Starting phenix.real_space_refine on Thu Nov 20 21:32:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbn_21594/11_2025/6wbn_21594.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbn_21594/11_2025/6wbn_21594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wbn_21594/11_2025/6wbn_21594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbn_21594/11_2025/6wbn_21594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wbn_21594/11_2025/6wbn_21594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbn_21594/11_2025/6wbn_21594.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 154 5.16 5 C 25886 2.51 5 N 5726 2.21 5 O 6594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38402 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "N" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 2, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "F" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "I" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "K" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "L" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "M" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "N" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M Time building chain proxies: 5.71, per 1000 atoms: 0.15 Number of scatterers: 38402 At special positions: 0 Unit cell: (109.62, 107.996, 230.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 42 15.00 O 6594 8.00 N 5726 7.00 C 25886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 40 " distance=0.00 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 66 " distance=0.00 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 84 " distance=0.00 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 136 " distance=0.00 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 216 " distance=0.00 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 228 " distance=0.00 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 246 " distance=0.00 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 66 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 265 " distance=0.00 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 347 " distance=0.00 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 265 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 265 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 265 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 265 " distance=2.03 Simple disulfide: pdb=" SG CYS M 66 " - pdb=" SG CYS M 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Simple disulfide: pdb=" SG CYS H 84 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS I 84 " - pdb=" SG CYS I 246 " distance=2.03 Simple disulfide: pdb=" SG CYS J 84 " - pdb=" SG CYS J 246 " distance=2.03 Simple disulfide: pdb=" SG CYS K 84 " - pdb=" SG CYS K 246 " distance=2.03 Simple disulfide: pdb=" SG CYS L 84 " - pdb=" SG CYS L 246 " distance=2.03 Simple disulfide: pdb=" SG CYS M 84 " - pdb=" SG CYS M 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 1.6 seconds 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 14 sheets defined 71.3% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.697A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 108 through 131 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix removed outlier: 3.788A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.697A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 removed outlier: 3.593A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.551A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix removed outlier: 3.788A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.692A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.697A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 removed outlier: 3.593A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix removed outlier: 3.788A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.692A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.697A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 removed outlier: 3.593A pdb=" N ILE D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix removed outlier: 3.788A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 312 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.696A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 100 through 108 Processing helix chain 'E' and resid 108 through 131 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix removed outlier: 3.788A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 312 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.697A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 100 through 108 Processing helix chain 'F' and resid 108 through 131 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 removed outlier: 3.595A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix removed outlier: 3.788A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN F 301 " --> pdb=" O VAL F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 312 removed outlier: 4.122A pdb=" N VAL F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 312 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.697A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 100 through 108 Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 204 Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.551A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix removed outlier: 3.789A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN G 301 " --> pdb=" O VAL G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR G 309 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 11 Processing helix chain 'H' and resid 32 through 54 Proline residue: H 46 - end of helix removed outlier: 3.697A pdb=" N PHE H 54 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 88 Processing helix chain 'H' and resid 100 through 108 Processing helix chain 'H' and resid 108 through 131 Proline residue: H 123 - end of helix Processing helix chain 'H' and resid 131 through 162 removed outlier: 3.593A pdb=" N ILE H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 204 Processing helix chain 'H' and resid 207 through 236 Processing helix chain 'H' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU H 253 " --> pdb=" O SER H 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H 255 " --> pdb=" O ILE H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 296 Proline residue: H 289 - end of helix removed outlier: 3.788A pdb=" N PHE H 296 " --> pdb=" O VAL H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN H 301 " --> pdb=" O VAL H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR H 309 " --> pdb=" O VAL H 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU H 312 " --> pdb=" O VAL H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU H 330 " --> pdb=" O ASN H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS H 346 " --> pdb=" O VAL H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU H 370 " --> pdb=" O LEU H 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 11 Processing helix chain 'I' and resid 32 through 54 Proline residue: I 46 - end of helix removed outlier: 3.696A pdb=" N PHE I 54 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 88 Processing helix chain 'I' and resid 100 through 108 Processing helix chain 'I' and resid 108 through 131 Proline residue: I 123 - end of helix Processing helix chain 'I' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE I 135 " --> pdb=" O ALA I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 204 Processing helix chain 'I' and resid 207 through 236 Processing helix chain 'I' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU I 253 " --> pdb=" O SER I 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA I 255 " --> pdb=" O ILE I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 296 Proline residue: I 289 - end of helix removed outlier: 3.787A pdb=" N PHE I 296 " --> pdb=" O VAL I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN I 301 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 312 removed outlier: 4.122A pdb=" N VAL I 308 " --> pdb=" O ASP I 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR I 309 " --> pdb=" O VAL I 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU I 312 " --> pdb=" O VAL I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU I 330 " --> pdb=" O ASN I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS I 346 " --> pdb=" O VAL I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 370 removed outlier: 3.692A pdb=" N LEU I 370 " --> pdb=" O LEU I 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 11 Processing helix chain 'J' and resid 32 through 54 Proline residue: J 46 - end of helix removed outlier: 3.696A pdb=" N PHE J 54 " --> pdb=" O ILE J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 88 Processing helix chain 'J' and resid 100 through 108 Processing helix chain 'J' and resid 108 through 131 Proline residue: J 123 - end of helix Processing helix chain 'J' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE J 135 " --> pdb=" O ALA J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 204 Processing helix chain 'J' and resid 207 through 236 Processing helix chain 'J' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU J 253 " --> pdb=" O SER J 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA J 255 " --> pdb=" O ILE J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 296 Proline residue: J 289 - end of helix removed outlier: 3.788A pdb=" N PHE J 296 " --> pdb=" O VAL J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN J 301 " --> pdb=" O VAL J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL J 308 " --> pdb=" O ASP J 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR J 309 " --> pdb=" O VAL J 305 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU J 312 " --> pdb=" O VAL J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU J 330 " --> pdb=" O ASN J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS J 346 " --> pdb=" O VAL J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU J 370 " --> pdb=" O LEU J 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 11 Processing helix chain 'K' and resid 32 through 54 Proline residue: K 46 - end of helix removed outlier: 3.697A pdb=" N PHE K 54 " --> pdb=" O ILE K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 88 Processing helix chain 'K' and resid 100 through 108 Processing helix chain 'K' and resid 108 through 131 Proline residue: K 123 - end of helix Processing helix chain 'K' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE K 135 " --> pdb=" O ALA K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 Processing helix chain 'K' and resid 207 through 236 Processing helix chain 'K' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU K 253 " --> pdb=" O SER K 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 296 Proline residue: K 289 - end of helix removed outlier: 3.787A pdb=" N PHE K 296 " --> pdb=" O VAL K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN K 301 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL K 308 " --> pdb=" O ASP K 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR K 309 " --> pdb=" O VAL K 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU K 312 " --> pdb=" O VAL K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 339 removed outlier: 3.822A pdb=" N LEU K 330 " --> pdb=" O ASN K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS K 346 " --> pdb=" O VAL K 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU K 370 " --> pdb=" O LEU K 366 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Processing helix chain 'L' and resid 32 through 54 Proline residue: L 46 - end of helix removed outlier: 3.697A pdb=" N PHE L 54 " --> pdb=" O ILE L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 88 Processing helix chain 'L' and resid 100 through 108 Processing helix chain 'L' and resid 108 through 131 Proline residue: L 123 - end of helix Processing helix chain 'L' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 204 Processing helix chain 'L' and resid 207 through 236 Processing helix chain 'L' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU L 253 " --> pdb=" O SER L 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA L 255 " --> pdb=" O ILE L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 296 Proline residue: L 289 - end of helix removed outlier: 3.788A pdb=" N PHE L 296 " --> pdb=" O VAL L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN L 301 " --> pdb=" O VAL L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL L 308 " --> pdb=" O ASP L 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR L 309 " --> pdb=" O VAL L 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 312 " --> pdb=" O VAL L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU L 330 " --> pdb=" O ASN L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS L 346 " --> pdb=" O VAL L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU L 370 " --> pdb=" O LEU L 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 11 Processing helix chain 'M' and resid 32 through 54 Proline residue: M 46 - end of helix removed outlier: 3.697A pdb=" N PHE M 54 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 88 Processing helix chain 'M' and resid 100 through 108 Processing helix chain 'M' and resid 108 through 131 Proline residue: M 123 - end of helix Processing helix chain 'M' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 204 Processing helix chain 'M' and resid 207 through 236 Processing helix chain 'M' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU M 253 " --> pdb=" O SER M 250 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA M 255 " --> pdb=" O ILE M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 296 Proline residue: M 289 - end of helix removed outlier: 3.788A pdb=" N PHE M 296 " --> pdb=" O VAL M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN M 301 " --> pdb=" O VAL M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL M 308 " --> pdb=" O ASP M 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR M 309 " --> pdb=" O VAL M 305 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU M 312 " --> pdb=" O VAL M 308 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU M 330 " --> pdb=" O ASN M 326 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS M 346 " --> pdb=" O VAL M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU M 370 " --> pdb=" O LEU M 366 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 32 through 54 Proline residue: N 46 - end of helix removed outlier: 3.696A pdb=" N PHE N 54 " --> pdb=" O ILE N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 88 Processing helix chain 'N' and resid 100 through 108 Processing helix chain 'N' and resid 108 through 131 Proline residue: N 123 - end of helix Processing helix chain 'N' and resid 131 through 162 removed outlier: 3.593A pdb=" N ILE N 135 " --> pdb=" O ALA N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 204 Processing helix chain 'N' and resid 207 through 236 Processing helix chain 'N' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU N 253 " --> pdb=" O SER N 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA N 255 " --> pdb=" O ILE N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 296 Proline residue: N 289 - end of helix removed outlier: 3.788A pdb=" N PHE N 296 " --> pdb=" O VAL N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN N 301 " --> pdb=" O VAL N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL N 308 " --> pdb=" O ASP N 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR N 309 " --> pdb=" O VAL N 305 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU N 312 " --> pdb=" O VAL N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU N 330 " --> pdb=" O ASN N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS N 346 " --> pdb=" O VAL N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU N 370 " --> pdb=" O LEU N 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 Processing sheet with id=AA8, first strand: chain 'H' and resid 64 through 65 Processing sheet with id=AA9, first strand: chain 'I' and resid 64 through 65 Processing sheet with id=AB1, first strand: chain 'J' and resid 64 through 65 Processing sheet with id=AB2, first strand: chain 'K' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'L' and resid 64 through 65 Processing sheet with id=AB4, first strand: chain 'M' and resid 64 through 65 Processing sheet with id=AB5, first strand: chain 'N' and resid 64 through 65 2367 hydrogen bonds defined for protein. 