Starting phenix.real_space_refine on Sat Jul 4 05:00:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rtj_24682/07_2026/7rtj_24682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtj_24682/07_2026/7rtj_24682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rtj_24682/07_2026/7rtj_24682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtj_24682/07_2026/7rtj_24682.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rtj_24682/07_2026/7rtj_24682.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rtj_24682/07_2026/7rtj_24682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rtj_24682/07_2026/7rtj_24682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtj_24682/07_2026/7rtj_24682.map" } resolution = 3.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6124 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8860 2.51 5 N 2140 2.21 5 O 2316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13352 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-3': 6, 'PGW:plan-1': 5, 'PGW:plan-2': 5} Unresolved non-hydrogen planarities: 57 Restraints were copied for chains: C, D Time building chain proxies: 4.04, per 1000 atoms: 0.30 Number of scatterers: 13352 At special positions: 0 Unit cell: (106.937, 106.937, 114.348, 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 28 16.00 P 8 15.00 O 2316 8.00 N 2140 7.00 C 8860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.34 Conformation dependent library (CDL) restraints added in 423.0 milliseconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 66.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 12 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.824A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 4.146A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 222 removed outlier: 3.710A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.701A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 299 removed outlier: 6.158A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.557A pdb=" N LYS A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 306 through 314 removed outlier: 3.632A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.601A pdb=" N ALA A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.825A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.146A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 222 removed outlier: 3.711A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 removed outlier: 3.702A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 299 removed outlier: 6.159A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 removed outlier: 3.557A pdb=" N LYS B 303 " --> pdb=" O PRO B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 306 through 314 removed outlier: 3.632A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.601A pdb=" N ALA B 408 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 56 Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.825A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 removed outlier: 4.147A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 222 removed outlier: 3.710A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 removed outlier: 3.702A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 removed outlier: 6.159A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 303 removed outlier: 3.557A pdb=" N LYS C 303 " --> pdb=" O PRO C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 306 through 314 removed outlier: 3.632A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'C' and resid 404 through 420 removed outlier: 3.602A pdb=" N ALA C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 56 Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.825A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 removed outlier: 4.146A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 222 removed outlier: 3.710A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 removed outlier: 3.701A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 299 removed outlier: 6.158A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 removed outlier: 3.556A pdb=" N LYS D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 306 through 314 removed outlier: 3.631A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 404 through 420 removed outlier: 3.601A pdb=" N ALA D 408 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR A 322 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 387 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 390 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 340 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 392 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 338 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 339 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 348 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR