Starting phenix.real_space_refine on Thu Mar 5 02:43:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtj_24682/03_2026/7rtj_24682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtj_24682/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rtj_24682/03_2026/7rtj_24682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtj_24682/03_2026/7rtj_24682.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtj_24682/03_2026/7rtj_24682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtj_24682/03_2026/7rtj_24682.cif" } 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-5986/lib/python3.9/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: 266 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: 266 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: 3.73, per 1000 atoms: 0.28 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: 1.35 Conformation dependent library (CDL) restraints added in 457.5 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: 0.41 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: 1.97 Time building geometry restraints manager: 1.68 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 - 31.75: 7824 31.75 - 63.50: 472 63.50 - 95.26: 20 95.26 - 127.01: 16 127.01 - 158.76: 12 Dihedral angle restraints: 8344 sinusoidal: 3664 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 8341 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.830 Find NCS groups from input model: 0.300 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 20.090 158.761 5320 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 covalent geometry : bond 0.00824 (13616) covalent geometry : angle 1.03471 (18384) hydrogen bonds : bond 0.13050 ( 732) hydrogen bonds : angle 5.43637 ( 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 : 0.359 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 288 average time/residue: 0.1091 time to fit residues: 47.0828 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 : 0.479 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.217033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.169011 restraints weight = 14325.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.159590 restraints weight = 18468.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.158322 restraints weight = 15335.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.157850 restraints weight = 14592.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157640 restraints weight = 13455.465| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.0857 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= 0.135 Angle : 0.652 8.308 18384 Z= 0.309 Chirality : 0.042 0.128 2140 Planarity : 0.005 0.064 2224 Dihedral : 17.293 163.479 2288 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.95 % Allowed : 25.37 % Favored : 70.69 % 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: 0.49 (0.23), residues: 1576 helix: 0.77 (0.17), residues: 1020 sheet: 0.64 (0.65), residues: 96 loop : -0.57 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 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 0.002 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00297 (13616) covalent geometry : angle 0.65209 (18384) hydrogen bonds : bond 0.03871 ( 732) hydrogen bonds : angle 4.24584 ( 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 337 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 0.450 Fit side-chains REVERT: A 366 PHE cc_start: 0.8694 (p90) cc_final: 0.8492 (p90) REVERT: C 366 PHE cc_start: 0.8694 (p90) cc_final: 0.8489 (p90) REVERT: D 366 PHE cc_start: 0.8646 (p90) cc_final: 0.8435 (p90) outliers start: 54 outliers final: 22 residues processed: 297 average time/residue: 0.1052 time to fit residues: 46.8038 Evaluate side-chains 282 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 B residue 381 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 Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 43 optimal weight: 0.0570 chunk 154 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.217942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.166545 restraints weight = 14574.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.155033 restraints weight = 18234.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153917 restraints weight = 17811.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154197 restraints weight = 14296.