7017 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: 7.45 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5807 1.32 - 1.44: 9642 1.44 - 1.56: 23527 1.56 - 1.69: 84 1.69 - 1.81: 182 Bond restraints: 39242 Sorted by residual: bond pdb=" N ASP B 256 " pdb=" CA ASP B 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.23e+00 bond pdb=" N ASP H 256 " pdb=" CA ASP H 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.20e+00 bond pdb=" N ASP D 256 " pdb=" CA ASP D 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.20e+00 bond pdb=" N ASP M 256 " pdb=" CA ASP M 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.12e+00 bond pdb=" N ASP I 256 " pdb=" CA ASP I 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.11e+00 ... (remaining 39237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 51411 2.04 - 4.08: 1532 4.08 - 6.12: 257 6.12 - 8.16: 14 8.16 - 10.20: 42 Bond angle restraints: 53256 Sorted by residual: angle pdb=" C THR G 258 " pdb=" N VAL G 259 " pdb=" CA VAL G 259 " ideal model delta sigma weight residual 122.59 125.27 -2.68 7.20e-01 1.93e+00 1.39e+01 angle pdb=" C THR I 258 " pdb=" N VAL I 259 " pdb=" CA VAL I 259 " ideal model delta sigma weight residual 122.59 125.26 -2.67 7.20e-01 1.93e+00 1.37e+01 angle pdb=" C THR D 258 " pdb=" N VAL D 259 " pdb=" CA VAL D 259 " ideal model delta sigma weight residual 122.59 125.25 -2.66 7.20e-01 1.93e+00 1.37e+01 angle pdb=" C THR H 258 " pdb=" N VAL H 259 " pdb=" CA VAL H 259 " ideal model delta sigma weight residual 122.59 125.25 -2.66 7.20e-01 1.93e+00 1.37e+01 angle pdb=" C THR E 258 " pdb=" N VAL E 259 " pdb=" CA VAL E 259 " ideal model delta sigma weight residual 122.59 125.24 -2.65 7.20e-01 1.93e+00 1.36e+01 ... (remaining 53251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 24161 33.84 - 67.67: 1065 67.67 - 101.51: 28 101.51 - 135.35: 28 135.35 - 169.19: 14 Dihedral angle restraints: 25296 sinusoidal: 11086 harmonic: 14210 Sorted by residual: dihedral pdb=" N1 PTY M 401 " pdb=" C2 PTY M 401 " pdb=" C3 PTY M 401 " pdb=" O11 PTY M 401 " ideal model delta sinusoidal sigma weight residual 65.33 -103.86 169.19 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N1 PTY N 402 " pdb=" C2 PTY N 402 " pdb=" C3 PTY N 402 " pdb=" O11 PTY N 402 " ideal model delta sinusoidal sigma weight residual 65.33 -103.84 169.17 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N1 PTY K 401 " pdb=" C2 PTY K 401 " pdb=" C3 PTY K 401 " pdb=" O11 PTY K 401 " ideal model delta sinusoidal sigma weight residual 65.33 -103.84 169.17 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 25293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3797 0.038 - 0.076: 1784 0.076 - 0.114: 584 0.114 - 0.152: 135 0.152 - 0.190: 14 Chirality restraints: 6314 Sorted by residual: chirality pdb=" CA LEU I 146 " pdb=" N LEU I 146 " pdb=" C LEU I 146 " pdb=" CB LEU I 146 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA LEU D 146 " pdb=" N LEU D 146 " pdb=" C LEU D 146 " pdb=" CB LEU D 146 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA LEU E 146 " pdb=" N LEU E 146 " pdb=" C LEU E 146 " pdb=" CB LEU E 146 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 6311 not shown) Planarity restraints: 6230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 122 " 0.024 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO I 123 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO I 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 123 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 122 " 0.024 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO B 123 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 122 " -0.024 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO D 123 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.020 5.00e-02 4.00e+02 ... (remaining 6227 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 230 2.60 - 3.18: 34704 3.18 - 3.75: 58957 3.75 - 4.33: 80152 4.33 - 4.90: 134418 Nonbonded interactions: 308461 Sorted by model distance: nonbonded pdb=" SG CYS N 66 " pdb=" SG CYS N 265 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS N 84 " pdb=" SG CYS N 246 " model vdw 2.030 3.760 nonbonded pdb=" NZ LYS I 148 " pdb=" O ASN J 369 " model vdw 2.069 3.120 nonbonded pdb=" NZ LYS M 148 " pdb=" O ASN N 369 " model vdw 2.073 3.120 nonbonded pdb=" O ASN H 369 " pdb=" NZ LYS N 148 " model vdw 2.076 3.120 ... (remaining 308456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'B' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'C' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'D' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'E' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'F' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'G' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'H' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'I' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'J' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'K' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'L' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'M' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'N' and (resid 2 through 373 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or resid 405)) } 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 31.960 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.010 0.049 39268 Z= 0.451 Angle : 0.876 10.199 53317 Z= 0.455 Chirality : 0.048 0.190 6314 Planarity : 0.004 0.035 6230 Dihedral : 16.955 169.187 15960 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.80 % Allowed : 11.41 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.12), residues: 4718 helix: 0.55 (0.09), residues: 3150 sheet: None (None), residues: 0 loop : -2.35 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 29 TYR 0.021 0.002 TYR N 345 PHE 0.021 0.002 PHE M 67 TRP 0.008 0.002 TRP F 104 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00986 (39242) covalent geometry : angle 0.87641 (53256) SS BOND : bond 0.00163 ( 26) SS BOND : angle 0.66832 ( 61) hydrogen bonds : bond 0.12113 ( 2367) hydrogen bonds : angle 5.35271 ( 7017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 377 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8348 (mpt-90) cc_final: 0.8122 (mmm-85) REVERT: I 256 ASP cc_start: 0.8345 (t0) cc_final: 0.8038 (t0) REVERT: K 200 LEU cc_start: 0.7787 (tt) cc_final: 0.7572 (mp) REVERT: N 89 GLN cc_start: 0.8555 (mp10) cc_final: 0.7695 (mt0) REVERT: N 200 LEU cc_start: 0.7770 (tt) cc_final: 0.7538 (mp) outliers start: 28 outliers final: 10 residues processed: 405 average time/residue: 0.9222 time to fit residues: 438.7873 Evaluate side-chains 264 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 254 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 88 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 0.0050 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 76 GLN A 89 GLN A 134 HIS A 208 ASN A 274 GLN B 76 GLN B 89 GLN B 134 HIS B 208 ASN B 264 GLN B 274 GLN B 353 ASN C 76 GLN C 89 GLN C 134 HIS C 208 ASN C 274 GLN D 76 GLN D 89 GLN D 134 HIS D 208 ASN D 264 GLN D 274 GLN E 76 GLN E 89 GLN E 134 HIS E 208 ASN E 264 GLN E 274 GLN F 76 GLN F 89 GLN F 134 HIS F 208 ASN F 274 GLN G 76 GLN G 89 GLN G 134 HIS G 208 ASN G 274 GLN G 353 ASN H 76 GLN H 134 HIS H 208 ASN H 264 GLN H 274 GLN I 76 GLN I 134 HIS I 208 ASN I 264 GLN I 274 GLN J 76 GLN J 134 HIS J 208 ASN J 274 GLN K 76 GLN K 134 HIS K 208 ASN K 274 GLN L 76 GLN L 89 GLN L 134 HIS L 208 ASN L 274 GLN L 353 ASN M 76 GLN M 89 GLN M 134 HIS M 208 ASN M 274 GLN M 353 ASN N 76 GLN N 89 GLN N 134 HIS N 208 ASN N 274 GLN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.108898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071456 restraints weight = 