B 322 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 387 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 390 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 340 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 392 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 338 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 339 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 348 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR C 322 " --> pdb=" O CYS C 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C 387 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 390 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 340 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 392 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 338 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C 339 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 348 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR D 322 " --> pdb=" O CYS D 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS D 387 " --> pdb=" O TYR D 322 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 390 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 340 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 392 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 338 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR D 339 " --> pdb=" O PHE D 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 348 " --> pdb=" O ALA D 358 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2148 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: 2.03 Time building geometry restraints manager: 1.76 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: 2088 1.32 - 1.44: 3376 1.44 - 1.56: 8084 1.56 - 1.68: 20 1.68 - 1.81: 48 Bond restraints: 13616 Sorted by residual: bond pdb=" C10 PGW B 507 " pdb=" C9 PGW B 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW C 507 " pdb=" C9 PGW C 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW A 505 " pdb=" C9 PGW A 505 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW D 507 " pdb=" C9 PGW D 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 ... (remaining 13611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 18018 2.97 - 5.93: 274 5.93 - 8.90: 52 8.90 - 11.87: 24 11.87 - 14.84: 16 Bond angle restraints: 18384 Sorted by residual: angle pdb=" N LEU C 91 " pdb=" CA LEU C 91 " pdb=" C LEU C 91 " ideal model delta sigma weight residual 112.54 106.05 6.49 1.22e+00 6.72e-01 2.83e+01 angle pdb=" N LEU D 91 " pdb=" CA LEU D 91 " pdb=" C LEU D 91 " ideal model delta sigma weight residual 112.54 106.06 6.48 1.22e+00 6.72e-01 2.82e+01 angle pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 112.54 106.06 6.48 1.22e+00 6.72e-01 2.82e+01 angle pdb=" N LEU B 91 " pdb=" CA LEU B 91 " pdb=" C LEU B 91 " ideal model delta sigma weight residual 112.54 106.11 6.43 1.22e+00 6.72e-01 2.78e+01 angle pdb=" C10 PGW D 507 " pdb=" C9 PGW D 507 " pdb=" C8 PGW D 507 " ideal model delta sigma weight residual 127.02 112.18 14.84 3.00e+00 1.11e-01 2.45e+01 ... (remaining 18379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.71: 7629 28.71 - 57.42: 595 57.42 - 86.13: 24 86.13 - 114.84: 8 114.84 - 143.56: 4 Dihedral angle restraints: 8260 sinusoidal: 3580 harmonic: 4680 Sorted by residual: dihedral pdb=" C5' CMP D 503 " pdb=" O5' CMP D 503 " pdb=" P CMP D 503 " pdb=" O1P CMP D 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.67 -112.67 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' CMP B 503 " pdb=" O5' CMP B 503 " pdb=" P CMP B 503 " pdb=" O1P CMP B 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.64 -112.64 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" C5' CMP C 503 " pdb=" O5' CMP C 503 " pdb=" P CMP C 503 " pdb=" O1P CMP C 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.62 -112.62 1 2.00e+01 2.50e-03 3.32e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1560 0.052 - 0.104: 447 0.104 - 0.157: 113 0.157 - 0.209: 8 0.209 - 0.261: 12 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CA PRO C 405 " pdb=" N PRO C 405 " pdb=" C PRO C 405 " pdb=" CB PRO C 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO D 405 " pdb=" N PRO D 405 " pdb=" C PRO D 405 " pdb=" CB PRO D 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO B 405 " pdb=" N PRO B 405 " pdb=" C PRO B 405 " pdb=" CB PRO B 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2137 not shown) Planarity restraints: 2224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 504 " 0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW D 504 " -0.148 2.00e-02 2.50e+03 pdb=" C8 PGW D 504 " 0.142 2.00e-02 2.50e+03 pdb=" C9 PGW D 504 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 504 " -0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW B 504 " 