Starting phenix.real_space_refine on Sun Aug 9 13:55:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cin_16680/08_2026/8cin_16680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cin_16680/08_2026/8cin_16680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cin_16680/08_2026/8cin_16680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cin_16680/08_2026/8cin_16680.map" model { file = "/net/cci-nas-00/data/ceres_data/8cin_16680/08_2026/8cin_16680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cin_16680/08_2026/8cin_16680.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 22335 2.51 5 N 5787 2.21 5 O 6909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35175 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8241 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "B" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8241 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "C" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8241 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "E" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Chain: "F" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1582 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Chain: "J" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Chain: "K" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1582 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1582 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "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: 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: "C" 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 Time building chain proxies: 7.38, per 1000 atoms: 0.21 Number of scatterers: 35175 At special positions: 0 Unit cell: (222.742, 216.899, 173.081, 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 144 16.00 O 6909 8.00 N 5787 7.00 C 22335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 585 " distance=2.02 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS A 733 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 846 " distance=2.03 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1038 " distance=2.03 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 533 " - pdb=" SG CYS B 585 " distance=2.02 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS B 666 " distance=2.03 Simple disulfide: pdb=" SG CYS B 733 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 846 " distance=2.03 Simple disulfide: pdb=" SG CYS B1027 " - pdb=" SG CYS B1038 " distance=2.03 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 533 " - pdb=" SG CYS C 585 " distance=2.02 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 846 " distance=2.03 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 138 " - pdb=" SG CYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " 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-ASN " NAG A1201 " - " ASN A 58 " " NAG A1202 " - " ASN A 277 " " NAG A1203 " - " ASN A 598 " " NAG A1204 " - " ASN A 611 " " NAG A1205 " - " ASN A 652 " " NAG A1206 " - " ASN A 704 " " NAG A1207 " - " ASN A1069 " " NAG A1208 " - " ASN A 326 " " NAG A1209 " - " ASN A 338 " " NAG B1201 " - " ASN B 58 " " NAG B1202 " - " ASN B 277 " " NAG B1203 " - " ASN B 598 " " NAG B1204 " - " ASN B 611 " " NAG B1205 " - " ASN B 652 " " NAG B1206 " - " ASN B 704 " " NAG B1207 " - " ASN B1069 " " NAG B1208 " - " ASN B 326 " " NAG B1209 " - " ASN B 338 " " NAG C1201 " - " ASN C 58 " " NAG C1202 " - " ASN C 277 " " NAG C1203 " - " ASN C 598 " " NAG C1204 " - " ASN C 611 " " NAG C1205 " - " ASN C 652 " " NAG C1206 " - " ASN C 704 " " NAG C1207 " - " ASN C1069 " " NAG C1208 " - " ASN C 326 " " NAG C1209 " - " ASN C 338 " " NAG D 1 " - " ASN A 712 " " NAG G 1 " - " ASN A 796 " " NAG I 1 " - " ASN A1093 " " NAG M 1 " - " ASN A1129 " " NAG N 1 " - " ASN B 712 " " NAG O 1 " - " ASN B 796 " " NAG P 1 " - " ASN B1093 " " NAG Q 1 " - " ASN B1129 " " NAG R 1 " - " ASN C 712 " " NAG S 1 " - " ASN C 796 " " NAG T 1 " - " ASN C1093 " " NAG U 1 " - " ASN C1129 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8328 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 87 sheets defined 21.7% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.523A pdb=" N TRP A 348 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 4.050A pdb=" N TYR A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 4.587A pdb=" N ASN A 383 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 4.109A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.668A pdb=" N SER A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 741 through 750 removed outlier: 3.811A pdb=" N GLN A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 778 Processing helix chain 'A' and resid 811 through 821 Processing helix chain 'A' and resid 831 through 837 removed outlier: 3.831A pdb=" N CYS A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 851 Processing helix chain 'A' and resid 861 through 880 Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 892 through 904 Processing helix chain 'A' and resid 907 through 914 removed outlier: 4.063A pdb=" N LEU A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 Processing helix chain 'A' and resid 940 through 960 Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'A' and resid 980 through 1028 removed outlier: 3.871A pdb=" N VAL A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1142 removed outlier: 4.176A pdb=" N GLU A1139 " --> pdb=" O PRO A1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.519A pdb=" N TRP B 348 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 4.064A pdb=" N TYR B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 384 removed outlier: 4.586A pdb=" N ASN B 383 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 removed outlier: 4.122A pdb=" N SER B 403 " --> pdb=" O ASN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.663A pdb=" N SER B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 500 Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 741 through 750 removed outlier: 3.810A pdb=" N GLN B 750 " --> pdb=" O ASN B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 778 Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 831 through 837 removed outlier: 3.831A pdb=" N CYS B 835 " --> pdb=" O GLN B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 851 Processing helix chain 'B' and resid 861 through 880 Processing helix chain 'B' and resid 881 through 885 Processing helix chain 'B' and resid 892 through 904 Processing helix chain 'B' and resid 907 through 914 removed outlier: 4.057A pdb=" N LEU B 911 " --> pdb=" O THR B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 Processing helix chain 'B' and resid 940 through 960 Processing helix chain 'B' and resid 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 971 through 979 Processing helix chain 'B' and resid 980 through 1027 removed outlier: 3.871A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 987 " --> pdb=" O GLU B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1142 removed outlier: 4.171A pdb=" N GLU B1139 " --> pdb=" O PRO B1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 344 through 348 removed outlier: 3.516A pdb=" N TRP C 348 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 4.056A pdb=" N TYR C 364 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 384 removed outlier: 4.589A pdb=" N ASN C 383 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 removed outlier: 4.095A pdb=" N SER C 403 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'C' and resid 433 through 438 removed outlier: 3.667A pdb=" N SER C 438 " --> pdb=" O ASN C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 500 Processing helix chain 'C' and resid 732 through 739 Processing helix chain 'C' and resid 741 through 750 removed outlier: 3.813A pdb=" N GLN C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 778 Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 831 through 837 removed outlier: 3.832A pdb=" N CYS C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 851 Processing helix chain 'C' and resid 861 through 880 Processing helix chain 'C' and resid 881 through 885 Processing helix chain 'C' and resid 892 through 904 Processing helix chain 'C' and resid 907 through 914 removed outlier: 4.054A pdb=" N LEU C 911 " --> pdb=" O THR C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 Processing helix chain 'C' and resid 940 through 960 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 971 through 979 Processing helix chain 'C' and resid 980 through 1028 removed outlier: 3.872A pdb=" N VAL C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1142 removed outlier: 4.172A pdb=" N GLU C1139 " --> pdb=" O PRO C1135 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.501A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'F' and