Starting phenix.real_space_refine on Sat Sep 12 21:22:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rtj_24682/09_2026/7rtj_24682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtj_24682/09_2026/7rtj_24682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rtj_24682/09_2026/7rtj_24682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtj_24682/09_2026/7rtj_24682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rtj_24682/09_2026/7rtj_24682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtj_24682/09_2026/7rtj_24682.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rtj_24682/09_2026/7rtj_24682.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rtj_24682/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13352 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNAv2': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNAv2': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-3': 6, 'PGW:plan-1': 5, 'PGW:plan-2': 5} Unresolved non-hydrogen planarities: 57 Restraints were copied for chains: C, D Time building chain proxies: 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: 1.15 Conformation dependent library (CDL) restraints added in 579.5 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: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 12 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.824A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 4.146A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 222 removed outlier: 3.710A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.701A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 299 removed outlier: 6.158A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.557A pdb=" N LYS A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 306 through 314 removed outlier: 3.632A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.601A pdb=" N ALA A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.825A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.146A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 222 removed outlier: 3.711A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 removed outlier: 3.702A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 299 removed outlier: 6.159A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 removed outlier: 3.557A pdb=" N LYS B 303 " --> pdb=" O PRO B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 306 through 314 removed outlier: 3.632A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.601A pdb=" N ALA B 408 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 56 Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.825A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 removed outlier: 4.147A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 222 removed outlier: 3.710A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 removed outlier: 3.702A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 removed outlier: 6.159A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 303 removed outlier: 3.557A pdb=" N LYS C 303 " --> pdb=" O PRO C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 306 through 314 removed outlier: 3.632A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'C' and resid 404 through 420 removed outlier: 3.602A pdb=" N ALA C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 56 Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.825A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 removed outlier: 4.146A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 222 removed outlier: 3.710A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 removed outlier: 3.701A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 299 removed outlier: 6.158A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 removed outlier: 3.556A pdb=" N LYS D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 306 through 314 removed outlier: 3.631A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 404 through 420 removed outlier: 3.601A pdb=" N ALA D 408 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR A 322 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 387 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 390 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 340 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 392 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 338 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 339 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 348 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR B 322 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 387 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 390 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 340 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 392 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 338 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 339 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 348 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR C 322 " --> pdb=" O CYS C 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C 387 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 390 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 340 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 392 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 338 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C 339 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 348 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR D 322 " --> pdb=" O CYS D 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS D 387 " --> pdb=" O TYR D 322 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 390 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 340 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 392 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 338 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR D 339 " --> pdb=" O PHE D 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 