE cc_start: 0.9193 (m-80) cc_final: 0.8813 (m-10) REVERT: C 238 PHE cc_start: 0.9324 (p90) cc_final: 0.8979 (p90) REVERT: C 241 LEU cc_start: 0.8014 (mt) cc_final: 0.7679 (mp) REVERT: C 273 LEU cc_start: 0.9225 (tp) cc_final: 0.8895 (mm) REVERT: C 278 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: C 557 LEU cc_start: 0.8460 (mt) cc_final: 0.8166 (mt) REVERT: C 559 PHE cc_start: 0.8545 (p90) cc_final: 0.8243 (p90) REVERT: C 581 ILE cc_start: 0.8157 (mm) cc_final: 0.7923 (mm) REVERT: C 719 VAL cc_start: 0.9657 (t) cc_final: 0.9440 (m) REVERT: C 772 ASP cc_start: 0.8740 (t0) cc_final: 0.8457 (t70) REVERT: C 881 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8666 (m) REVERT: C 926 SER cc_start: 0.8480 (m) cc_final: 0.8172 (t) REVERT: C 1132 ASN cc_start: 0.7704 (t0) cc_final: 0.7204 (t0) outliers start: 44 outliers final: 35 residues processed: 215 average time/residue: 0.1648 time to fit residues: 61.5521 Evaluate side-chains 220 residues out of total 3298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 883 TRP Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1029 CYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1048 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 761 ASN Chi-restraints excluded: chain C residue 881 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1029 CYS Chi-restraints excluded: chain F residue 48 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 232 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 329 optimal weight: 50.0000 chunk 369 optimal weight: 50.0000 chunk 296 optimal weight: 5.9990 chunk 336 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.123964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075783 restraints weight = 110625.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077097 restraints weight = 71456.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077160 restraints weight = 44153.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077541 restraints weight = 43977.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077964 restraints weight = 37229.864| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.313 31090 Z= 0.172 Angle : 0.693 59.200 42452 Z= 0.371 Chirality : 0.045 0.691 4930 Planarity : 0.004 0.054 5374 Dihedral : 4.041 24.130 5271 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.27 % Allowed : 13.89 % Favored : 84.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3734 helix: 1.54 (0.21), residues: 636 sheet: 0.64 (0.15), residues: 1073 loop : 0.18 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.000 ARG F 76 TYR 0.028 0.001 TYR K 85 PHE 0.025 0.001 PHE C 272 TRP 0.012 0.001 TRP B 64 HIS 0.006 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00407 (30982) covalent geometry : angle 0.68818 (42179) SS BOND : bond 0.00174 ( 51) SS BOND : angle 0.85478 ( 102) hydrogen bonds : bond 0.03453 ( 1265) hydrogen bonds : angle 5.33640 ( 3558) link_BETA1-4 : bond 0.00266 ( 13) link_BETA1-4 : angle 1.02146 ( 39) link_NAG-ASN : bond 0.00176 ( 44) link_NAG-ASN : angle 1.44437 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6369.27 seconds wall clock time: 110 minutes 42.75 seconds (6642.75 seconds total)