resid 125 through 131 Processing helix chain 'F' and resid 185 through 192 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 135 through 140 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'J' and resid 135 through 140 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 125 through 131 Processing helix chain 'K' and resid 185 through 192 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 removed outlier: 7.363A pdb=" N ASN A 58 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR A 264 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA A 259 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR A 90 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER A 200 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 5.626A pdb=" N ASP B 569 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 319 " --> pdb=" O CYS B 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 52 removed outlier: 7.445A pdb=" N THR A 269 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP A 285 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 271 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 283 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS A 273 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 removed outlier: 6.639A pdb=" N ARG A 97 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN A 116 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.473A pdb=" N GLN A 129 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 306 through 314 removed outlier: 6.730A pdb=" N VAL A 590 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN A 312 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY A 588 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY A 589 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 323 removed outlier: 4.210A pdb=" N GLU A 319 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP A 569 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE A 560 " --> pdb=" O PHE C 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 357 removed outlier: 6.729A pdb=" N CYS A 356 " --> pdb=" O CYS A 520 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 447 through 449 Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AB3, first strand: chain 'A' and resid 649 through 650 removed outlier: 6.328A pdb=" N ALA A 667 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 697 through 699 removed outlier: 3.652A pdb=" N LYS C 785 " --> pdb=" O ASN A 698 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 706 through 710 Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 723 removed outlier: 7.009A pdb=" N GLY A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N SER A1050 " --> pdb=" O GLY A1054 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A1056 " --> pdb=" O PRO A1048 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A1058 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A1046 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A1060 " --> pdb=" O LEU A1044 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 728 through 731 removed outlier: 4.529A pdb=" N LYS A 728 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.989A pdb=" N ILE A 783 " --> pdb=" O ASN B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1115 through 1117 Processing sheet with id=AC1, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id=AC2, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.366A pdb=" N ASN B 58 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR B 264 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 259 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR B 90 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER B 200 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 39 through 40 removed outlier: 5.627A pdb=" N ASP C 569 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU C 319 " --> pdb=" O CYS C 533 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 44 through 52 removed outlier: 7.442A pdb=" N THR B 269 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP B 285 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 271 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA B 283 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS B 273 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.637A pdb=" N ARG B 97 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN B 116 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 129 through 130 removed outlier: 6.474A pdb=" N GLN B 129 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 306 through 314 removed outlier: 6.732A pdb=" N VAL B 590 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN B 312 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLY B 588 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY B 589 " --> pdb=" O GLN B 608 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 349 through 353 Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 357 removed outlier: 6.722A pdb=" N CYS B 356 " --> pdb=" O CYS B 520 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AD2, first strand: chain 'B' and resid 468 through 469 Processing sheet with id=AD3, first strand: chain 'B' and resid 649 through 650 removed outlier: 6.333A pdb=" N ALA B 667 " --> pdb=" O PRO B 660 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 706 through 710 Processing sheet with id=AD5, first strand: chain 'B' and resid 713 through 723 removed outlier: 7.007A pdb=" N GLY B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER B1050 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B1056 " --> pdb=" O PRO B1048 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B1058 " --> pdb=" O SER B1046 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B1046 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B1060 " --> pdb=" O LEU B1044 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 728 through 731 removed outlier: 4.539A pdb=" N LYS B 728 " --> pdb=" O LEU B 856 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 783 through 785 removed outlier: 5.987A pdb=" N ILE B 783 " --> pdb=" O ASN C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1115 through 1117 Processing sheet with id=AD9, first strand: chain 'B' and resid 1089 through 1092 Processing sheet with id=AE1, first strand: chain 'C' and resid 23 through 27 removed outlier: 7.369A pdb=" N ASN C 58 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR C 264 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA C 259 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR C 90 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER C 200 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 44 through 52 removed outlier: 7.445A pdb=" N THR C 269 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASP C 285 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 271 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA C 283 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS C 273 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 79 through 80 removed outlier: 6.636A pdb=" N ARG C 97 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN C 116 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 129 through 130 removed outlier: 6.470A pdb=" N GLN C 129 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 306 through 314 removed outlier: 6.732A pdb=" N VAL C 590 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN C 312 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY C 588 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY C 589 " --> pdb=" O GLN C 608 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 349 through 353 Processing sheet with id=AE7, first strand: chain 'C' and resid 356 through 357 removed outlier: 6.725A pdb=" N CYS C 356 " --> pdb=" O CYS C 520 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AE9, first strand: chain 'C' and resid 468 through 469 Processing sheet with id=AF1, first strand: chain 'C' and resid 649 through 650 removed outlier: 6.338A pdb=" N ALA C 667 " --> pdb=" O PRO C 660 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 706 through 710 Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 723 removed outlier: 7.006A pdb=" N GLY C1054 " --> pdb=" O SER C1050 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER C1050 " --> pdb=" O GLY C1054 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1056 " --> pdb=" O PRO C1048 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C1058 " --> pdb=" O SER C1046 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C1046 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C1060 " --> pdb=" O LEU C1044 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 728 through 731 removed outlier: 4.536A pdb=" N LYS C 728 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1115 through 1117 Processing sheet with id=AF6, first