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154545 restraints weight = 12377.958| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13616 Z= 0.127 Angle : 0.647 9.451 18384 Z= 0.302 Chirality : 0.041 0.126 2140 Planarity : 0.005 0.063 2224 Dihedral : 15.905 143.706 2288 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.46 % Allowed : 25.22 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1576 helix: 0.88 (0.17), residues: 1016 sheet: 0.35 (0.62), residues: 96 loop : -0.57 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.010 0.001 TYR A 175 PHE 0.008 0.001 PHE C 26 TRP 0.013 0.001 TRP C 264 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00283 (13616) covalent geometry : angle 0.64686 (18384) hydrogen bonds : bond 0.03604 ( 732) hydrogen bonds : angle 4.04086 ( 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: 61 poor density : 293 time to evaluate : 0.474 Fit side-chains REVERT: A 270 TYR cc_start: 0.3512 (OUTLIER) cc_final: 0.2555 (m-80) REVERT: A 366 PHE cc_start: 0.8803 (p90) cc_final: 0.8536 (p90) REVERT: B 270 TYR cc_start: 0.3599 (OUTLIER) cc_final: 0.2689 (m-80) REVERT: C 270 TYR cc_start: 0.3583 (OUTLIER) cc_final: 0.2678 (m-80) REVERT: C 366 PHE cc_start: 0.8786 (p90) cc_final: 0.8538 (p90) REVERT: D 270 TYR cc_start: 0.3645 (OUTLIER) cc_final: 0.2725 (m-80) REVERT: D 366 PHE cc_start: 0.8798 (p90) cc_final: 0.8543 (p90) outliers start: 61 outliers final: 29 residues processed: 325 average time/residue: 0.1036 time to fit residues: 51.2071 Evaluate side-chains 305 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 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 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 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: 10.0000 chunk 131 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.214637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.161465 restraints weight = 14462.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.149985 restraints weight = 20095.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.150033 restraints weight = 17006.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.150112 restraints weight = 14467.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.150164 restraints weight = 13904.983| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13616 Z= 0.155 Angle : 0.664 9.531 18384 Z= 0.313 Chirality : 0.042 0.120 2140 Planarity : 0.005 0.066 2224 Dihedral : 15.185 137.427 2288 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.19 % Allowed : 25.15 % 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: 0.68 (0.23), residues: 1576 helix: 0.95 (0.17), residues: 1020 sheet: 0.22 (0.62), residues: 96 loop : -0.45 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 417 TYR 0.014 0.001 TYR D 175 PHE 0.009 0.001 PHE C 26 TRP 0.013 0.001 TRP A 264 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00367 (13616) covalent geometry : angle 0.66363 (18384) hydrogen bonds : bond 0.03666 ( 732) hydrogen bonds : angle 4.00675 ( 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 359 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 288 time to evaluate : 0.467 Fit side-chains REVERT: A 270 TYR cc_start: 0.3770 (OUTLIER) cc_final: 0.3092 (m-80) REVERT: A 366 PHE cc_start: 0.8872 (p90) cc_final: 0.8593 (p90) REVERT: B 270 TYR cc_start: 0.3802 (OUTLIER) cc_final: 0.2832 (m-80) REVERT: B 394 LYS cc_start: 0.7818 (ttpp) cc_final: 0.7416 (tttp) REVERT: C 270 TYR cc_start: 0.3696 (OUTLIER) cc_final: 0.2748 (m-80) REVERT: C 366 PHE cc_start: 0.8829 (p90) cc_final: 0.8594 (p90) REVERT: C 394 LYS cc_start: 0.7822 (ttpp) cc_final: 0.7421 (tttp) REVERT: D 270 TYR cc_start: 0.3785 (OUTLIER) cc_final: 0.2831 (m-80) REVERT: D 366 PHE cc_start: 0.8861 (p90) cc_final: 0.8621 (p90) REVERT: D 394 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7323 (tttp) outliers start: 71 outliers final: 48 residues processed: 323 average time/residue: 0.0923 time to fit residues: 45.1285 Evaluate side-chains 323 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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: 0.0770 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.218130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162749 restraints weight = 14665.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.152854 restraints weight = 18508.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152406 restraints weight = 15158.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152479 restraints weight = 13460.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152715 restraints weight = 11655.840| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1585 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= 0.121 Angle : 0.645 9.839 18384 Z= 0.301 Chirality : 0.041 0.129 2140 Planarity : 0.005 0.064 2224 Dihedral : 13.653 134.354 2288 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.80 % Allowed : 26.97 % Favored : 69.23 % 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: 0.83 (0.23), residues: 1576 helix: 1.08 (0.17), residues: 1016 sheet: 0.26 (0.63), residues: 96 loop : -0.38 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.007 0.001 TYR A 175 PHE 0.012 0.001 PHE A 26 TRP 0.013 0.001 TRP C 264 HIS 0.001 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00262 (13616) covalent geometry : angle 0.64483 (18384) hydrogen bonds : bond 0.03281 ( 732) hydrogen bonds : angle 3.85410 ( 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 339 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 287 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3706 (OUTLIER) cc_final: 0.2931 (m-80) REVERT: A 366 PHE cc_start: 0.8853 (p90) cc_final: 0.8572 (p90) REVERT: B 270 TYR cc_start: 0.3708 (OUTLIER) cc_final: 0.2755 (m-80) REVERT: B 394 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7333 (tttp) REVERT: C 270 TYR cc_start: 0.3709 (OUTLIER) cc_final: 0.2760 (m-80) REVERT: C 366 PHE cc_start: 0.8822 (p90) cc_final: 0.8551 (p90) REVERT: D 270 TYR cc_start: 0.3676 (OUTLIER) cc_final: 0.2934 (m-80) REVERT: D 366 PHE cc_start: 0.8844 (p90) cc_final: 0.8567 (p90) outliers start: 52 outliers final: 29 residues processed: 309 average time/residue: 0.0979 time to fit residues: 46.1378 Evaluate side-chains 305 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 94 LEU 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 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 94 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.216088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.163212 restraints weight = 14624.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 123)---------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150656 restraints weight = 19055.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.149117 restraints weight = 17219.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.149161 restraints weight = 11783.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.149142 restraints weight = 9826.948| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13616 Z= 0.138 Angle : 0.672 10.548 18384 Z= 0.311 Chirality : 0.042 0.148 2140 Planarity : 0.005 0.067 2224 Dihedral : 13.223 134.416 2288 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.68 % Allowed : 26.46 % Favored : 68.86 % 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: 0.74 (0.23), residues: 1576 helix: 1.01 (0.17), residues: 1016 sheet: 0.18 (0.63), residues: 96 loop : -0.43 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 417 TYR 0.011 0.001 TYR C 175 PHE 0.008 0.001 PHE B 26 TRP 0.013 0.001 TRP A 264 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00321 (13616) covalent geometry : angle 0.67209 (18384) hydrogen bonds : bond 0.03409 ( 732) hydrogen bonds : angle 3.91268 ( 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 338 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 274 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3631 (OUTLIER) cc_final: 0.2911 (m-80) REVERT: A 366 PHE cc_start: 0.8912 (p90) cc_final: 0.8633 (p90) REVERT: B 270 TYR cc_start: 0.3617 (OUTLIER) cc_final: 0.2903 (m-80) REVERT: B 366 PHE cc_start: 0.8969 (p90) cc_final: 0.8750 (p90) REVERT: B 394 LYS cc_start: 0.7586 (ttpp) cc_final: 0.7316 (tttp) REVERT: C 270 TYR cc_start: 0.3606 (OUTLIER) cc_final: 0.2900 (m-80) REVERT: C 366 PHE cc_start: 0.8889 (p90) cc_final: 0.8612 (p90) REVERT: C 394 LYS cc_start: 0.7612 (ttpp) cc_final: 0.7245 (tttp) REVERT: D 270 TYR cc_start: 0.3620 (OUTLIER) cc_final: 0.2909 (m-80) REVERT: D 366 PHE cc_start: 0.8920 (p90) cc_final: 0.8638 (p90) outliers start: 64 outliers final: 38 residues processed: 308 average time/residue: 0.0959 time to fit residues: 44.9306 Evaluate side-chains 313 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 308 GLU 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 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 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 LEU 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 46 LEU Chi-restraints excluded: chain D residue 54 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 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=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: 0.7980 chunk 154 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 152 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.216580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.164705 restraints weight = 14520.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152625 restraints weight = 19643.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.152302 restraints weight = 17428.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.152424 restraints weight = 14849.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.152476 restraints weight = 14360.931| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13616 Z= 0.130 Angle : 0.671 9.950 18384 Z= 0.310 Chirality : 0.041 0.145 2140 Planarity : 0.005 0.069 2224 Dihedral : 12.984 133.389 2288 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.95 % Allowed : 27.41 % Favored : 68.64 % 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: 0.80 (0.23), residues: 1576 helix: 1.06 (0.17), residues: 1012 sheet: 0.17 (0.63), residues: 96 loop : -0.38 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 417 TYR 0.009 0.001 TYR D 175 PHE 0.011 0.001 PHE C 26 TRP 0.014 0.001 TRP A 264 HIS 0.002 0.001 HIS D 149 Details of bonding type rmsd covalent geometry : bond 0.00301 (13616) covalent geometry : angle 0.67113 (18384) hydrogen bonds : bond 0.03340 ( 732) hydrogen bonds : angle 3.89337 ( 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 