84531.157| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.60 r_work: 0.3033 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39268 Z= 0.127 Angle : 0.586 7.500 53317 Z= 0.292 Chirality : 0.040 0.124 6314 Planarity : 0.004 0.035 6230 Dihedral : 15.340 136.258 8704 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.33 % Allowed : 14.71 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.12), residues: 4718 helix: 1.60 (0.09), residues: 3234 sheet: None (None), residues: 0 loop : -2.05 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 254 TYR 0.016 0.001 TYR E 345 PHE 0.010 0.001 PHE H 54 TRP 0.009 0.001 TRP H 104 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00267 (39242) covalent geometry : angle 0.58666 (53256) SS BOND : bond 0.00198 ( 26) SS BOND : angle 0.27105 ( 61) hydrogen bonds : bond 0.03913 ( 2367) hydrogen bonds : angle 4.10851 ( 7017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 307 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8095 (tm-30) REVERT: A 140 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8283 (ptpp) REVERT: B 9 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8198 (tm-30) REVERT: C 5 GLN cc_start: 0.8859 (tt0) cc_final: 0.8629 (tp40) REVERT: C 9 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8121 (tm-30) REVERT: D 5 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8286 (tm-30) REVERT: D 9 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8176 (tm-30) REVERT: E 5 GLN cc_start: 0.8967 (tt0) cc_final: 0.8725 (tp40) REVERT: E 9 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8171 (tm-30) REVERT: F 5 GLN cc_start: 0.8915 (mt0) cc_final: 0.8677 (tp40) REVERT: F 9 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8163 (tm-30) REVERT: G 9 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8225 (tm-30) REVERT: H 5 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7842 (tm-30) REVERT: H 9 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7905 (tm-30) REVERT: H 143 MET cc_start: 0.8804 (mtp) cc_final: 0.8600 (mtm) REVERT: I 5 GLN cc_start: 0.8627 (mt0) cc_final: 0.8215 (tm-30) REVERT: I 9 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7924 (tm-30) REVERT: I 256 ASP cc_start: 0.8774 (t0) cc_final: 0.8569 (t0) REVERT: J 9 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7838 (tm-30) REVERT: K 5 GLN cc_start: 0.8515 (mt0) cc_final: 0.8204 (tm-30) REVERT: K 9 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7966 (tm-30) REVERT: L 9 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7885 (tm-30) REVERT: L 143 MET cc_start: 0.8653 (mtp) cc_final: 0.8355 (mtm) REVERT: M 5 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7826 (tm-30) REVERT: M 9 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7910 (tm-30) REVERT: M 57 GLU cc_start: 0.8493 (pm20) cc_final: 0.8188 (pm20) REVERT: N 5 GLN cc_start: 0.8648 (mt0) cc_final: 0.8224 (tm-30) REVERT: N 9 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7981 (tm-30) outliers start: 117 outliers final: 44 residues processed: 383 average time/residue: 0.7319 time to fit residues: 339.9285 Evaluate side-chains 319 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 274 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 37 MET Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 354 ILE Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 183 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 399 optimal weight: 7.9990 chunk 445 optimal weight: 9.9990 chunk 209 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 129 optimal weight: 0.0010 chunk 78 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN C 264 GLN F 89 GLN H 353 ASN I 89 GLN I 264 GLN I 353 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 264 GLN N 353 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.107123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069673 restraints weight = 85420.490| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.59 r_work: 0.2987 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 39268 Z= 0.142 Angle : 0.559 7.734 53317 Z= 0.278 Chirality : 0.040 0.259 6314 Planarity : 0.004 0.035 6230 Dihedral : 12.858 102.491 8704 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.53 % Allowed : 18.01 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.13), residues: 4718 helix: 2.08 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.87 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 254 TYR 0.021 0.001 TYR I 345 PHE 0.014 0.001 PHE E 129 TRP 0.007 0.001 TRP C 104 HIS 0.002 0.001 HIS M 134 Details of bonding type rmsd covalent geometry : bond 0.00332 (39242) covalent geometry : angle 0.55919 (53256) SS BOND : bond 0.00127 ( 26) SS BOND : angle 0.37458 ( 61) hydrogen bonds : bond 0.03743 ( 2367) hydrogen bonds : angle 3.91529 ( 7017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 288 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8433 (tp40) REVERT: A 9 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8192 (tm-30) REVERT: B 9 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8289 (tm-30) REVERT: C 5 GLN cc_start: 0.8878 (tt0) cc_final: 0.8661 (tp40) REVERT: C 9 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8259 (tm-30) REVERT: D 5 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8288 (tm-30) REVERT: D 9 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8217 (tm-30) REVERT: D 89 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8241 (mt0) REVERT: E 9 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8277 (tm-30) REVERT: F 9 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8303 (tm-30) REVERT: F 196 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7846 (p) REVERT: G 5 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8218 (tm-30) REVERT: G 9 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8244 (tm-30) REVERT: H 5 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7809 (tm-30) REVERT: H 9 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7901 (tm-30) REVERT: I 5 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: I 9 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7843 (tm-30) REVERT: I 152 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6192 (mtm110) REVERT: J 9 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7849 (tm-30) REVERT: K 9 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7879 (tm-30) REVERT: K 89 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8530 (mt0) REVERT: K 138 ASP cc_start: 0.7850 (m-30) cc_final: 0.7602 (m-30) REVERT: L 9 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7891 (tm-30) REVERT: L 89 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: L 143 MET cc_start: 0.8671 (mtp) cc_final: 0.8395 (mtm) REVERT: L 152 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6260 (mtm110) REVERT: M 5 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7919 (tm-30) REVERT: M 9 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7856 (tm-30) REVERT: N 9 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7923 (tm-30) outliers start: 89 outliers final: 30 residues processed: 341 average time/residue: 0.8277 time to fit residues: 337.7494 Evaluate side-chains 300 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 152 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 56 GLN Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 336 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 379 optimal weight: 3.9990 chunk 360 optimal weight: 8.9990 chunk 445 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 chunk 454 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN C 89 GLN D 89 GLN D 264 GLN E 264 GLN E 353 ASN F 89 GLN H 89 GLN H 264 GLN I 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 353 ASN L 89 GLN M 89 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 264 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.104433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.066660 restraints weight = 85734.128| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.57 r_work: 0.2901 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 39268 Z= 0.274 Angle : 0.644 8.127 53317 Z= 