strand: chain 'C' and resid 1089 through 1092 Processing sheet with id=AF7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.563A pdb=" N TRP E 34 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN E 50 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR E 52 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER E 56 " --> pdb=" O TYR E 52 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'E' and resid 128 through 132 removed outlier: 5.114A pdb=" N ALA E 145 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 192 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY E 147 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E 190 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU E 149 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER E 188 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS E 151 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU E 186 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 128 through 132 removed outlier: 5.114A pdb=" N ALA E 145 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 192 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY E 147 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E 190 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU E 149 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER E 188 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS E 151 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU E 186 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 159 through 162 removed outlier: 4.607A pdb=" N TYR E 202 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.365A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AG6, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'F' and resid 118 through 122 removed outlier: 5.945A pdb=" N TYR F 176 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 118 through 122 removed outlier: 5.945A pdb=" N TYR F 176 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 157 through 159 removed outlier: 4.231A pdb=" N TRP F 152 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.563A pdb=" N TRP H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR H 52 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER H 56 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AH4, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.931A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.931A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 159 through 162 removed outlier: 4.623A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AH8, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.565A pdb=" N TRP J 34 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR J 52 " --> pdb=" O SER J 56 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER J 56 " --> pdb=" O TYR J 52 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AI1, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.107A pdb=" N ALA J 145 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 192 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY J 147 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL J 190 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU J 149 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER J 188 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS J 151 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU J 186 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.107A pdb=" N ALA J 145 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 192 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY J 147 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL J 190 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU J 149 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER J 188 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS J 151 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU J 186 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 159 through 162 removed outlier: 4.616A pdb=" N TYR J 202 " --> pdb=" O VAL J 219 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.362A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AI6, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AI7, first strand: chain 'K' and resid 118 through 122 removed outlier: 5.947A pdb=" N TYR K 176 " --> pdb=" O ASP K 142 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 118 through 122 removed outlier: 5.947A pdb=" N TYR K 176 " --> pdb=" O ASP K 142 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 157 through 159 removed outlier: 4.231A pdb=" N TRP K 152 " --> pdb=" O VAL K 159 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.366A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AJ3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AJ4, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.947A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.947A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.230A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) 1595 hydrogen bonds defined for protein. 4155 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: 9.26 Time building geometry restraints manager: 3.65 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: 11157 1.34 - 1.46: 8324 1.46 - 1.58: 16333 1.58 - 1.70: 0 1.70 - 1.81: 171 Bond restraints: 35985 Sorted by residual: bond pdb=" C1 NAG B1207 " pdb=" O5 NAG B1207 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG C1207 " pdb=" O5 NAG C1207 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG A1207 " pdb=" O5 NAG A1207 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 35980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 47422 1.25 - 2.50: 1263 2.50 - 3.76: 301 3.76 - 5.01: 16 5.01 - 6.26: 21 Bond angle restraints: 49023 Sorted by residual: angle pdb=" N ILE B 839 " pdb=" CA ILE B 839 " pdb=" C ILE B 839 " ideal model delta sigma weight residual 113.47 108.23 5.24 1.01e+00 9.80e-01 2.69e+01 angle pdb=" N ILE A 839 " pdb=" CA ILE A 839 " pdb=" C ILE A 839 " ideal model delta sigma weight residual 113.47 108.25 5.22 1.01e+00 9.80e-01 2.67e+01 angle pdb=" N ILE C 839 " pdb=" CA ILE C 839 " pdb=" C ILE C 839 " ideal model delta sigma weight residual 113.47 108.30 5.17 1.01e+00 9.80e-01 2.62e+01 angle pdb=" C THR B 310 " pdb=" N SER B 311 " pdb=" CA SER B 311 " ideal model delta sigma weight residual 122.08 117.33 4.75 1.84e+00 2.95e-01 6.65e+00 angle pdb=" C THR C 310 " pdb=" N SER C 311 " pdb=" CA SER C 311 " ideal model delta sigma weight residual 122.08 117.37 4.71 1.84e+00 2.95e-01 6.57e+00 ... (remaining 49018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21171 17.90 - 35.79: 733 35.79 - 53.69: 154 53.69 - 71.59: 25 71.59 - 89.49: 15 Dihedral angle restraints: 22098 sinusoidal: 9111 harmonic: 12987 Sorted by residual: dihedral pdb=" CA THR A 594 " pdb=" C THR A 594 " pdb=" N PRO A 595 " pdb=" CA PRO A 595 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR B 594 " pdb=" C THR B 594 " pdb=" N PRO B 595 " pdb=" CA PRO B 595 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR C 594 " pdb=" C THR C 594 " pdb=" N PRO C 595 " pdb=" CA PRO C 595 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 22095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3502 0.032 - 0.063: 1434 0.063 - 0.095: 447 0.095 - 0.127: 317 0.127 - 0.159: 36 Chirality restraints: 5736 Sorted by residual: chirality pdb=" C1 NAG C1203 " pdb=" ND2 ASN C 598 " pdb=" C2 NAG C1203 " pdb=" O5 NAG C1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" C1 NAG A1203 " pdb=" ND2 ASN A 598 " pdb=" C2 NAG A1203 " pdb=" O5 NAG A1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" C1 NAG B1203 " pdb=" ND2 ASN B 598 " pdb=" C2 NAG B1203 " pdb=" O5 NAG B1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 5733 not shown) Planarity restraints: 6279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 156 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO J 157 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO J 157 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 156 " -0.030 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO E 157 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 157 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 157 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO H 157 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " 0.022 5.00e-02 4.00e+02 ... (remaining 6276 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6173 2.77 - 3.30: 31759 3.30 - 3.84: 57175 3.84 - 4.37: 69651 4.37 - 4.90: 121486 Nonbonded interactions: 286244 Sorted by model distance: nonbonded pdb=" O THR C 388 " pdb=" OG1 THR C 518 " model vdw 2.238 3.040 nonbonded pdb=" O THR A 388 " pdb=" OG1 THR A 518 " model vdw 2.240 3.040 nonbonded pdb=" O THR B 388 " pdb=" OG1 THR B 518 " model vdw 2.240 3.040 nonbonded pdb=" O THR B 103 " pdb=" NH1 ARG B 232 " model vdw 2.256 3.120 