332 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3566 (OUTLIER) cc_final: 0.2861 (m-80) REVERT: A 366 PHE cc_start: 0.8857 (p90) cc_final: 0.8567 (p90) REVERT: B 270 TYR cc_start: 0.3590 (OUTLIER) cc_final: 0.2929 (m-80) REVERT: B 366 PHE cc_start: 0.8869 (p90) cc_final: 0.8631 (p90) REVERT: B 394 LYS cc_start: 0.7634 (ttpp) cc_final: 0.7324 (tttp) REVERT: C 270 TYR cc_start: 0.3618 (OUTLIER) cc_final: 0.2950 (m-80) REVERT: C 366 PHE cc_start: 0.8831 (p90) cc_final: 0.8555 (p90) REVERT: D 270 TYR cc_start: 0.3603 (OUTLIER) cc_final: 0.2934 (m-80) REVERT: D 366 PHE cc_start: 0.8871 (p90) cc_final: 0.8606 (p90) outliers start: 54 outliers final: 37 residues processed: 301 average time/residue: 0.0976 time to fit residues: 44.3740 Evaluate side-chains 307 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 54 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 121 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4280 r_free = 0.4280 target = 0.216386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.168375 restraints weight = 14461.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.157363 restraints weight = 18117.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.156557 restraints weight = 17526.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156342 restraints weight = 15594.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156388 restraints weight = 14370.792| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1754 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= 0.137 Angle : 0.680 9.999 18384 Z= 0.316 Chirality : 0.042 0.151 2140 Planarity : 0.005 0.073 2224 Dihedral : 12.734 133.531 2288 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.31 % Allowed : 26.75 % Favored : 68.93 % 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: 0.83 (0.23), residues: 1576 helix: 1.09 (0.17), residues: 1012 sheet: 0.17 (0.63), residues: 96 loop : -0.40 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 417 TYR 0.011 0.001 TYR D 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 covalent geometry : bond 0.00318 (13616) covalent geometry : angle 0.67977 (18384) hydrogen bonds : bond 0.03428 ( 732) hydrogen bonds : angle 3.91953 ( 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 326 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 267 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3690 (OUTLIER) cc_final: 0.3038 (m-80) REVERT: A 366 PHE cc_start: 0.8810 (p90) cc_final: 0.8565 (p90) REVERT: B 270 TYR cc_start: 0.3649 (OUTLIER) cc_final: 0.3076 (m-80) REVERT: B 366 PHE cc_start: 0.8829 (p90) cc_final: 0.8599 (p90) REVERT: B 394 LYS cc_start: 0.7614 (ttpp) cc_final: 0.7324 (tttp) REVERT: C 270 TYR cc_start: 0.3638 (OUTLIER) cc_final: 0.3064 (m-80) REVERT: C 366 PHE cc_start: 0.8791 (p90) cc_final: 0.8542 (p90) REVERT: D 270 TYR cc_start: 0.3650 (OUTLIER) cc_final: 0.3069 (m-80) REVERT: D 366 PHE cc_start: 0.8821 (p90) cc_final: 0.8567 (p90) outliers start: 59 outliers final: 40 residues processed: 291 average time/residue: 0.0965 time to fit residues: 42.0934 Evaluate side-chains 309 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 308 GLU 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 203 ILE 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 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 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 104 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.216310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.171292 restraints weight = 14686.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 86)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158185 restraints weight = 18914.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157843 restraints weight = 19352.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157856 restraints weight = 16662.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.157805 restraints weight = 17693.910| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13616 Z= 0.131 Angle : 0.687 11.304 18384 Z= 0.317 Chirality : 0.042 0.140 2140 Planarity : 0.005 0.075 2224 Dihedral : 12.399 133.145 2288 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.65 % Allowed : 27.49 % Favored : 68.86 % 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: 0.85 (0.23), residues: 1576 helix: 1.10 (0.17), residues: 1012 sheet: 0.18 (0.63), residues: 96 loop : -0.37 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 417 TYR 0.009 0.001 TYR B 175 PHE 0.008 0.001 PHE B 26 TRP 0.012 0.001 TRP A 264 HIS 0.002 0.000 HIS D 149 Details of bonding type rmsd covalent geometry : bond 0.00299 (13616) covalent geometry : angle 0.68701 (18384) hydrogen bonds : bond 0.03340 ( 732) hydrogen bonds : angle 3.91491 ( 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 323 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3685 (OUTLIER) cc_final: 0.3100 (m-80) REVERT: A 366 PHE cc_start: 0.8732 (p90) cc_final: 0.8480 (p90) REVERT: B 270 TYR cc_start: 