0.148 2.00e-02 2.50e+03 pdb=" C8 PGW B 504 " -0.142 2.00e-02 2.50e+03 pdb=" C9 PGW B 504 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 502 " -0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW A 502 " 0.148 2.00e-02 2.50e+03 pdb=" C8 PGW A 502 " -0.142 2.00e-02 2.50e+03 pdb=" C9 PGW A 502 " 0.137 2.00e-02 2.50e+03 ... (remaining 2221 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2059 2.76 - 3.29: 12876 3.29 - 3.83: 21815 3.83 - 4.36: 23707 4.36 - 4.90: 42020 Nonbonded interactions: 102477 Sorted by model distance: nonbonded pdb=" O ARG D 417 " pdb=" NH1 ARG D 417 " model vdw 2.224 3.120 nonbonded pdb=" O ARG A 417 " pdb=" NH1 ARG A 417 " model vdw 2.224 3.120 nonbonded pdb=" O ARG C 417 " pdb=" NH1 ARG C 417 " model vdw 2.224 3.120 nonbonded pdb=" O ARG B 417 " pdb=" NH1 ARG B 417 " model vdw 2.225 3.120 nonbonded pdb=" O ILE C 178 " pdb=" OG1 THR C 182 " model vdw 2.253 3.040 ... (remaining 102472 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or (resid 506 and (name C01 or name C02 or name C03 or name \ C1 or name C19 or name C2 or name C20 or name C3 or name C4 or name C5 or name C \ 6 or name O01 or name O02 or name O03 or name O04)) or (resid 508 and (name C01 \ or name C02 or name C03 or name C1 or name C15 or name C16 or name C17 or name C \ 18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or n \ ame C5 or name C6 or name O01 or name O02 or name O03 or name O04)) or resid 509 \ )) selection = (chain 'B' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) selection = (chain 'C' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) selection = (chain 'D' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.860 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 : 0.008 0.190 13616 Z= 0.411 Angle : 1.035 14.836 18384 Z= 0.510 Chirality : 0.053 0.261 2140 Planarity : 0.008 0.143 2224 Dihedral : 18.102 143.556 5236 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.17 % Allowed : 26.17 % Favored : 72.66 % 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: 0.00 (0.22), residues: 1576 helix: 0.39 (0.17), residues: 1028 sheet: 0.95 (0.65), residues: 96 loop : -0.90 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 111 TYR 0.012 0.001 TYR B 175 PHE 0.009 0.002 PHE A 302 TRP 0.019 0.002 TRP B 264 HIS 0.004 0.001 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00824 / 0.41 (13616) covalent geometry : angle 1.03471 / 0.51 (18384) hydrogen bonds : bond 0.13050 / 8.58 ( 732) hydrogen bonds : angle 5.43637 / 3.83 ( 2148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 0.493 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 288 average time/residue: 0.1025 time to fit residues: 44.4117 Evaluate side-chains 270 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.217296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.163833 restraints weight = 14344.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 87)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.152565 restraints weight = 18796.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.152621 restraints weight = 16461.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.152656 restraints weight = 14234.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.153311 restraints weight = 12645.721| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13616 Z= 0.134 Angle : 0.650 8.283 18384 Z= 0.308 Chirality : 0.042 0.127 2140 Planarity : 0.005 0.062 2224 Dihedral : 12.441 164.388 2204 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.80 % Allowed : 25.15 % Favored : 71.05 % 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: 0.52 (0.22), residues: 1576 helix: 0.81 (0.17), residues: 996 sheet: 0.64 (0.65), residues: 96 loop : -0.51 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 29 TYR 0.009 0.001 TYR D 175 PHE 0.006 0.001 PHE A 366 TRP 0.011 0.001 TRP D 264 HIS 0.003 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13616) covalent geometry : angle 0.65016 / 0.31 (18384) hydrogen bonds : bond 0.03904 / 2.61 ( 732) hydrogen bonds : angle 4.27873 / 3.03 ( 2148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 0.490 Fit side-chains REVERT: A 366 PHE cc_start: 0.8798 (p90) cc_final: 0.8571 (p90) REVERT: B 366 PHE cc_start: 0.8794 (p90) cc_final: 0.8584 (p90) REVERT: D 366 PHE cc_start: 0.8775 (p90) cc_final: 0.8540 (p90) outliers start: 52 outliers final: 20 residues processed: 288 average time/residue: 0.1010 time to fit residues: 43.5987 Evaluate side-chains 281 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 261 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 348 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 43 optimal weight: 0.0020 chunk 154 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.217052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.171470 restraints weight = 14541.