nonbonded pdb=" O THR C 103 " pdb=" NH1 ARG C 232 " model vdw 2.260 3.120 ... (remaining 286239 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 31.730 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.170 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:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.004 0.036 36090 Z= 0.179 Angle : 0.527 6.261 49284 Z= 0.270 Chirality : 0.044 0.159 5736 Planarity : 0.004 0.045 6240 Dihedral : 9.970 89.486 13608 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.70 % Allowed : 3.21 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.29 (0.13), residues: 4425 helix: 1.92 (0.19), residues: 759 sheet: 0.63 (0.14), residues: 1290 loop : -0.62 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1009 TYR 0.016 0.001 TYR A1062 PHE 0.014 0.001 PHE A 372 TRP 0.008 0.001 TRP C 431 HIS 0.003 0.000 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (35985) covalent geometry : angle 0.51941 / 0.27 (49023) SS BOND : bond 0.00267 / 0.15 ( 54) SS BOND : angle 0.59521 / 0.39 ( 108) hydrogen bonds : bond 0.11743 / 7.71 ( 1489) hydrogen bonds : angle 6.56871 / 4.60 ( 4155) link_BETA1-4 : bond 0.00332 / 0.21 ( 12) link_BETA1-4 : angle 1.01469 / 0.66 ( 36) link_NAG-ASN : bond 0.00274 / 0.17 ( 39) link_NAG-ASN : angle 1.76590 / 1.16 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 325 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8836 (tt0) cc_final: 0.8580 (tm-30) REVERT: A 152 PHE cc_start: 0.6813 (p90) cc_final: 0.6560 (p90) REVERT: A 352 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8440 (ttt-90) REVERT: A 569 ASP cc_start: 0.8297 (t70) cc_final: 0.7859 (t0) REVERT: A 656 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8022 (mp0) REVERT: A 1137 GLN cc_start: 0.9029 (tp40) cc_final: 0.8607 (tm-30) REVERT: B 49 GLN cc_start: 0.8861 (tt0) cc_final: 0.8486 (tm-30) REVERT: B 152 PHE cc_start: 0.6780 (p90) cc_final: 0.6550 (p90) REVERT: B 352 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8421 (ttt-90) REVERT: B 569 ASP cc_start: 0.8246 (t70) cc_final: 0.7795 (t0) REVERT: B 656 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7954 (mp0) REVERT: B 1137 GLN cc_start: 0.9023 (tp40) cc_final: 0.8560 (tm-30) REVERT: C 49 GLN cc_start: 0.8821 (tt0) cc_final: 0.8528 (tm-30) REVERT: C 152 PHE cc_start: 0.6684 (p90) cc_final: 0.6463 (p90) REVERT: C 569 ASP cc_start: 0.8376 (t70) cc_final: 0.8035 (t0) REVERT: C 656 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7962 (mp0) REVERT: C 775 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8199 (mm-30) REVERT: C 1137 GLN cc_start: 0.9028 (tp40) cc_final: 0.8557 (tm-30) REVERT: E 162 TRP cc_start: 0.7455 (m100) cc_final: 0.7158 (m100) REVERT: E 205 ASN cc_start: 0.7024 (t0) cc_final: 0.6765 (m110) REVERT: F 195 TYR cc_start: 0.5216 (m-80) cc_final: 0.4740 (m-80) REVERT: J 205 ASN cc_start: 0.6956 (t0) cc_final: 0.6717 (m110) REVERT: K 195 TYR cc_start: 0.5404 (m-80) cc_final: 0.5069 (m-80) REVERT: L 85 GLU cc_start: 0.8614 (tt0) cc_final: 0.8389 (mt-10) outliers start: 27 outliers final: 10 residues processed: 343 average time/residue: 0.6332 time to fit residues: 265.0991 Evaluate side-chains 185 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 HIS A 309 GLN A 400 ASN A 608 GLN A1000 GLN B 309 GLN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN B 608 GLN B1000 GLN C 202 HIS C 309 GLN ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 GLN C1000 GLN E 50 ASN E 58 ASN E 200 GLN E 207 ASN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN H 58 ASN H 200 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN J 58 ASN J 200 GLN J 207 ASN K 16 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052095 restraints weight = 81918.304| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.01 r_work: 0.2650 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 36090 Z= 0.259 Angle : 0.579 6.363 49284 Z= 0.302 Chirality : 0.046 0.187 5736 Planarity : 0.004 0.057 6240 Dihedral : 5.941 57.320 5878 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.63 % Allowed : 6.58 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.25 (0.13), residues: 4425 helix: 1.78 (0.19), residues: 783 sheet: 0.63 (0.14), residues: 1260 loop : -0.63 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 232 TYR 0.023 0.001 TYR F 176 PHE 0.023 0.002 PHE L 122 TRP 0.027 0.001 TRP H 162 HIS 0.005 0.001 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.26 (35985) covalent geometry : angle 0.56893 / 0.30 (49023) SS BOND : bond 0.00428 / 0.28 ( 54) SS BOND : angle 1.19507 / 0.85 ( 108) hydrogen bonds : bond 0.04604 / 3.00 ( 1489) hydrogen bonds : angle 5.66987 / 3.94 ( 4155) link_BETA1-4 : bond 0.00100 / 0.06 ( 12) link_BETA1-4 : angle 1.21278 / 0.77 ( 36) link_NAG-ASN : bond 0.00357 / 0.22 ( 39) link_NAG-ASN : angle 1.94900 / 1.25 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.9050 (tt0) cc_final: 0.8678 (tm-30) REVERT: A 152 PHE cc_start: 0.6855 (p90) cc_final: 0.6577 (p90) REVERT: A 319 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: A 352 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8830 (ttt-90) REVERT: A 466 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: A 569 ASP cc_start: 0.8601 (t70) cc_final: 0.8149 (t0) REVERT: A 656 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8610 (mp0) REVERT: A 1137 GLN cc_start: 0.9072 (tp40) cc_final: 0.8589 (tm-30) REVERT: B 49 GLN cc_start: 0.9080 (tt0) cc_final: 0.8685 (tm-30) REVERT: B 152 PHE cc_start: 0.6855 (p90) cc_final: 0.6636 (p90) REVERT: B 319 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: B 352 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8794 (ttt-90) REVERT: B 466 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: B 569 ASP cc_start: 0.8628 (t70) cc_final: 0.8173 (t0) REVERT: B 656 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8605 (mp0) REVERT: B 1137 GLN cc_start: 0.9069 (tp40) cc_final: 0.8607 (tm-30) REVERT: C 49 GLN cc_start: 0.9037 (tt0) cc_final: 0.8687 (tm-30) REVERT: C 152 PHE cc_start: 0.6786 (p90) cc_final: 0.6507 (p90) REVERT: C 319 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: C 466 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: C 569 ASP cc_start: 0.8641 (t70) cc_final: 0.8320 (t0) REVERT: C 656 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8549 (mp0) REVERT: C 775 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8722 (mm-30) REVERT: C 1137 GLN cc_start: 0.9071 (tp40) cc_final: 0.8591 (tm-30) REVERT: E 72 ASP cc_start: 0.7832 (t70) cc_final: 0.7450 (p0) REVERT: F 85 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8310 (mt-10) REVERT: F 195 TYR cc_start: 0.5356 (m-80) cc_final: 0.4619 (m-80) REVERT: H 30 ASP cc_start: 0.8682 (m-30) cc_final: 0.8413 (m-30) REVERT: H 72 ASP cc_start: 0.7735 (t70) cc_final: 0.7455 (p0) REVERT: J 72 ASP cc_start: 0.7736 (t70) cc_final: 0.7439 (p0) REVERT: K 85 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8343 (mt-10) REVERT: K 195 TYR cc_start: 0.5285 (m-80) cc_final: 0.4829 (m-80) REVERT: L 85 GLU cc_start: 0.8574 (tt0) cc_final: 0.8100 (mt-10) REVERT: L 128 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7715 (pp20) REVERT: L 195 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5372 (m-80) outliers start: 63 outliers final: 24 residues processed: 244 average time/residue: 0.6194 time to fit residues: 185.4958 Evaluate side-chains 206 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain L residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 240 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 422 optimal weight: 20.0000 chunk 238 optimal weight: 0.9990 chunk 432 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 357 optimal weight: 30.0000 chunk 360 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 757 GLN A1000 GLN B 757 GLN B1000 GLN C 400 ASN C 757 GLN C1000 GLN F 16 GLN ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.091230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053681 restraints weight = 81074.543| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.03 r_work: 0.2691 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36090 Z= 0.124 Angle : 0.504 6.325 49284 Z= 0.263 Chirality : 0.043 0.168 5736 Planarity : 0.004 0.059 6240 Dihedral : 5.397 58.289 5876 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.50 % Allowed : 7.25 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.40 (0.13), residues: 4425 helix: 2.08 (0.19), residues: 759 sheet: 0.76 (0.14), residues: 1260 loop : -0.60 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 232 TYR 0.018 0.001 TYR L 176 PHE 0.020 0.001 PHE K 122 TRP 0.015 0.001 TRP H 162 HIS 0.003 0.000 HIS F 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (35985) covalent geometry : angle 0.49618 / 0.26 (49023) SS BOND : bond 0.00222 / 0.14 ( 54) SS