0.3738 (OUTLIER) cc_final: 0.3155 (m-80) REVERT: B 366 PHE cc_start: 0.8762 (p90) cc_final: 0.8539 (p90) REVERT: C 34 LEU cc_start: 0.8991 (mm) cc_final: 0.8784 (mt) REVERT: C 270 TYR cc_start: 0.3674 (OUTLIER) cc_final: 0.3145 (m-80) REVERT: C 364 GLN cc_start: 0.8617 (pm20) cc_final: 0.8357 (pm20) REVERT: C 366 PHE cc_start: 0.8722 (p90) cc_final: 0.8476 (p90) REVERT: D 270 TYR cc_start: 0.3687 (OUTLIER) cc_final: 0.3110 (m-80) REVERT: D 334 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.5706 (ptp) REVERT: D 366 PHE cc_start: 0.8785 (p90) cc_final: 0.8494 (p90) outliers start: 50 outliers final: 34 residues processed: 293 average time/residue: 0.0971 time to fit residues: 43.0929 Evaluate side-chains 304 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 243 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 46 LEU Chi-restraints excluded: chain B residue 54 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 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 46 LEU Chi-restraints excluded: chain D residue 54 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 334 MET 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: 1.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 119 optimal weight: 0.0970 chunk 76 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.215140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.169868 restraints weight = 14570.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 90)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.156233 restraints weight = 18632.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156032 restraints weight = 19254.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156038 restraints weight = 16688.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.155989 restraints weight = 16816.055| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13616 Z= 0.138 Angle : 0.698 10.334 18384 Z= 0.323 Chirality : 0.042 0.144 2140 Planarity : 0.005 0.077 2224 Dihedral : 12.342 133.457 2288 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.02 % Allowed : 27.41 % 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: 0.84 (0.23), residues: 1576 helix: 1.10 (0.17), residues: 1012 sheet: 0.18 (0.63), residues: 96 loop : -0.39 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 417 TYR 0.011 0.001 TYR C 175 PHE 0.006 0.001 PHE A 366 TRP 0.012 0.001 TRP D 264 HIS 0.002 0.001 HIS D 149 Details of bonding type rmsd covalent geometry : bond 0.00322 (13616) covalent geometry : angle 0.69809 (18384) hydrogen bonds : bond 0.03433 ( 732) hydrogen bonds : angle 3.92877 ( 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 316 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3636 (OUTLIER) cc_final: 0.2959 (m-80) REVERT: B 270 TYR cc_start: 0.3612 (OUTLIER) cc_final: 0.2947 (m-80) REVERT: C 270 TYR cc_start: 0.3607 (OUTLIER) cc_final: 0.2989 (m-80) REVERT: C 364 GLN cc_start: 0.8635 (pm20) cc_final: 0.8339 (pm20) REVERT: C 366 PHE cc_start: 0.8750 (p90) cc_final: 0.8547 (p90) REVERT: D 270 TYR cc_start: 0.3635 (OUTLIER) cc_final: 0.2963 (m-80) REVERT: D 366 PHE cc_start: 0.8818 (p90) cc_final: 0.8571 (p90) outliers start: 55 outliers final: 37 residues processed: 287 average time/residue: 0.0986 time to fit residues: 43.1119 Evaluate side-chains 299 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 243 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 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 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 334 MET 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: 4.9990 chunk 29 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.214537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162774 restraints weight = 14599.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.151764 restraints weight = 18060.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150728 restraints weight = 17487.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150734 restraints weight = 15111.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150813 restraints weight = 13792.155| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13616 Z= 0.153 Angle : 0.714 10.316 18384 Z= 0.333 Chirality : 0.043 0.144 2140 Planarity : 0.005 0.076 2224 Dihedral : 12.495 133.673 2288 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.65 % Allowed : 27.92 % 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: 0.75 (0.23), residues: 1576 helix: 1.01 (0.17), residues: 1012 sheet: 0.18 (0.63), residues: 96 loop : -0.40 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 417 TYR 0.012 0.001 TYR C 175 PHE 0.009 0.001 PHE B 366 TRP 0.013 0.001 TRP C 264 HIS 0.003 0.001 HIS D 149 Details of bonding type rmsd covalent geometry : bond 0.00366 (13616) covalent geometry : angle 0.71372 (18384) hydrogen bonds : bond 0.03564 ( 732) hydrogen bonds : angle 4.00303 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2447.15 seconds wall clock time: 43 minutes 2.82 seconds (2582.82 seconds total)