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.163441 restraints weight = 19601.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.160660 restraints weight = 18872.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.160913 restraints weight = 16658.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.160510 restraints weight = 13693.288| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13616 Z= 0.129 Angle : 0.648 9.222 18384 Z= 0.302 Chirality : 0.042 0.125 2140 Planarity : 0.005 0.064 2224 Dihedral : 11.214 145.199 2204 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.68 % Allowed : 24.78 % Favored : 70.54 % 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: 0.55 (0.23), residues: 1576 helix: 0.85 (0.17), residues: 1024 sheet: 0.39 (0.63), residues: 96 loop : -0.56 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.010 0.001 TYR A 175 PHE 0.006 0.001 PHE C 366 TRP 0.013 0.001 TRP A 264 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13616) covalent geometry : angle 0.64773 / 0.30 (18384) hydrogen bonds : bond 0.03648 / 2.44 ( 732) hydrogen bonds : angle 4.06760 / 2.91 ( 2148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 290 time to evaluate : 0.391 Fit side-chains REVERT: A 270 TYR cc_start: 0.3582 (OUTLIER) cc_final: 0.2643 (m-80) REVERT: A 366 PHE cc_start: 0.8762 (p90) cc_final: 0.8504 (p90) REVERT: B 270 TYR cc_start: 0.3654 (OUTLIER) cc_final: 0.2733 (m-80) REVERT: B 366 PHE cc_start: 0.8721 (p90) cc_final: 0.8505 (p90) REVERT: C 270 TYR cc_start: 0.3637 (OUTLIER) cc_final: 0.2718 (m-80) REVERT: D 270 TYR cc_start: 0.3705 (OUTLIER) cc_final: 0.2769 (m-80) REVERT: D 366 PHE cc_start: 0.8748 (p90) cc_final: 0.8505 (p90) outliers start: 64 outliers final: 37 residues processed: 318 average time/residue: 0.0968 time to fit residues: 47.1644 Evaluate side-chains 315 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 PHE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 133 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.215883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.168955 restraints weight = 14440.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.156174 restraints weight = 18823.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154918 restraints weight = 18544.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154937 restraints weight = 16376.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154772 restraints weight = 16287.647| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13616 Z= 0.138 Angle : 0.653 9.766 18384 Z= 0.307 Chirality : 0.041 0.123 2140 Planarity : 0.005 0.065 2224 Dihedral : 10.836 137.190 2204 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.56 % Allowed : 24.78 % Favored : 69.66 % 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: 0.73 (0.23), residues: 1576 helix: 0.98 (0.17), residues: 1020 sheet: 0.30 (0.62), residues: 96 loop : -0.40 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.011 0.001 TYR A 175 PHE 0.006 0.001 PHE A 366 TRP 0.013 0.001 TRP C 264 HIS 0.002 0.001 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13616) covalent geometry : angle 0.65341 / 0.31 (18384) hydrogen bonds : bond 0.03548 / 2.37 ( 732) hydrogen bonds : angle 3.96935 / 2.84 ( 2148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 0.497 Fit side-chains REVERT: A 270 TYR cc_start: 0.3670 (OUTLIER) cc_final: 0.2808 (m-80) REVERT: A 366 PHE cc_start: 0.8831 (p90) cc_final: 0.8578 (p90) REVERT: B 270 TYR cc_start: 0.3684 (OUTLIER) cc_final: 0.2805 (m-80) REVERT: B 366 PHE cc_start: 0.8798 (p90) cc_final: 0.8529 (p90) REVERT: C 91 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7370 (tt) REVERT: C 270 TYR cc_start: 0.3711 (OUTLIER) cc_final: 0.2822 (m-80) REVERT: C 394 LYS cc_start: 0.7661 (ttpp) cc_final: 0.7330 (tttp) REVERT: D 270 TYR cc_start: 0.3664 (OUTLIER) cc_final: 0.2797 (m-80) REVERT: D 366 PHE cc_start: 0.8819 (p90) cc_final: 0.8581 (p90) REVERT: D 394 LYS cc_start: 0.7661 (ttpp) cc_final: 0.7348 (tttp) outliers start: 76 outliers final: 44 residues processed: 332 average time/residue: 0.0938 time to fit residues: 47.6815 Evaluate side-chains 328 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 7 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 46 optimal weight: 0.0000 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.217608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173918 restraints weight = 14587.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.161328 restraints weight = 19216.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.158782 restraints weight = 20923.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.158703 restraints weight = 16916.