BOND : angle 0.81545 / 0.55 ( 108) hydrogen bonds : bond 0.03830 / 2.48 ( 1489) hydrogen bonds : angle 5.38878 / 3.74 ( 4155) link_BETA1-4 : bond 0.00227 / 0.16 ( 12) link_BETA1-4 : angle 1.02066 / 0.65 ( 36) link_NAG-ASN : bond 0.00223 / 0.16 ( 39) link_NAG-ASN : angle 1.75194 / 1.12 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.9024 (tt0) cc_final: 0.8655 (tm-30) REVERT: A 152 PHE cc_start: 0.6853 (p90) cc_final: 0.6572 (p90) REVERT: A 466 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: A 569 ASP cc_start: 0.8586 (t70) cc_final: 0.8129 (t0) REVERT: A 629 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.7969 (mtm-85) REVERT: A 656 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8627 (mp0) REVERT: A 1137 GLN cc_start: 0.9067 (tp40) cc_final: 0.8582 (tm-30) REVERT: B 49 GLN cc_start: 0.9051 (tt0) cc_final: 0.8666 (tm-30) REVERT: B 195 TYR cc_start: 0.8346 (m-80) cc_final: 0.8101 (m-80) REVERT: B 352 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8711 (ttt-90) REVERT: B 466 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8262 (mp0) REVERT: B 512 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6292 (mt) REVERT: B 569 ASP cc_start: 0.8569 (t70) cc_final: 0.8202 (t0) REVERT: B 656 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8617 (mp0) REVERT: B 1137 GLN cc_start: 0.9083 (tp40) cc_final: 0.8607 (tm-30) REVERT: C 49 GLN cc_start: 0.9010 (tt0) cc_final: 0.8679 (tm-30) REVERT: C 152 PHE cc_start: 0.6761 (p90) cc_final: 0.6494 (p90) REVERT: C 466 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: C 569 ASP cc_start: 0.8622 (t70) cc_final: 0.8280 (t0) REVERT: C 656 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8588 (mp0) REVERT: C 775 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8669 (mm-30) REVERT: C 1137 GLN cc_start: 0.9077 (tp40) cc_final: 0.8599 (tm-30) REVERT: E 72 ASP cc_start: 0.7823 (t70) cc_final: 0.7483 (p0) REVERT: E 123 SER cc_start: 0.8757 (m) cc_final: 0.8543 (p) REVERT: F 85 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8250 (mt-10) REVERT: H 17 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7970 (m) REVERT: H 72 ASP cc_start: 0.7728 (t70) cc_final: 0.7435 (p0) REVERT: J 17 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8063 (m) REVERT: J 72 ASP cc_start: 0.7741 (t70) cc_final: 0.7503 (p0) REVERT: K 85 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8249 (mt-10) REVERT: K 195 TYR cc_start: 0.5268 (m-80) cc_final: 0.4589 (m-80) REVERT: L 85 GLU cc_start: 0.8533 (tt0) cc_final: 0.8046 (mt-10) REVERT: L 128 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7942 (pp20) REVERT: L 195 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.5549 (m-10) outliers start: 58 outliers final: 26 residues processed: 227 average time/residue: 0.6519 time to fit residues: 181.6363 Evaluate side-chains 200 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1087 GLU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain L residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 232 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 367 optimal weight: 9.9990 chunk 36 optimal weight: 0.0570 chunk 390 optimal weight: 1.9990 chunk 336 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 286 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1000 GLN B1000 GLN C1000 GLN E 207 ASN J 207 ASN L 6 GLN L 188 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.090129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.052444 restraints weight = 81587.062| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.03 r_work: 0.2660 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 36090 Z= 0.203 Angle : 0.531 6.372 49284 Z= 0.276 Chirality : 0.044 0.180 5736 Planarity : 0.004 0.053 6240 Dihedral : 5.168 59.644 5874 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.74 % Allowed : 8.05 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.34 (0.13), residues: 4425 helix: 2.00 (0.19), residues: 759 sheet: 0.63 (0.14), residues: 1281 loop : -0.58 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 79 TYR 0.016 0.001 TYR A1062 PHE 0.015 0.001 PHE K 122 TRP 0.017 0.001 TRP H 162 HIS 0.002 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (35985) covalent geometry : angle 0.52227 / 0.27 (49023) SS BOND : bond 0.00301 / 0.19 ( 54) SS BOND : angle 0.79980 / 0.54 ( 108) hydrogen bonds : bond 0.04134 / 2.69 ( 1489) hydrogen bonds : angle 5.29582 / 3.68 ( 4155) link_BETA1-4 : bond 0.00070 / 0.05 ( 12) link_BETA1-4 : angle 1.14807 / 0.72 ( 36) link_NAG-ASN : bond 0.00287 / 0.18 ( 39) link_NAG-ASN : angle 1.87950 / 1.21 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.9052 (tt0) cc_final: 0.8675 (tm-30) REVERT: A 152 PHE cc_start: 0.6885 (p90) cc_final: 0.6618 (p90) REVERT: A 319 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: A 466 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: A 569 ASP cc_start: 0.8615 (t70) cc_final: 0.8153 (t0) REVERT: A 629 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7971 (mtm-85) REVERT: A 656 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8632 (mp0) REVERT: B 49 GLN cc_start: 0.9069 (tt0) cc_final: 0.8670 (tm-30) REVERT: B 152 PHE cc_start: 0.7024 (p90) cc_final: 0.6810 (p90) REVERT: B 195 TYR cc_start: 0.8333 (m-80) cc_final: 0.8058 (m-80) REVERT: B 319 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: B 352 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8814 (ttt-90) REVERT: B 466 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: B 512 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6276 (mt) REVERT: B 569 ASP cc_start: 0.8622 (t70) cc_final: 0.8236 (t0) REVERT: B 656 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8617 (mp0) REVERT: C 49 GLN cc_start: 0.9034 (tt0) cc_final: 0.8692 (tm-30) REVERT: C 319 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: C 466 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: C 569 ASP cc_start: 0.8641 (t70) cc_final: 0.8303 (t0) REVERT: C 656 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8593 (mp0) REVERT: C 775 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8704 (mm-30) REVERT: E 72 ASP cc_start: 0.7850 (t70) cc_final: 0.7540 (p0) REVERT: E 123 SER cc_start: 0.8760 (m) cc_final: 0.8553 (p) REVERT: F 85 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8258 (mt-10) REVERT: F 198 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7284 (tp40) REVERT: H 17 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7930 (m) REVERT: H 72 ASP cc_start: 0.7771 (t70) cc_final: 0.7502 (p0) REVERT: J 17 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8040 (m) REVERT: J 72 ASP cc_start: 0.7773 (t70) cc_final: 0.7555 (p0) REVERT: K 85 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8272 (mt-10) REVERT: K 195 TYR cc_start: 0.5333 (m-80) cc_final: 0.4562 (m-80) REVERT: L 85 GLU cc_start: 0.8522 (tt0) cc_final: 0.8021 (mt-10) REVERT: L 128 GLU cc_start: 0.8298 (tt0) cc_final: 0.7950 (pp20) outliers start: 67 outliers final: 33 residues processed: 229 average time/residue: 0.5837 time to fit residues: 164.9867 Evaluate side-chains 199 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 188 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 184 optimal weight: 0.7980 chunk 308 optimal weight: 1.9990 chunk 387 optimal weight: 9.9990 chunk 431 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 chunk 255 optimal weight: 0.8980 chunk 338 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.8413 > 50:) chunk 336 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 358 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1000 GLN B1000 GLN C1000 GLN ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.089615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051881 restraints weight = 81658.774| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.04 r_work: 0.2646 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 36090 Z= 0.246 Angle : 0.554 6.398 49284 Z= 0.289 Chirality : 0.045 0.181 5736 Planarity : 0.004 0.045 6240 Dihedral : 5.165 58.556 5874 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.79 % Allowed : 7.85 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.26 (0.13), residues: 4425 helix: 1.91 (0.19), residues: 759 sheet: 0.56 (0.14), residues: 1281 loop : -0.61 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 79 TYR 0.016 0.001 TYR A1062 PHE 0.017 0.001 PHE C 372 TRP 0.017 0.001 TRP H 162 HIS 0.005 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 (35985) covalent geometry : angle 0.54571 / 0.29 (49023) SS BOND : bond 0.00375 / 0.24 ( 54) SS BOND : angle 0.84955 / 0.56 ( 108) hydrogen bonds : bond 0.04317 / 2.81 ( 1489) hydrogen bonds : angle 5.32472 / 3.70 ( 4155) link_BETA1-4 : bond 0.00063 / 0.04 ( 12) link_BETA1-4 : angle 1.13670 / 0.71 ( 36) link_NAG-ASN : bond 0.00293 / 