0.320 Chirality : 0.043 0.156 6314 Planarity : 0.004 0.035 6230 Dihedral : 12.461 96.609 8695 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.47 % Allowed : 17.02 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.13), residues: 4718 helix: 2.07 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.75 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 254 TYR 0.021 0.002 TYR G 345 PHE 0.019 0.002 PHE N 67 TRP 0.010 0.002 TRP M 104 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00659 (39242) covalent geometry : angle 0.64418 (53256) SS BOND : bond 0.00241 ( 26) SS BOND : angle 0.52425 ( 61) hydrogen bonds : bond 0.04332 ( 2367) hydrogen bonds : angle 4.05597 ( 7017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 278 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8483 (tm-30) REVERT: A 9 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 5 GLN cc_start: 0.8957 (tt0) cc_final: 0.8685 (tm-30) REVERT: B 9 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8299 (tm-30) REVERT: B 29 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7827 (mmm-85) REVERT: C 5 GLN cc_start: 0.8913 (tt0) cc_final: 0.8703 (tm-30) REVERT: C 9 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 31 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8474 (mt-10) REVERT: C 143 MET cc_start: 0.8979 (mtm) cc_final: 0.8717 (mtp) REVERT: D 5 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8360 (tm-30) REVERT: D 9 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 254 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8747 (ttm110) REVERT: E 5 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8458 (tp40) REVERT: E 9 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8316 (tm-30) REVERT: E 29 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7745 (mmm-85) REVERT: F 9 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8347 (tm-30) REVERT: F 29 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7951 (mmm-85) REVERT: G 5 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8295 (tm-30) REVERT: G 9 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8250 (tm-30) REVERT: H 5 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7824 (tm-30) REVERT: H 9 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7845 (tm-30) REVERT: H 138 ASP cc_start: 0.7938 (m-30) cc_final: 0.7713 (m-30) REVERT: I 9 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7838 (tm-30) REVERT: I 138 ASP cc_start: 0.7906 (m-30) cc_final: 0.7629 (m-30) REVERT: I 152 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6146 (mtm110) REVERT: J 9 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7806 (tm-30) REVERT: J 138 ASP cc_start: 0.7906 (m-30) cc_final: 0.7618 (m-30) REVERT: K 9 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7841 (tm-30) REVERT: K 138 ASP cc_start: 0.7967 (m-30) cc_final: 0.7708 (m-30) REVERT: L 9 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7859 (tm-30) REVERT: L 57 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: L 143 MET cc_start: 0.8696 (mtp) cc_final: 0.8410 (mtm) REVERT: M 5 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7884 (tm-30) REVERT: M 9 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7843 (tm-30) REVERT: M 354 ILE cc_start: 0.8023 (mm) cc_final: 0.7730 (mt) REVERT: N 9 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7932 (tm-30) REVERT: N 89 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8822 (mt0) outliers start: 157 outliers final: 63 residues processed: 393 average time/residue: 0.7385 time to fit residues: 352.5827 Evaluate side-chains 326 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 258 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 152 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 189 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 471 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 366 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 403 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN D 89 GLN D 264 GLN E 264 GLN G 264 GLN I 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.106003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.068681 restraints weight = 85080.786| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.57 r_work: 0.2961 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39268 Z= 0.140 Angle : 0.560 9.402 53317 Z= 0.277 Chirality : 0.040 0.144 6314 Planarity : 0.004 0.035 6230 Dihedral : 11.839 92.656 8695 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.70 % Allowed : 18.73 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.13), residues: 4718 helix: 2.28 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.72 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 128 TYR 0.017 0.001 TYR B 345 PHE 0.014 0.001 PHE D 129 TRP 0.013 0.001 TRP M 104 HIS 0.002 0.001 HIS M 134 Details of bonding type rmsd covalent geometry : bond 0.00327 (39242) covalent geometry : angle 0.55996 (53256) SS BOND : bond 0.00125 ( 26) SS BOND : angle 0.41245 ( 61) hydrogen bonds : bond 0.03634 ( 2367) hydrogen bonds : angle 3.78230 ( 7017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 282 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8372 (tm-30) REVERT: A 9 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8197 (tm-30) REVERT: B 5 GLN cc_start: 0.8939 (tt0) cc_final: 0.8639 (tm-30) REVERT: B 9 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 29 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7798 (mmm-85) REVERT: C 5 GLN cc_start: 0.8872 (tt0) cc_final: 0.8662 (tm-30) REVERT: C 9 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8184 (tm-30) REVERT: C 143 MET cc_start: 0.9011 (mtm) cc_final: 0.8736 (mtp) REVERT: D 5 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8313 (tm-30) REVERT: D 9 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8167 (tm-30) REVERT: E 5 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8364 (tp40) REVERT: E 9 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8237 (tm-30) REVERT: F 9 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8307 (tm-30) REVERT: G 5 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8201 (tm-30) REVERT: G 9 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8167 (tm-30) REVERT: G 31 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8498 (mt-10) REVERT: G 147 ASP cc_start: 0.9009 (m-30) cc_final: 0.8777 (p0) REVERT: H 5 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7804 (tm-30) REVERT: H 9 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7774 (tm-30) REVERT: H 138 ASP cc_start: 0.7975 (m-30) cc_final: 0.7718 (m-30) REVERT: I 9 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7757 (tm-30) REVERT: I 138 ASP cc_start: 0.7979 (m-30) cc_final: 0.7682 (m-30) REVERT: I 152 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6130 (mtm110) REVERT: J 9 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7711 (tm-30) REVERT: J 138 ASP cc_start: 0.7899 (m-30) cc_final: 0.7609 (m-30) REVERT: K 9 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7773 (tm-30) REVERT: K 138 ASP cc_start: 0.7987 (m-30) cc_final: 0.7708 (m-30) REVERT: L 9 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7801 (tm-30) REVERT: L 143 MET cc_start: 0.8718 (mtp) cc_final: 0.8503 (mtm) REVERT: L 152 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6304 (mtm110) REVERT: M 5 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7779 (tm-30) REVERT: M 9 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7828 (tm-30) REVERT: M 57 GLU cc_start: 0.8709 (pm20) cc_final: 0.8297 (pm20) REVERT: M 354 ILE cc_start: 0.7968 (mm) cc_final: 0.7711 (mt) REVERT: N 9 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7798 (tm-30) REVERT: N 138 ASP cc_start: 0.7897 (m-30) cc_final: 0.7668 (m-30) outliers start: 95 outliers final: 45 residues processed: 341 average time/residue: 0.7973 time to fit residues: 326.9036 Evaluate side-chains 307 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 152 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 105 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 403 