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.157850 restraints weight = 15210.171| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13616 Z= 0.124 Angle : 0.647 9.809 18384 Z= 0.302 Chirality : 0.041 0.128 2140 Planarity : 0.004 0.065 2224 Dihedral : 10.485 134.918 2204 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.17 % Allowed : 26.68 % Favored : 69.15 % 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 (0.23), residues: 1576 helix: 1.02 (0.17), residues: 1016 sheet: 0.24 (0.63), residues: 96 loop : -0.38 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.008 0.001 TYR A 175 PHE 0.012 0.001 PHE A 26 TRP 0.013 0.001 TRP C 264 HIS 0.002 0.000 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13616) covalent geometry : angle 0.64744 / 0.30 (18384) hydrogen bonds : bond 0.03333 / 2.22 ( 732) hydrogen bonds : angle 3.87059 / 2.77 ( 2148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7411 (tt) REVERT: A 270 TYR cc_start: 0.3945 (OUTLIER) cc_final: 0.2936 (m-80) REVERT: A 366 PHE cc_start: 0.8785 (p90) cc_final: 0.8549 (p90) REVERT: B 91 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7363 (tt) REVERT: B 270 TYR cc_start: 0.3899 (OUTLIER) cc_final: 0.2925 (m-80) REVERT: B 366 PHE cc_start: 0.8779 (p90) cc_final: 0.8496 (p90) REVERT: B 394 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7345 (tttp) REVERT: C 270 TYR cc_start: 0.3891 (OUTLIER) cc_final: 0.2960 (m-80) REVERT: C 394 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7327 (tttp) REVERT: D 91 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7371 (tt) REVERT: D 270 TYR cc_start: 0.3902 (OUTLIER) cc_final: 0.2929 (m-80) REVERT: D 366 PHE cc_start: 0.8785 (p90) cc_final: 0.8556 (p90) outliers start: 57 outliers final: 30 residues processed: 306 average time/residue: 0.1014 time to fit residues: 47.0999 Evaluate side-chains 305 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 131 optimal weight: 0.0070 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.217753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.171092 restraints weight = 14565.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 88)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.157423 restraints weight = 17872.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.156730 restraints weight = 17975.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.156659 restraints weight = 15854.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.156566 restraints weight = 14837.865| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13616 Z= 0.127 Angle : 0.659 10.618 18384 Z= 0.306 Chirality : 0.041 0.153 2140 Planarity : 0.005 0.068 2224 Dihedral : 10.390 134.292 2204 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.39 % Allowed : 27.27 % Favored : 68.35 % 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: 0.76 (0.23), residues: 1576 helix: 1.00 (0.17), residues: 1016 sheet: 0.21 (0.63), residues: 96 loop : -0.35 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.009 0.001 TYR A 175 PHE 0.010 0.001 PHE D 26 TRP 0.013 0.001 TRP C 264 HIS 0.002 0.000 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (13616) covalent geometry : angle 0.65936 / 0.31 (18384) hydrogen bonds : bond 0.03297 / 2.20 ( 732) hydrogen bonds : angle 3.88449 / 2.78 ( 2148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3660 (OUTLIER) cc_final: 0.2927 (m-80) REVERT: A 366 PHE cc_start: 0.8783 (p90) cc_final: 0.8514 (p90) REVERT: B 270 TYR cc_start: 0.3638 (OUTLIER) cc_final: 0.2926 (m-80) REVERT: B 366 PHE cc_start: 0.8817 (p90) cc_final: 0.8500 (p90) REVERT: B 394 LYS cc_start: 0.7588 (ttpp) cc_final: 0.7294 (tttp) REVERT: C 270 TYR cc_start: 0.3707 (OUTLIER) cc_final: 0.3007 (m-80) REVERT: C 366 PHE cc_start: 0.8807 (p90) cc_final: 0.8598 (p90) REVERT: C 394 LYS cc_start: 0.7603 (ttpp) cc_final: 0.7319 (tttp) REVERT: D 270 TYR cc_start: 0.3705 (OUTLIER) cc_final: 0.2973 (m-80) REVERT: D 366 PHE cc_start: 0.8802 (p90) cc_final: 0.8560 (p90) outliers start: 60 outliers final: 35 residues processed: 308 average time/residue: 0.1016 time to fit residues: 47.4293 Evaluate side-chains 307 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 104 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.216083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.167675 restraints weight = 14441.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 92)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154550 restraints weight = 19596.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154546 restraints weight = 17731.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154610 restraints weight = 16095.