348 " --> pdb=" O ALA D 358 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.53 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: 18002 2.97 - 5.93: 274 5.93 - 8.90: 64 8.90 - 11.87: 28 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 - 22.53: 7318 22.53 - 45.07: 790 45.07 - 67.60: 136 67.60 - 90.14: 4 90.14 - 112.67: 12 Dihedral angle restraints: 8260 sinusoidal: 3580 harmonic: 4680 Sorted by residual: dihedral pdb=" C5' CMP D 503 " pdb=" O5' CMP D 503 " pdb=" P CMP D 503 " pdb=" O1P CMP D 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.67 -112.67 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' CMP B 503 " pdb=" O5' CMP B 503 " pdb=" P CMP B 503 " pdb=" O1P CMP B 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.64 -112.64 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" C5' CMP C 503 " pdb=" O5' CMP C 503 " pdb=" P CMP C 503 " pdb=" O1P CMP C 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.62 -112.62 1 2.00e+01 2.50e-03 3.32e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1556 0.052 - 0.104: 447 0.104 - 0.157: 113 0.157 - 0.209: 12 0.209 - 0.261: 12 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CA PRO C 405 " pdb=" N PRO C 405 " pdb=" C PRO C 405 " pdb=" CB PRO C 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO D 405 " pdb=" N PRO D 405 " pdb=" C PRO D 405 " pdb=" CB PRO D 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO B 405 " pdb=" N PRO B 405 " pdb=" C PRO B 405 " pdb=" CB PRO B 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2137 not shown) Planarity restraints: 2224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 504 " 0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW D 504 " -0.148 2.00e-02 2.50e+03 pdb=" C8 PGW D 504 " 0.142 2.00e-02 2.50e+03 pdb=" C9 PGW D 504 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 504 " -0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW B 504 " 0.148 2.00e-02 2.50e+03 pdb=" C8 PGW B 504 " -0.142 2.00e-02 2.50e+03 pdb=" C9 PGW B 504 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 502 " -0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW A 502 " 0.148 2.00e-02 2.50e+03 pdb=" C8 PGW A 502 " -0.142 2.00e-02 2.50e+03 pdb=" C9 PGW A 502 " 0.137 2.00e-02 2.50e+03 ... (remaining 2221 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2059 2.76 - 3.29: 12876 3.29 - 3.83: 21815 3.83 - 4.36: 23707 4.36 - 4.90: 42020 Nonbonded interactions: 102477 Sorted by model distance: nonbonded pdb=" O ARG D 417 " pdb=" NH1 ARG D 417 " model vdw 2.224 3.120 nonbonded pdb=" O ARG A 417 " pdb=" NH1 ARG A 417 " model vdw 2.224 3.120 nonbonded pdb=" O ARG C 417 " pdb=" NH1 ARG C 417 " model vdw 2.224 3.120 nonbonded pdb=" O ARG B 417 " pdb=" NH1 ARG B 417 " model vdw 2.225 3.120 nonbonded pdb=" O ILE C 178 " pdb=" OG1 THR C 182 " model vdw 2.253 3.040 ... (remaining 102472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or (resid 506 and (name C01 or name C02 or name C03 or name \ C1 or name C19 or name C2 or name C20 or name C3 or name C4 or name C5 or name C \ 6 or name O01 or name O02 or name O03 or name O04)) or (resid 508 and (name C01 \ or name C02 or name C03 or name C1 or name C15 or name C16 or name C17 or name C \ 18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or n \ ame C5 or name C6 or name O01 or name O02 or name O03 or name O04)) or resid 509 \ )) selection = (chain 'B' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) selection = (chain 'C' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) selection = (chain 'D' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.650 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.190 13616 Z= 0.409 Angle : 1.064 14.836 18384 Z= 0.507 Chirality : 0.053 0.261 2140 Planarity : 0.008 0.143 2224 Dihedral : 17.903 112.672 5236 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.17 % Allowed : 26.17 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.22), residues: 1576 helix: 0.39 (0.17), residues: 1028 sheet: 0.95 (0.65), residues: 96 loop : -0.90 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 111 TYR 0.012 0.001 TYR B 175 PHE 0.009 0.002 PHE A 302 TRP 0.019 0.002 TRP B 264 HIS 0.004 0.001 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00824 / 0.41 (13616) covalent geometry : angle 1.06398 / 0.51 (18384) hydrogen bonds : bond 0.13050 / 8.58 ( 732) hydrogen bonds : angle 5.43637 / 3.83 ( 2148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 0.473 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 288 average time/residue: 0.1059 time to fit residues: 46.0415 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 : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.216957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.161331 restraints weight = 14357.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.149419 restraints weight = 18219.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.148419 restraints weight = 15817.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.148173 restraints weight = 11486.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.148721 restraints weight = 9461.699| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13616 Z= 0.132 Angle : 0.688 8.812 18384 Z= 0.313 Chirality : 0.042 0.127 2140 Planarity : 0.005 0.064 2224 Dihedral : 9.500 57.513 2204 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.39 % Allowed : 24.78 % Favored : 70.83 % 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: 0.48 (0.23), residues: 1576 helix: 0.77 (0.17), residues: 1012 sheet: 0.65 (0.65), residues: 96 loop : -0.55 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 377 TYR 0.009 0.001 TYR D 175 PHE 0.008 0.001 PHE A 366 TRP 0.011 0.001 TRP D 264 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13616) covalent geometry : angle 0.68801 / 0.31 (18384) hydrogen bonds : bond 0.03777 / 2.52 ( 732) hydrogen bonds : angle 4.22610 / 3.00 ( 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 