0.19 ( 39) link_NAG-ASN : angle 1.91375 / 1.23 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 164 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.9062 (tt0) cc_final: 0.8669 (tm-30) REVERT: A 152 PHE cc_start: 0.6932 (p90) cc_final: 0.6688 (p90) REVERT: A 319 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: A 466 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: A 569 ASP cc_start: 0.8648 (t70) cc_final: 0.8170 (t0) REVERT: A 656 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8621 (mp0) REVERT: B 49 GLN cc_start: 0.9085 (tt0) cc_final: 0.8665 (tm-30) REVERT: B 152 PHE cc_start: 0.7108 (p90) cc_final: 0.6854 (p90) REVERT: B 195 TYR cc_start: 0.8351 (m-80) cc_final: 0.8086 (m-80) REVERT: B 319 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: B 352 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8810 (ttt-90) REVERT: B 466 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8285 (mp0) REVERT: B 512 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6321 (mt) REVERT: B 569 ASP cc_start: 0.8620 (t70) cc_final: 0.8242 (t0) REVERT: B 656 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8621 (mp0) REVERT: C 49 GLN cc_start: 0.9038 (tt0) cc_final: 0.8675 (tm-30) REVERT: C 152 PHE cc_start: 0.6912 (p90) cc_final: 0.6638 (p90) REVERT: C 319 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: C 466 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: C 569 ASP cc_start: 0.8659 (t70) cc_final: 0.8320 (t0) REVERT: C 656 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8583 (mp0) REVERT: C 775 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8743 (mm-30) REVERT: E 72 ASP cc_start: 0.7828 (t70) cc_final: 0.7522 (p0) REVERT: E 162 TRP cc_start: 0.7613 (m100) cc_final: 0.7337 (m100) REVERT: F 85 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8241 (mt-10) REVERT: F 198 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7496 (tp40) REVERT: H 17 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7929 (m) REVERT: H 72 ASP cc_start: 0.7788 (t70) cc_final: 0.7516 (p0) REVERT: H 89 ASP cc_start: 0.7679 (m-30) cc_final: 0.7461 (m-30) REVERT: H 207 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7213 (m-40) REVERT: J 17 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8042 (m) REVERT: J 72 ASP cc_start: 0.7829 (t70) cc_final: 0.7616 (p0) REVERT: K 85 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8190 (mt-10) REVERT: K 198 GLN cc_start: 0.7278 (tp40) cc_final: 0.6963 (tp40) REVERT: L 85 GLU cc_start: 0.8519 (tt0) cc_final: 0.8070 (mt-10) REVERT: L 128 GLU cc_start: 0.8311 (tt0) cc_final: 0.8011 (pp20) REVERT: L 144 TYR cc_start: 0.8301 (t80) cc_final: 0.8085 (t80) REVERT: L 195 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.5568 (m-80) outliers start: 69 outliers final: 33 residues processed: 219 average time/residue: 0.5828 time to fit residues: 158.8541 Evaluate side-chains 198 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1087 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 195 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 30 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 278 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 chunk 126 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1000 GLN B 960 GLN B1000 GLN C 316 GLN C1000 GLN J 207 ASN K 192 HIS L 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.091502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054148 restraints weight = 81058.050| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.30 r_work: 0.2682 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36090 Z= 0.107 Angle : 0.493 6.588 49284 Z= 0.256 Chirality : 0.043 0.155 5736 Planarity : 0.004 0.047 6240 Dihedral : 4.760 56.965 5874 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.58 % Allowed : 8.34 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4425 helix: 2.29 (0.19), residues: 741 sheet: 0.77 (0.14), residues: 1224 loop : -0.63 (0.13), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 79 TYR 0.015 0.001 TYR B1062 PHE 0.012 0.001 PHE C 128 TRP 0.023 0.001 TRP H 162 HIS 0.004 0.000 HIS F 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (35985) covalent geometry : angle 0.48561 / 0.25 (49023) SS BOND : bond 0.00240 / 0.16 ( 54) SS BOND : angle 0.71139 / 0.46 ( 108) hydrogen bonds : bond 0.03489 / 2.26 ( 1489) hydrogen bonds : angle 5.04900 / 3.50 ( 4155) link_BETA1-4 : bond 0.00278 / 0.18 ( 12) link_BETA1-4 : angle 0.94605 / 0.60 ( 36) link_NAG-ASN : bond 0.00210 / 0.15 ( 39) link_NAG-ASN : angle 1.64360 / 1.05 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8909 (tt0) cc_final: 0.8558 (tm-30) REVERT: A 152 PHE cc_start: 0.6828 (p90) cc_final: 0.6606 (p90) REVERT: A 319 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: A 466 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: A 569 ASP cc_start: 0.8409 (t70) cc_final: 0.7907 (t0) REVERT: A 656 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8502 (mp0) REVERT: B 49 GLN cc_start: 0.8934 (tt0) cc_final: 0.8546 (tm-30) REVERT: B 152 PHE cc_start: 0.6960 (p90) cc_final: 0.6678 (p90) REVERT: B 195 TYR cc_start: 0.8257 (m-80) cc_final: 0.8032 (m-80) REVERT: B 319 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: B 352 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8643 (ttt-90) REVERT: B 466 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: B 569 ASP cc_start: 0.8375 (t70) cc_final: 0.7945 (t0) REVERT: B 656 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8493 (mp0) REVERT: C 49 GLN cc_start: 0.8897 (tt0) cc_final: 0.8578 (tm-30) REVERT: C 152 PHE cc_start: 0.6807 (p90) cc_final: 0.6471 (p90) REVERT: C 319 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: C 466 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: C 569 ASP cc_start: 0.8459 (t70) cc_final: 0.7885 (t0) REVERT: C 625 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.7187 (t) REVERT: C 656 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8446 (mp0) REVERT: C 775 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8404 (mm-30) REVERT: E 72 ASP cc_start: 0.7766 (t70) cc_final: 0.7523 (p0) REVERT: E 162 TRP cc_start: 0.7590 (m100) cc_final: 0.7381 (m100) REVERT: F 85 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8174 (mt-10) REVERT: F 198 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7686 (tp-100) REVERT: H 17 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7920 (m) REVERT: H 72 ASP cc_start: 0.7778 (t70) cc_final: 0.7501 (p0) REVERT: H 89 ASP cc_start: 0.7615 (m-30) cc_final: 0.7394 (m-30) REVERT: H 174 PHE cc_start: 0.6606 (m-80) cc_final: 0.6401 (m-80) REVERT: H 207 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.7209 (m-40) REVERT: J 17 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8016 (m) REVERT: K 85 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8303 (mt-10) REVERT: K 195 TYR cc_start: 0.5630 (m-80) cc_final: 0.5193 (m-80) REVERT: K 198 GLN cc_start: 0.7558 (tp40) cc_final: 0.7344 (tp40) REVERT: L 85 GLU cc_start: 0.8504 (tt0) cc_final: 0.8039 (mt-10) REVERT: L 128 GLU cc_start: 0.8315 (tt0) cc_final: 0.8012 (pp20) REVERT: L 144 TYR cc_start: 0.8261 (t80) cc_final: 0.7994 (t80) outliers start: 61 outliers final: 25 residues processed: 219 average time/residue: 0.6101 time to fit residues: 164.9325 Evaluate side-chains 191 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 153 optimal weight: 0.7980 chunk 320 optimal weight: 10.0000 chunk 30 optimal weight: 0.1980 chunk 125 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 415 optimal weight: 20.0000 chunk 98 optimal weight: 0.