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.154696 restraints weight = 15252.965| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13616 Z= 0.141 Angle : 0.672 10.102 18384 Z= 0.314 Chirality : 0.042 0.148 2140 Planarity : 0.005 0.070 2224 Dihedral : 10.498 133.997 2204 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.80 % Allowed : 27.63 % Favored : 68.57 % 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: 0.79 (0.23), residues: 1576 helix: 1.03 (0.17), residues: 1012 sheet: 0.22 (0.63), residues: 96 loop : -0.35 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.012 0.001 TYR B 175 PHE 0.010 0.001 PHE B 26 TRP 0.013 0.001 TRP A 264 HIS 0.003 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13616) covalent geometry : angle 0.67230 / 0.31 (18384) hydrogen bonds : bond 0.03428 / 2.29 ( 732) hydrogen bonds : angle 3.92155 / 2.80 ( 2148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 279 time to evaluate : 0.487 Fit side-chains REVERT: A 270 TYR cc_start: 0.3622 (OUTLIER) cc_final: 0.2901 (m-80) REVERT: A 366 PHE cc_start: 0.8821 (p90) cc_final: 0.8551 (p90) REVERT: B 270 TYR cc_start: 0.3633 (OUTLIER) cc_final: 0.2957 (m-80) REVERT: B 366 PHE cc_start: 0.8839 (p90) cc_final: 0.8549 (p90) REVERT: B 394 LYS cc_start: 0.7641 (ttpp) cc_final: 0.7318 (tttp) REVERT: C 270 TYR cc_start: 0.3617 (OUTLIER) cc_final: 0.2947 (m-80) REVERT: C 394 LYS cc_start: 0.7650 (ttpp) cc_final: 0.7312 (tttp) REVERT: D 270 TYR cc_start: 0.3634 (OUTLIER) cc_final: 0.2952 (m-80) REVERT: D 366 PHE cc_start: 0.8820 (p90) cc_final: 0.8575 (p90) REVERT: D 394 LYS cc_start: 0.7625 (ttpp) cc_final: 0.7322 (tttp) outliers start: 52 outliers final: 39 residues processed: 302 average time/residue: 0.0933 time to fit residues: 42.8241 Evaluate side-chains 304 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 54 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 ASN B 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.210688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.165375 restraints weight = 14467.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.152314 restraints weight = 20002.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.151264 restraints weight = 23444.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.151185 restraints weight = 19071.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.150690 restraints weight = 18012.213| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13616 Z= 0.186 Angle : 0.725 9.893 18384 Z= 0.342 Chirality : 0.043 0.140 2140 Planarity : 0.005 0.073 2224 Dihedral : 11.118 134.510 2204 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.46 % Allowed : 27.12 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1576 helix: 0.92 (0.17), residues: 1020 sheet: 0.12 (0.62), residues: 96 loop : -0.45 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 29 TYR 0.016 0.001 TYR C 175 PHE 0.007 0.001 PHE A 366 TRP 0.015 0.002 TRP C 264 HIS 0.005 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (13616) covalent geometry : angle 0.72519 / 0.34 (18384) hydrogen bonds : bond 0.03854 / 2.56 ( 732) hydrogen bonds : angle 4.07513 / 2.90 ( 2148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 252 time to evaluate : 0.479 Fit side-chains REVERT: A 270 TYR cc_start: 0.3791 (OUTLIER) cc_final: 0.3162 (m-80) REVERT: A 366 PHE cc_start: 0.8826 (p90) cc_final: 0.8572 (p90) REVERT: B 270 TYR cc_start: 0.3775 (OUTLIER) cc_final: 0.3184 (m-80) REVERT: B 366 PHE cc_start: 0.8846 (p90) cc_final: 0.8543 (p90) REVERT: C 270 TYR cc_start: 0.3728 (OUTLIER) cc_final: 0.3168 (m-80) REVERT: D 270 TYR cc_start: 0.3774 (OUTLIER) cc_final: 0.3181 (m-80) REVERT: D 366 PHE cc_start: 0.8850 (p90) cc_final: 0.8596 (p90) outliers start: 61 outliers final: 45 residues processed: 280 average time/residue: 0.0929 time to fit residues: 40.2684 Evaluate side-chains 297 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 7 optimal weight: 0.0570 chunk 155 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 342 ASN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.211474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.168345 restraints weight = 14689.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.162704 restraints weight = 19705.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.160420 restraints weight = 19294.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.159913 restraints weight = 17510.