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 397 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 130 optimal weight: 0.0020 chunk 424 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN C 264 GLN F 264 GLN J 89 GLN K 89 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.106489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069488 restraints weight = 85226.162| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.62 r_work: 0.2988 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39268 Z= 0.120 Angle : 0.541 9.846 53317 Z= 0.267 Chirality : 0.039 0.127 6314 Planarity : 0.004 0.034 6230 Dihedral : 11.243 82.025 8695 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.27 % Allowed : 18.38 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.13), residues: 4718 helix: 2.38 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.74 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 75 TYR 0.015 0.001 TYR B 345 PHE 0.012 0.001 PHE K 141 TRP 0.025 0.002 TRP K 74 HIS 0.002 0.001 HIS K 134 Details of bonding type rmsd covalent geometry : bond 0.00272 (39242) covalent geometry : angle 0.54140 (53256) SS BOND : bond 0.00101 ( 26) SS BOND : angle 0.41300 ( 61) hydrogen bonds : bond 0.03345 ( 2367) hydrogen bonds : angle 3.67427 ( 7017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 293 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 9 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 5 GLN cc_start: 0.8908 (tt0) cc_final: 0.8621 (tm-30) REVERT: B 9 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 29 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7694 (mmm-85) REVERT: B 74 TRP cc_start: 0.8843 (t60) cc_final: 0.8354 (t-100) REVERT: C 5 GLN cc_start: 0.8894 (tt0) cc_final: 0.8692 (tm-30) REVERT: C 9 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8188 (tm-30) REVERT: C 143 MET cc_start: 0.9035 (mtm) cc_final: 0.8765 (mtp) REVERT: D 5 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8374 (tm-30) REVERT: D 9 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8197 (tm-30) REVERT: E 5 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8317 (tp40) REVERT: E 9 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8301 (tm-30) REVERT: E 29 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7417 (mmm-85) REVERT: F 9 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8319 (tm-30) REVERT: F 147 ASP cc_start: 0.8990 (m-30) cc_final: 0.8747 (p0) REVERT: G 5 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8195 (tm-30) REVERT: G 9 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8207 (tm-30) REVERT: G 31 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8453 (mt-10) REVERT: G 143 MET cc_start: 0.9159 (mtp) cc_final: 0.8778 (mtp) REVERT: G 147 ASP cc_start: 0.8978 (m-30) cc_final: 0.8733 (p0) REVERT: H 5 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7789 (tm-30) REVERT: H 9 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7803 (tm-30) REVERT: H 138 ASP cc_start: 0.7929 (m-30) cc_final: 0.7716 (m-30) REVERT: H 215 SER cc_start: 0.9135 (m) cc_final: 0.8919 (p) REVERT: I 9 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7791 (tm-30) REVERT: I 74 TRP cc_start: 0.8627 (t60) cc_final: 0.8387 (t60) REVERT: I 138 ASP cc_start: 0.8012 (m-30) cc_final: 0.7755 (m-30) REVERT: J 9 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7769 (tm-30) REVERT: J 150 TYR cc_start: 0.6751 (t80) cc_final: 0.6525 (t80) REVERT: J 215 SER cc_start: 0.9118 (m) cc_final: 0.8905 (p) REVERT: K 9 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7788 (tm-30) REVERT: K 138 ASP cc_start: 0.8012 (m-30) cc_final: 0.7750 (m-30) REVERT: L 9 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7796 (tm-30) REVERT: L 143 MET cc_start: 0.8715 (mtp) cc_final: 0.8458 (mtm) REVERT: M 5 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7787 (tm-30) REVERT: M 9 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7834 (tm-30) REVERT: M 57 GLU cc_start: 0.8670 (pm20) cc_final: 0.8289 (pm20) REVERT: M 138 ASP cc_start: 0.7855 (m-30) cc_final: 0.7607 (m-30) REVERT: M 354 ILE cc_start: 0.7908 (mm) cc_final: 0.7681 (mt) REVERT: N 9 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7822 (tm-30) REVERT: N 138 ASP cc_start: 0.7905 (m-30) cc_final: 0.7681 (m-30) REVERT: N 352 GLU cc_start: 0.9526 (tm-30) cc_final: 0.8982 (mp0) outliers start: 115 outliers final: 47 residues processed: 380 average time/residue: 0.7143 time to fit residues: 332.2083 Evaluate side-chains 310 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 56 GLN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 267 optimal weight: 20.0000 chunk 370 optimal weight: 7.9990 chunk 352 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 264 optimal weight: 8.9990 chunk 443 optimal weight: 0.0870 chunk 462 optimal weight: 7.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN C 264 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.106321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.069416 restraints weight = 85420.324| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.60 r_work: 0.2984 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39268 Z= 0.127 Angle : 0.559 10.414 53317 Z= 0.271 Chirality : 0.039 0.144 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.922 70.613 8695 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.27 % Allowed : 18.73 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.13), residues: 4718 helix: 2.43 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.70 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 75 TYR 0.015 0.001 TYR B 345 PHE 0.010 0.001 PHE M 141 TRP 0.022 0.002 TRP K 74 HIS 0.002 0.001 HIS H 134 Details of bonding type rmsd covalent geometry : bond 0.00294 (39242) covalent geometry : angle 0.55898 (53256) SS BOND : bond 0.00120 ( 26) SS BOND : angle 0.43164 ( 61) hydrogen bonds : bond 0.03378 ( 2367) hydrogen bonds : angle 3.65724 ( 7017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 278 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 9 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8287 (tm-30) REVERT: B 5 GLN cc_start: 0.8893 (tt0) cc_final: 0.8610 (tm-30) REVERT: B 9 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 29 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.7732 (mmm-85) REVERT: B 74 TRP cc_start: 0.8868 (t60) cc_final: 0.8458 (t-100) REVERT: C 9 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 143 MET cc_start: 0.9013 (mtm) cc_final: 0.8763 (mtp) REVERT: D 5 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8399 (tm-30) REVERT: D 9 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8226 (tm-30) REVERT: E 5 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8343 (tp40) REVERT: E 9 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8330 (tm-30) REVERT: E 29 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7534 (mmm-85) REVERT: F 9 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8343 (tm-30) REVERT: F 143 MET cc_start: 0.9144 (mtp) cc_final: 0.8794 (mtp) REVERT: F 147 ASP cc_start: 0.8996 (m-30) cc_final: 0.8759 (p0) REVERT: G 5 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8194 (tm-30) REVERT: G 9 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8235 (tm-30) REVERT: G 31 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8435 (mt-10) REVERT: G 143 MET cc_start: 0.9128 (mtp) cc_final: 0.8778 (mtp) REVERT: G 147 ASP cc_start: 0.8983 (m-30) cc_final: 0.8742 (p0) REVERT: H 5 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7787 (tm-30) REVERT: H 9 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7839 (tm-30) REVERT: I 9 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7787 (tm-30) REVERT: I 57 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: I 138 ASP cc_start: 0.8025 (m-30) cc_final: 0.7699 (m-30) REVERT: I 215 SER cc_start: 0.9242 (m) cc_final: 0.9035 (p) REVERT: J 9 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7787 (tm-30) REVERT: J 150 TYR cc_start: 0.6752 (t80) cc_final: 0.6513 (t80) REVERT: J 215 SER cc_start: 0.9117 (m) cc_final: 0.8916 (p) REVERT: K 9 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7817 (tm-30) REVERT: K 89 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8349 (mt0) REVERT: K 138 ASP cc_start: 0.7996 (m-30) cc_final: 0.7776 (m-30) REVERT: K 215 SER cc_start: 0.9221 (m) cc_final: 0.8940 (p) REVERT: K 219 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8573 (mp) REVERT: L 9 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7812 (tm-30) REVERT: L 215 SER cc_start: 0.9226 (m) cc_final: 0.8986 (p) REVERT: M 5 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7836 (tm-30) REVERT: M 9 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7860 (tm-30) REVERT: M 57 GLU cc_start: 0.8666 (pm20) cc_final: 0.8281 (pm20) REVERT: M 138 ASP cc_start: 0.7905 (m-30) cc_final: 0.7700 (m-30) REVERT: N 9 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7838 (tm-30) REVERT: N 215 SER cc_start: 0.9095 (m) cc_final: 0.8882 (p) outliers start: 115 outliers final: 57 residues processed: 367 average time/residue: 0.6698 time to fit residues: 303.3970 Evaluate side-chains 315 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 56 GLN Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 377 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 444 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 376 optimal weight: 0.0970 chunk 38 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 289 optimal weight: 9.9990 chunk 316 optimal weight: 1.9990 chunk 305 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 GLN I 89 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.105881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.069002 restraints weight = 85247.509| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.59 r_work: 0.2984 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39268 Z= 0.138 Angle : 0.573 10.698 53317 Z= 0.279 Chirality : 0.040 0.246 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.808 59.766 8695 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.93 % Allowed : 19.27 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.13), residues: 4718 helix: 2.47 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.60 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 75 TYR 0.015 0.001 TYR A 345 PHE 0.010 0.001 PHE N 141 TRP 0.032 0.002 TRP H 74 HIS 0.002 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00325 (39242) covalent geometry : angle 0.57312 (53256) SS BOND : bond 0.00134 ( 26) SS BOND : angle 0.46040 ( 61) hydrogen bonds : bond 0.03438 ( 2367) hydrogen bonds : angle 3.66759 ( 7017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 260 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8420 (tm-30) REVERT: A 9 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8295 (tm-30) REVERT: A 37 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8360 (ttt) REVERT: B 5 GLN cc_start: 0.8898 (tt0) cc_final: 0.8613 (tm-30) REVERT: B 9 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 29 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7757 (mmm-85) REVERT: B 74 TRP cc_start: 0.8822 (t60) cc_final: 0.8444 (t-100) REVERT: C 9 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 89 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: C 143 MET cc_start: 0.9052 (mtm) cc_final: 0.8830 (mtp) REVERT: D 5 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8421 (tm-30) REVERT: D 9 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8266 (tm-30) REVERT: E 5 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8348 (tp40) REVERT: E 9 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8322 (tm-30) REVERT: E 29 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7502 (mmm-85) REVERT: F 5 GLN cc_start: 0.8552 (tp40) cc_final: 0.8339 (tp40) REVERT: F 9 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8352 (tm-30) REVERT: F 147 ASP cc_start: 0.8977 (m-30) cc_final: 0.8752 (p0) REVERT: G 5 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8235 (tm-30) REVERT: G 9 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8243 (tm-30) REVERT: G 31 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8452 (mt-10) REVERT: G 143 MET cc_start: 0.9148 (mtp) cc_final: 0.8770 (mtp) REVERT: G 147 ASP cc_start: 0.8969 (m-30) cc_final: 0.8737 (p0) REVERT: H 5 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7760 (tm-30) REVERT: H 9 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7854 (tm-30) REVERT: I 9 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7810 (tm-30) REVERT: I 57 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: I 138 ASP cc_start: 0.8093 (m-30) cc_final: 0.7820 (m-30) REVERT: J 9 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7827 (tm-30) REVERT: J 150 TYR cc_start: 0.6820 (t80) cc_final: 0.6600 (t80) REVERT: K 9 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7862 (tm-30) REVERT: K 89 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8374 (mt0) REVERT: K 138 ASP cc_start: 0.8063 (m-30) cc_final: 0.7807 (m-30) REVERT: L 9 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7835 (tm-30) REVERT: L 143 MET cc_start: 0.9042 (mtm) cc_final: 0.8745 (mtm) REVERT: L 146 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7825 (tp) REVERT: L 215 SER cc_start: 0.9229 (m) cc_final: 0.9001 (p) REVERT: M 5 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7830 (tm-30) REVERT: M 9 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7894 (tm-30) REVERT: M 57 GLU cc_start: 0.8680 (pm20) cc_final: 0.8314 (pm20) REVERT: N 9 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7863 (tm-30) outliers start: 103 outliers final: 62 residues processed: 337 average time/residue: 0.6959 time to fit residues: 288.6822 Evaluate side-chains 310 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 56 GLN Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 355 optimal weight: 50.0000 chunk 282 optimal weight: 2.9990 chunk 472 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 421 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 464 optimal weight: 1.9990 chunk 399 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.105056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.068119 restraints weight = 85872.086| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.56 r_work: 0.2945 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39268 Z= 0.169 Angle : 0.605 13.783 53317 Z= 0.294 Chirality : 0.041 0.306 6314 Planarity : 0.004 0.033 6230 Dihedral : 11.000 64.934 8695 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.02 % Allowed : 19.21 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.13), residues: 4718 helix: 2.43 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.59 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 75 TYR 0.016 0.001 TYR A 345 PHE 0.017 0.001 PHE K 141 TRP 0.040 0.002 TRP H 74 HIS 0.002 0.001 HIS H 134 Details of bonding type rmsd covalent geometry : bond 0.00403 (39242) covalent geometry : angle 0.60476 (53256) SS BOND : bond 0.00166 ( 26) SS BOND : angle 0.52086 ( 61) hydrogen bonds : bond 0.03669 ( 2367) hydrogen bonds : angle 3.74501 ( 7017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 244 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 9 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8261 (tm-30) REVERT: A 37 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8369 (ttt) REVERT: B 5 GLN cc_start: 0.8902 (tt0) cc_final: 0.8639 (tm-30) REVERT: B 9 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 29 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7858 (mmm-85) REVERT: B 74 TRP cc_start: 0.8847 (t60) cc_final: 0.8568 (t-100) REVERT: C 5 GLN cc_start: 0.8576 (tp40) cc_final: 0.8268 (tp40) REVERT: C 9 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8141 (tm-30) REVERT: C 143 MET cc_start: 0.9043 (mtm) cc_final: 0.8813 (mtp) REVERT: D 5 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8439 (tm-30) REVERT: D 9 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8266 (tm-30) REVERT: E 5 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8450 (tm-30) REVERT: E 9 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8302 (tm-30) REVERT: E 29 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7766 (mmt90) REVERT: F 5 GLN cc_start: 0.8569 (tp40) cc_final: 0.8338 (tp40) REVERT: F 9 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8324 (tm-30) REVERT: F 143 MET cc_start: 0.9129 (mtp) cc_final: 0.8739 (mtp) REVERT: F 147 ASP cc_start: 0.8992 (m-30) cc_final: 0.8767 (p0) REVERT: G 5 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8241 (tm-30) REVERT: G 9 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8223 (tm-30) REVERT: G 31 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8461 (mt-10) REVERT: G 143 MET cc_start: 0.9148 (mtp) cc_final: 0.8788 (mtp) REVERT: G 147 ASP cc_start: 0.8974 (m-30) cc_final: 0.8720 (p0) REVERT: H 5 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7781 (tm-30) REVERT: H 9 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7853 (tm-30) REVERT: I 9 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7804 (tm-30) REVERT: I 138 ASP cc_start: 0.8061 (m-30) cc_final: 0.7783 (m-30) REVERT: J 9 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7798 (tm-30) REVERT: J 150 TYR cc_start: 0.6788 (t80) cc_final: 0.6566 (t80) REVERT: K 9 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7845 (tm-30) REVERT: K 57 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: K 89 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8403 (mt0) REVERT: K 138 ASP cc_start: 0.8073 (m-30) cc_final: 0.7834 (m-30) REVERT: L 9 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7777 (tm-30) REVERT: L 31 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8198 (mt-10) REVERT: L 143 MET cc_start: 0.8974 (mtm) cc_final: 0.8693 (mtm) REVERT: M 5 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7804 (tm-30) REVERT: M 9 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7835 (tm-30) REVERT: M 57 GLU cc_start: 0.8734 (pm20) cc_final: 0.8369 (pm20) REVERT: M 352 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: N 9 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7825 (tm-30) outliers start: 106 outliers final: 75 residues processed: 334 average time/residue: 0.7091 time to fit residues: 290.1483 Evaluate side-chains 311 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 232 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 56 GLN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 352 GLU Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 0.0170 chunk 307 optimal weight: 0.0770 chunk 63 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 361 optimal weight: 0.6980 chunk 186 optimal weight: 20.0000 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 353 ASN I 89 GLN J 353 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.107368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071330 restraints weight = 84883.744| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.58 r_work: 0.3042 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 39268 Z= 0.104 Angle : 0.569 12.287 53317 Z= 0.274 Chirality : 0.040 0.364 6314 Planarity : 0.004 0.035 6230 Dihedral : 10.396 68.780 8695 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.74 % Allowed : 20.32 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.13), residues: 4718 helix: 2.49 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.65 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 152 TYR 0.015 0.001 TYR B 345 PHE 0.014 0.001 PHE F 129 TRP 0.026 0.002 TRP H 74 HIS 0.001 0.001 HIS K 134 Details of bonding type rmsd covalent geometry : bond 0.00220 (39242) covalent geometry : angle 0.56922 (53256) SS BOND : bond 0.00052 ( 26) SS BOND : angle 0.41398 ( 61) hydrogen bonds : bond 0.02995 ( 2367) hydrogen bonds : angle 3.55505 ( 7017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 261 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8418 (tm-30) REVERT: A 9 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8310 (tm-30) REVERT: B 5 GLN cc_start: 0.8883 (tt0) cc_final: 0.8619 (tm-30) REVERT: B 9 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 29 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7717 (mmm-85) REVERT: C 5 GLN cc_start: 0.8613 (tp40) cc_final: 0.8294 (tp40) REVERT: C 9 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8229 (tm-30) REVERT: D 5 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8464 (tm-30) REVERT: D 9 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8338 (tm-30) REVERT: E 5 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8322 (tp40) REVERT: E 9 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8341 (tm-30) REVERT: E 29 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7358 (mtt180) REVERT: F 5 GLN cc_start: 0.8529 (tp40) cc_final: 0.8284 (tp40) REVERT: F 9 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8355 (tm-30) REVERT: F 147 ASP cc_start: 0.8973 (m-30) cc_final: 0.8742 (p0) REVERT: G 5 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8220 (tm-30) REVERT: G 9 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8270 (tm-30) REVERT: G 31 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8431 (mt-10) REVERT: G 143 MET cc_start: 0.9161 (mtp) cc_final: 0.8800 (mtp) REVERT: G 147 ASP cc_start: 0.8967 (m-30) cc_final: 0.8684 (p0) REVERT: H 5 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7735 (tm-30) REVERT: H 9 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7858 (tm-30) REVERT: I 9 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7792 (tm-30) REVERT: I 138 ASP cc_start: 0.8017 (m-30) cc_final: 0.7729 (m-30) REVERT: J 9 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7764 (tm-30) REVERT: K 9 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7864 (tm-30) REVERT: K 57 GLU cc_start: 0.8674 (pm20) cc_final: 0.8281 (pm20) REVERT: K 138 ASP cc_start: 0.8022 (m-30) cc_final: 0.7804 (m-30) REVERT: L 9 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7796 (tm-30) REVERT: L 56 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8535 (pp30) REVERT: L 57 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8347 (pm20) REVERT: L 143 MET cc_start: 0.9028 (mtm) cc_final: 0.8773 (mtm) REVERT: M 5 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7796 (tm-30) REVERT: M 9 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7943 (tm-30) REVERT: M 57 GLU cc_start: 0.8677 (pm20) cc_final: 0.8321 (pm20) REVERT: M 352 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: N 9 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7892 (tm-30) outliers start: 61 outliers final: 40 residues processed: 315 average time/residue: 0.7356 time to fit residues: 282.6450 Evaluate side-chains 277 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 352 GLU Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 414 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 427 optimal weight: 4.9990 chunk 353 optimal weight: 0.8980 chunk 267 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 361 optimal weight: 6.9990 chunk 419 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 464 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.105484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.068766 restraints weight = 85408.344| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.57 r_work: 0.2965 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 39268 Z= 0.150 Angle : 0.594 12.371 53317 Z= 0.288 Chirality : 0.041 0.363 6314 Planarity : 0.004 0.033 6230 Dihedral : 10.602 69.601 8695 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.76 % Allowed : 20.92 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.13), residues: 4718 helix: 2.46 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.68 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.017 0.001 TYR C 345 PHE 0.011 0.001 PHE K 141 TRP 0.044 0.003 TRP A 74 HIS 0.001 0.000 HIS M 134 Details of bonding type rmsd covalent geometry : bond 0.00354 (39242) covalent geometry : angle 0.59374 (53256) SS BOND : bond 0.00149 ( 26) SS BOND : angle 0.51594 ( 61) hydrogen bonds : bond 0.03499 ( 2367) hydrogen bonds : angle 3.67419 ( 7017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12223.49 seconds wall clock time: 209 minutes 16.86 seconds (12556.86 seconds total)