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1000 GLN B 309 GLN B1000 GLN C1000 GLN E 207 ASN K 192 HIS L 81 GLN L 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.091226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.053788 restraints weight = 81298.668| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.30 r_work: 0.2674 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36090 Z= 0.128 Angle : 0.500 7.910 49284 Z= 0.261 Chirality : 0.043 0.160 5736 Planarity : 0.004 0.043 6240 Dihedral : 4.643 55.911 5873 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.48 % Allowed : 8.78 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.45 (0.13), residues: 4425 helix: 2.32 (0.19), residues: 741 sheet: 0.78 (0.14), residues: 1254 loop : -0.61 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 232 TYR 0.016 0.001 TYR L 195 PHE 0.017 0.001 PHE F 122 TRP 0.025 0.001 TRP H 162 HIS 0.003 0.000 HIS J 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (35985) covalent geometry : angle 0.49356 / 0.26 (49023) SS BOND : bond 0.00233 / 0.15 ( 54) SS BOND : angle 0.64254 / 0.43 ( 108) hydrogen bonds : bond 0.03582 / 2.32 ( 1489) hydrogen bonds : angle 5.00283 / 3.47 ( 4155) link_BETA1-4 : bond 0.00174 / 0.11 ( 12) link_BETA1-4 : angle 1.02725 / 0.65 ( 36) link_NAG-ASN : bond 0.00153 / 0.10 ( 39) link_NAG-ASN : angle 1.64406 / 1.05 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8919 (tt0) cc_final: 0.8559 (tm-30) REVERT: A 319 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: A 466 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: A 569 ASP cc_start: 0.8403 (t70) cc_final: 0.7893 (t0) REVERT: A 656 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8511 (mp0) REVERT: B 49 GLN cc_start: 0.8940 (tt0) cc_final: 0.8548 (tm-30) REVERT: B 152 PHE cc_start: 0.6885 (p90) cc_final: 0.6592 (p90) REVERT: B 195 TYR cc_start: 0.8264 (m-80) cc_final: 0.8012 (m-80) REVERT: B 319 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: B 352 ARG cc_start: 0.8985 (ttp80) cc_final: 0.8643 (ttt-90) REVERT: B 466 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: B 569 ASP cc_start: 0.8397 (t70) cc_final: 0.7948 (t0) REVERT: B 656 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8497 (mp0) REVERT: C 49 GLN cc_start: 0.8907 (tt0) cc_final: 0.8581 (tm-30) REVERT: C 152 PHE cc_start: 0.6775 (p90) cc_final: 0.6528 (p90) REVERT: C 319 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8282 (pm20) REVERT: C 466 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: C 569 ASP cc_start: 0.8457 (t70) cc_final: 0.8051 (t0) REVERT: C 625 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7193 (t) REVERT: C 656 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8448 (mp0) REVERT: C 775 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8432 (mm-30) REVERT: E 72 ASP cc_start: 0.7731 (t70) cc_final: 0.7521 (p0) REVERT: F 85 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8190 (mt-10) REVERT: F 198 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7808 (tp-100) REVERT: H 17 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7922 (m) REVERT: H 72 ASP cc_start: 0.7764 (t70) cc_final: 0.7517 (p0) REVERT: H 89 ASP cc_start: 0.7627 (m-30) cc_final: 0.7407 (m-30) REVERT: H 207 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7189 (m-40) REVERT: J 17 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7926 (m) REVERT: K 85 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8224 (mt-10) REVERT: K 195 TYR cc_start: 0.6229 (m-80) cc_final: 0.5486 (m-80) REVERT: K 198 GLN cc_start: 0.7764 (tp40) cc_final: 0.7305 (tp40) REVERT: L 85 GLU cc_start: 0.8507 (tt0) cc_final: 0.8034 (mt-10) REVERT: L 128 GLU cc_start: 0.8328 (tt0) cc_final: 0.8039 (pp20) REVERT: L 144 TYR cc_start: 0.8273 (t80) cc_final: 0.8017 (t80) REVERT: L 195 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.5563 (m-80) outliers start: 57 outliers final: 28 residues processed: 210 average time/residue: 0.5816 time to fit residues: 152.3999 Evaluate side-chains 189 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain L residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 305 optimal weight: 4.9990 chunk 202 optimal weight: 0.0040 chunk 241 optimal weight: 4.9990 chunk 411 optimal weight: 7.9990 chunk 357 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 285 optimal weight: 0.0170 chunk 198 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 427 optimal weight: 8.9990 overall best weight: 1.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1000 GLN B 309 GLN B1000 GLN C 309 GLN C1000 GLN E 207 ASN K 192 HIS L 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053438 restraints weight = 81458.627| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.03 r_work: 0.2684 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 36090 Z= 0.150 Angle : 0.507 7.939 49284 Z= 0.264 Chirality : 0.043 0.163 5736 Planarity : 0.004 0.047 6240 Dihedral : 4.585 54.888 5870 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.35 % Allowed : 9.04 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.44 (0.13), residues: 4425 helix: 2.31 (0.19), residues: 741 sheet: 0.78 (0.14), residues: 1254 loop : -0.62 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 79 TYR 0.015 0.001 TYR B1062 PHE 0.019 0.001 PHE E 174 TRP 0.029 0.001 TRP H 162 HIS 0.002 0.000 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (35985) covalent geometry : angle 0.49991 / 0.26 (49023) SS BOND : bond 0.00247 / 0.15 ( 54) SS BOND : angle 0.67846 / 0.45 ( 108) hydrogen bonds : bond 0.03685 / 2.39 ( 1489) hydrogen bonds : angle 5.00387 / 3.47 ( 4155) link_BETA1-4 : bond 0.00162 / 0.10 ( 12) link_BETA1-4 : angle 1.05250 / 0.66 ( 36) link_NAG-ASN : bond 0.00180 / 0.11 ( 39) link_NAG-ASN : angle 1.68677 / 1.08 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8911 (tt0) cc_final: 0.8593 (tm-30) REVERT: A 319 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: A 466 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: A 569 ASP cc_start: 0.8404 (t70) cc_final: 0.7900 (t0) REVERT: A 656 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8496 (mp0) REVERT: B 49 GLN cc_start: 0.8930 (tt0) cc_final: 0.8553 (tm-30) REVERT: B 152 PHE cc_start: 0.6875 (p90) cc_final: 0.6586 (p90) REVERT: B 195 TYR cc_start: 0.8278 (m-80) cc_final: 0.8048 (m-80) REVERT: B 319 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: B 352 ARG cc_start: 0.8989 (ttp80) cc_final: 0.8639 (ttt-90) REVERT: B 466 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: B 569 ASP cc_start: 0.8394 (t70) cc_final: 0.7960 (t0) REVERT: B 656 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8485 (mp0) REVERT: C 49 GLN cc_start: 0.8897 (tt0) cc_final: 0.8584 (tm-30) REVERT: C 152 PHE cc_start: 0.6747 (p90) cc_final: 0.6491 (p90) REVERT: C 319 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: C 466 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: C 569 ASP cc_start: 0.8451 (t70) cc_final: 0.8047 (t0) REVERT: C 625 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.7133 (t) REVERT: C 656 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8436 (mp0) REVERT: C 775 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8485 (mm-30) REVERT: E 72 ASP cc_start: 0.7756 (t70) cc_final: 0.7529 (p0) REVERT: F 85 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8207 (mt-10) REVERT: F 192 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.7057 (m170) REVERT: F 195 TYR cc_start: 0.5959 (m-80) cc_final: 0.5735 (m-80) REVERT: H 17 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7959 (m) REVERT: H 72 ASP cc_start: 0.7762 (t70) cc_final: 0.7537 (p0) REVERT: H 89 ASP cc_start: 0.7696 (m-30) cc_final: 0.7474 (m-30) REVERT: H 207 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7180 (m-40) REVERT: J 17 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7898 (m) REVERT: K 85 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8292 (mt-10) REVERT: K 198 GLN cc_start: 0.7853 (tp40) cc_final: 0.7622 (tp-100) REVERT: L 85 GLU cc_start: 0.8518 (tt0) cc_final: 0.8059 (mt-10) REVERT: L 128 GLU cc_start: 0.8370 (tt0) cc_final: 0.8089 (pp20) REVERT: L 144 TYR cc_start: 0.8304 (t80) cc_final: 0.8045 (t80) REVERT: L 195 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.5190 (m-80) outliers start: 52 outliers final: 30 residues processed: 197 average time/residue: 0.6707 time to fit residues: 163.3215 Evaluate side-chains 189 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1087 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain F residue 192 HIS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 195 TYR Chi-restraints excluded: chain L residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 98 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 253 optimal weight: 0.9980 chunk 411 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 389 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 236 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1000 GLN B 309 GLN B1000 GLN C1000 GLN E 207 ASN J 207 ASN K 192 HIS L 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.090561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053011 restraints weight = 81017.970| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.02 r_work: 0.2673 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36090 Z= 0.179 Angle : 0.523 7.953 49284 Z= 0.272 Chirality : 0.043 0.168 5736 Planarity : 0.004 0.051 6240 Dihedral : 4.625 54.393 5870 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.40 % Allowed : 9.17 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.13), residues: 4425 helix: 2.42 (0.19), residues: 723 sheet: 0.71 (0.14), residues: 1278 loop : -0.57 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 79 TYR 0.015 0.001 TYR B1062 PHE 0.042 0.001 PHE A 152 TRP 0.037 0.001 TRP H 162 HIS 0.004 0.001 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (35985) covalent geometry : angle 0.51543 / 0.27 (49023) SS BOND : bond 0.00277 / 0.17 ( 54) SS BOND : angle 0.69019 / 0.47 ( 108) hydrogen