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.159117 restraints weight = 15002.828| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13616 Z= 0.138 Angle : 0.703 11.562 18384 Z= 0.326 Chirality : 0.042 0.133 2140 Planarity : 0.005 0.074 2224 Dihedral : 10.651 133.084 2204 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.39 % Allowed : 27.78 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1576 helix: 0.96 (0.17), residues: 1012 sheet: 0.30 (0.63), residues: 96 loop : -0.38 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.009 0.001 TYR C 175 PHE 0.008 0.001 PHE B 26 TRP 0.013 0.001 TRP C 264 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13616) covalent geometry : angle 0.70276 / 0.33 (18384) hydrogen bonds : bond 0.03461 / 2.31 ( 732) hydrogen bonds : angle 3.99943 / 2.84 ( 2148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3629 (OUTLIER) cc_final: 0.3084 (m-80) REVERT: A 366 PHE cc_start: 0.8739 (p90) cc_final: 0.8496 (p90) REVERT: B 270 TYR cc_start: 0.3642 (OUTLIER) cc_final: 0.3104 (m-80) REVERT: B 366 PHE cc_start: 0.8726 (p90) cc_final: 0.8463 (p90) REVERT: B 394 LYS cc_start: 0.7692 (ttpp) cc_final: 0.7373 (tttp) REVERT: C 270 TYR cc_start: 0.3706 (OUTLIER) cc_final: 0.3145 (m-80) REVERT: C 394 LYS cc_start: 0.7700 (ttpp) cc_final: 0.7371 (tttp) REVERT: D 270 TYR cc_start: 0.3642 (OUTLIER) cc_final: 0.3094 (m-80) REVERT: D 366 PHE cc_start: 0.8761 (p90) cc_final: 0.8508 (p90) outliers start: 60 outliers final: 39 residues processed: 305 average time/residue: 0.1069 time to fit residues: 49.3529 Evaluate side-chains 311 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 124 optimal weight: 0.0370 chunk 128 optimal weight: 0.3980 chunk 119 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.214955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.166311 restraints weight = 14613.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158241 restraints weight = 18058.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156325 restraints weight = 14982.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.155741 restraints weight = 13868.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155400 restraints weight = 13499.263| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13616 Z= 0.134 Angle : 0.708 10.441 18384 Z= 0.330 Chirality : 0.042 0.129 2140 Planarity : 0.005 0.075 2224 Dihedral : 10.413 133.303 2204 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.29 % Allowed : 28.51 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1576 helix: 1.02 (0.17), residues: 1012 sheet: 0.36 (0.62), residues: 96 loop : -0.35 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 391 TYR 0.009 0.001 TYR C 175 PHE 0.007 0.001 PHE A 366 TRP 0.012 0.001 TRP C 264 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (13616) covalent geometry : angle 0.70843 / 0.33 (18384) hydrogen bonds : bond 0.03435 / 2.28 ( 732) hydrogen bonds : angle 3.99828 / 2.84 ( 2148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 0.508 Fit side-chains REVERT: A 270 TYR cc_start: 0.3631 (OUTLIER) cc_final: 0.2967 (m-80) REVERT: A 366 PHE cc_start: 0.8760 (p90) cc_final: 0.8533 (p90) REVERT: B 270 TYR cc_start: 0.3629 (OUTLIER) cc_final: 0.2978 (m-80) REVERT: B 366 PHE cc_start: 0.8737 (p90) cc_final: 0.8511 (p90) REVERT: B 394 LYS cc_start: 0.7610 (ttpp) cc_final: 0.7374 (tttp) REVERT: C 270 TYR cc_start: 0.3622 (OUTLIER) cc_final: 0.3018 (m-80) REVERT: C 394 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7329 (tttp) REVERT: D 270 TYR cc_start: 0.3635 (OUTLIER) cc_final: 0.2982 (m-80) REVERT: D 366 PHE cc_start: 0.8752 (p90) cc_final: 0.8541 (p90) REVERT: D 394 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7316 (tttp) outliers start: 45 outliers final: 31 residues processed: 292 average time/residue: 0.1085 time to fit residues: 47.9615 Evaluate side-chains 299 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 152 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.208064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.163994 restraints weight = 14637.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 101)---------------| | r_work = 0.3660 r_free = 0.3660 target = 0.152026 restraints weight = 19641.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.151667 restraints weight = 21513.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.151484 restraints weight = 18776.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.151304 restraints weight = 18070.008| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13616 Z= 0.182 Angle : 0.736 10.237 18384 Z= 0.347 Chirality : 0.044 0.130 2140 Planarity : 0.005 0.078 2224 Dihedral : 10.937 133.948 2204 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.07 % Allowed : 29.31 % Favored : 67.62 % 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: 0.67 (0.22), residues: 1576 helix: 0.93 (0.17), residues: 1020 sheet: 0.38 (0.62), residues: 96 loop : -0.45 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 29 TYR 0.015 0.001 TYR B 175 PHE 0.008 0.001 PHE A 366 TRP 0.013 0.002 TRP B 264 HIS 0.004 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (13616) covalent geometry : angle 0.73620 / 0.35 (18384) hydrogen bonds : bond 0.03761 / 2.50 ( 732) hydrogen bonds : angle 4.09802 / 2.90 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.29 seconds wall clock time: 42 minutes 21.49 seconds (2541.49 seconds total)