bonds : bond 0.03852 / 2.50 ( 1489) hydrogen bonds : angle 5.03751 / 3.49 ( 4155) link_BETA1-4 : bond 0.00136 / 0.09 ( 12) link_BETA1-4 : angle 1.06999 / 0.67 ( 36) link_NAG-ASN : bond 0.00202 / 0.13 ( 39) link_NAG-ASN : angle 1.73139 / 1.11 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8922 (tt0) cc_final: 0.8590 (tm-30) REVERT: A 152 PHE cc_start: 0.6960 (p90) cc_final: 0.6759 (p90) REVERT: A 319 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: A 466 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: A 569 ASP cc_start: 0.8423 (t70) cc_final: 0.7917 (t0) REVERT: A 656 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8494 (mp0) REVERT: B 49 GLN cc_start: 0.8945 (tt0) cc_final: 0.8559 (tm-30) REVERT: B 152 PHE cc_start: 0.6871 (p90) cc_final: 0.6593 (p90) REVERT: B 319 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8320 (pm20) REVERT: B 352 ARG cc_start: 0.8999 (ttp80) cc_final: 0.8633 (ttt-90) REVERT: B 466 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: B 569 ASP cc_start: 0.8413 (t70) cc_final: 0.7985 (t0) REVERT: B 656 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8490 (mp0) REVERT: C 49 GLN cc_start: 0.8909 (tt0) cc_final: 0.8606 (tm-30) REVERT: C 152 PHE cc_start: 0.6830 (p90) cc_final: 0.6561 (p90) REVERT: C 319 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: C 466 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: C 569 ASP cc_start: 0.8452 (t70) cc_final: 0.8064 (t0) REVERT: C 625 THR cc_start: 0.7369 (OUTLIER) cc_final: 0.7150 (t) REVERT: C 656 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8428 (mp0) REVERT: C 775 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8498 (mm-30) REVERT: E 72 ASP cc_start: 0.7758 (t70) cc_final: 0.7526 (p0) REVERT: F 85 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8200 (mt-10) REVERT: F 195 TYR cc_start: 0.5979 (m-80) cc_final: 0.5498 (m-80) REVERT: H 17 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7935 (m) REVERT: H 72 ASP cc_start: 0.7792 (t70) cc_final: 0.7589 (p0) REVERT: H 89 ASP cc_start: 0.7708 (m-30) cc_final: 0.7489 (m-30) REVERT: H 207 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.7121 (m-40) REVERT: J 17 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7931 (m) REVERT: K 85 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8236 (mt-10) REVERT: K 195 TYR cc_start: 0.6234 (m-80) cc_final: 0.5394 (m-80) REVERT: K 198 GLN cc_start: 0.7901 (tp40) cc_final: 0.7366 (tp-100) REVERT: L 85 GLU cc_start: 0.8513 (tt0) cc_final: 0.8058 (mt-10) REVERT: L 128 GLU cc_start: 0.8397 (tt0) cc_final: 0.8122 (pp20) REVERT: L 144 TYR cc_start: 0.8310 (t80) cc_final: 0.8059 (t80) REVERT: L 195 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.5250 (m-80) outliers start: 54 outliers final: 29 residues processed: 198 average time/residue: 0.6365 time to fit residues: 157.0188 Evaluate side-chains 189 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 195 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 380 optimal weight: 7.9990 chunk 438 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 326 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1000 GLN B 309 GLN B1000 GLN C1000 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 ASN K 192 HIS L 188 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.090976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053526 restraints weight = 81283.876| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.32 r_work: 0.2665 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36090 Z= 0.134 Angle : 0.508 8.017 49284 Z= 0.265 Chirality : 0.043 0.163 5736 Planarity : 0.004 0.056 6240 Dihedral : 4.559 53.869 5870 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.17 % Allowed : 9.40 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.50 (0.13), residues: 4425 helix: 2.47 (0.19), residues: 723 sheet: 0.79 (0.14), residues: 1263 loop : -0.59 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 79 TYR 0.015 0.001 TYR B1062 PHE 0.036 0.001 PHE A 152 TRP 0.048 0.001 TRP H 162 HIS 0.008 0.000 HIS J 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (35985) covalent geometry : angle 0.50114 / 0.26 (49023) SS BOND : bond 0.00237 / 0.15 ( 54) SS BOND : angle 0.65727 / 0.45 ( 108) hydrogen bonds : bond 0.03658 / 2.38 ( 1489) hydrogen bonds : angle 4.98313 / 3.45 ( 4155) link_BETA1-4 : bond 0.00184 / 0.12 ( 12) link_BETA1-4 : angle 1.01058 / 0.63 ( 36) link_NAG-ASN : bond 0.00156 / 0.10 ( 39) link_NAG-ASN : angle 1.66807 / 1.07 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8923 (tt0) cc_final: 0.8574 (tm-30) REVERT: A 319 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: A 466 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: A 569 ASP cc_start: 0.8419 (t70) cc_final: 0.7902 (t0) REVERT: A 656 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8506 (mp0) REVERT: B 49 GLN cc_start: 0.8933 (tt0) cc_final: 0.8530 (tm-30) REVERT: B 152 PHE cc_start: 0.6854 (p90) cc_final: 0.6589 (p90) REVERT: B 319 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: B 352 ARG cc_start: 0.8981 (ttp80) cc_final: 0.8610 (ttt-90) REVERT: B 466 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: B 569 ASP cc_start: 0.8426 (t70) cc_final: 0.7985 (t0) REVERT: B 656 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8496 (mp0) REVERT: C 49 GLN cc_start: 0.8904 (tt0) cc_final: 0.8563 (tm-30) REVERT: C 152 PHE cc_start: 0.6819 (p90) cc_final: 0.6523 (p90) REVERT: C 319 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: C 466 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: C 569 ASP cc_start: 0.8456 (t70) cc_final: 0.8054 (t0) REVERT: C 625 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.7146 (t) REVERT: C 656 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8443 (mp0) REVERT: C 775 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8480 (mm-30) REVERT: E 72 ASP cc_start: 0.7754 (t70) cc_final: 0.7500 (p0) REVERT: F 85 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8196 (mt-10) REVERT: H 17 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7865 (m) REVERT: H 72 ASP cc_start: 0.7809 (t70) cc_final: 0.7591 (p0) REVERT: H 89 ASP cc_start: 0.7658 (m-30) cc_final: 0.7442 (m-30) REVERT: H 207 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.7047 (m-40) REVERT: J 17 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7900 (m) REVERT: K 85 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8280 (mt-10) REVERT: K 195 TYR cc_start: 0.6173 (m-80) cc_final: 0.5358 (m-80) REVERT: L 85 GLU cc_start: 0.8488 (tt0) cc_final: 0.8046 (mt-10) REVERT: L 128 GLU cc_start: 0.8402 (tt0) cc_final: 0.7958 (pp20) REVERT: L 144 TYR cc_start: 0.8284 (t80) cc_final: 0.8040 (t80) REVERT: L 195 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.5268 (m-80) outliers start: 45 outliers final: 28 residues processed: 193 average time/residue: 0.6475 time to fit residues: 155.3914 Evaluate side-chains 188 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 911 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 195 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 170 optimal weight: 4.9990 chunk 368 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 267 optimal weight: 0.8980 chunk 366 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 335 optimal weight: 30.0000 chunk 76 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1000 GLN B 309 GLN B1000 GLN C1000 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS L 81 GLN L 188 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.090156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052590 restraints weight = 81587.066| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.98 r_work: 0.2663 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 36090 Z= 0.210 Angle : 0.544 7.846 49284 Z= 0.283 Chirality : 0.044 0.175 5736 Planarity : 0.004 0.054 6240 Dihedral : 4.676 53.685 5870 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.19 % Allowed : 9.43 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4425 helix: 2.15 (0.19), residues: 744 sheet: 0.68 (0.14), residues: 1284 loop : -0.55 (0.13), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 79 TYR 0.015 0.001 TYR A1062 PHE 0.024 0.001 PHE J 174 TRP 0.053 0.001 TRP H 162 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (35985) covalent geometry : angle 0.53605 / 0.28 (49023) SS BOND : bond 0.00299 / 0.18 ( 54) SS BOND : angle 0.75935 / 0.52 ( 108) hydrogen bonds : bond 0.04024 / 2.62 ( 1489) hydrogen bonds : angle 5.07379 / 3.52 ( 4155) link_BETA1-4 : bond 0.00073 / 0.05 ( 12) link_BETA1-4 : angle 1.10509 / 0.69 ( 36) link_NAG-ASN : bond 0.00254 / 0.16 ( 39) link_NAG-ASN : angle 1.78678 / 1.15 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14464.71 seconds wall clock time: 246 minutes 51.61 seconds (14811.61 seconds total)