347 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 287 time to evaluate : 0.474 Fit side-chains REVERT: A 318 GLU cc_start: 0.7512 (pt0) cc_final: 0.7290 (pt0) REVERT: A 366 PHE cc_start: 0.8870 (p90) cc_final: 0.8641 (p90) REVERT: B 318 GLU cc_start: 0.7460 (pt0) cc_final: 0.7228 (pt0) REVERT: B 366 PHE cc_start: 0.8855 (p90) cc_final: 0.8619 (p90) REVERT: C 318 GLU cc_start: 0.7453 (pt0) cc_final: 0.7232 (pt0) REVERT: C 366 PHE cc_start: 0.8850 (p90) cc_final: 0.8625 (p90) REVERT: D 318 GLU cc_start: 0.7489 (pt0) cc_final: 0.7257 (pt0) REVERT: D 366 PHE cc_start: 0.8834 (p90) cc_final: 0.8605 (p90) outliers start: 60 outliers final: 28 residues processed: 307 average time/residue: 0.1022 time to fit residues: 47.5091 Evaluate side-chains 286 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 257 ILE 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 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 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 94 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 C residue 381 VAL Chi-restraints excluded: chain D residue 24 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 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: 0.7980 chunk 120 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 154 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.214883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159074 restraints weight = 14931.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.146300 restraints weight = 20114.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.146809 restraints weight = 16589.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.147117 restraints weight = 13796.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.147665 restraints weight = 11741.384| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13616 Z= 0.125 Angle : 0.672 9.389 18384 Z= 0.303 Chirality : 0.042 0.131 2140 Planarity : 0.005 0.065 2224 Dihedral : 9.036 57.468 2204 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.46 % Allowed : 24.85 % 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: 0.54 (0.23), residues: 1576 helix: 0.86 (0.17), residues: 1024 sheet: 0.20 (0.64), residues: 96 loop : -0.57 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.010 0.001 TYR D 175 PHE 0.009 0.001 PHE B 26 TRP 0.012 0.001 TRP C 264 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (13616) covalent geometry : angle 0.67247 / 0.30 (18384) hydrogen bonds : bond 0.03611 / 2.41 ( 732) hydrogen bonds : angle 4.05400 / 2.90 ( 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 348 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 287 time to evaluate : 0.495 Fit side-chains REVERT: A 270 TYR cc_start: 0.3434 (OUTLIER) cc_final: 0.2487 (m-80) REVERT: A 366 PHE cc_start: 0.8855 (p90) cc_final: 0.8610 (p90) REVERT: B 270 TYR cc_start: 0.3516 (OUTLIER) cc_final: 0.2615 (m-80) REVERT: B 366 PHE cc_start: 0.8843 (p90) cc_final: 0.8613 (p90) REVERT: C 270 TYR cc_start: 0.3506 (OUTLIER) cc_final: 0.2617 (m-80) REVERT: C 366 PHE cc_start: 0.8847 (p90) cc_final: 0.8631 (p90) REVERT: D 270 TYR cc_start: 0.3575 (OUTLIER) cc_final: 0.2656 (m-80) REVERT: D 366 PHE cc_start: 0.8841 (p90) cc_final: 0.8605 (p90) outliers start: 61 outliers final: 22 residues processed: 315 average time/residue: 0.1067 time to fit residues: 50.9623 Evaluate side-chains 292 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 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 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 54 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 85 optimal weight: 0.0570 chunk 146 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.215932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.168761 restraints weight = 14448.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155378 restraints weight = 17938.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154996 restraints weight = 16496.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.155032 restraints weight = 13650.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.154492 restraints weight = 14137.720| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13616 Z= 0.142 Angle : 0.681 9.605 18384 Z= 0.308 Chirality : 0.042 0.143 2140 Planarity : 0.005 0.066 2224 Dihedral : 9.055 59.076 2204 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.97 % Allowed : 25.66 % Favored : 69.37 % 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: 0.64 (0.23), residues: 1576 helix: 0.93 (0.17), residues: 1024 sheet: 0.17 (0.62), residues: 96 loop : -0.47 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 377 TYR 0.012 0.001 TYR D 175 PHE 0.010 0.001 PHE C 26 TRP 0.013 0.001 TRP D 264 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (13616) covalent geometry : angle 0.68105 / 0.31 (18384) hydrogen bonds : bond 0.03572 / 2.38 ( 732) hydrogen bonds : angle 3.97495 / 2.84 ( 2148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 288 time to evaluate : 0.466 Fit side-chains REVERT: A 91 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7352 (tt) REVERT: A 270 TYR cc_start: 0.3660 (OUTLIER) cc_final: 0.2793 (m-80) REVERT: A 366 PHE cc_start: 0.8839 (p90) cc_final: 0.8594 (p90) REVERT: B 91 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7369 (tt) REVERT: B 270 TYR cc_start: 0.3663 (OUTLIER) cc_final: 0.2753 (m-80) REVERT: B 366 PHE cc_start: 0.8782 (p90) cc_final: 0.8565 (p90) REVERT: B 394 LYS cc_start: 0.7814 (ttpp) cc_final: 0.7401 (tttp) REVERT: C 91 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7363 (tt) REVERT: C 270 TYR cc_start: 0.3703 (OUTLIER) cc_final: 0.2780 (m-80) REVERT: C 394 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7265 (tttp) REVERT: D 91 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7338 (tt) REVERT: D 270 TYR cc_start: 0.3610 (OUTLIER) cc_final: 0.2739 (m-80) REVERT: D 366 PHE cc_start: 0.8812 (p90) cc_final: 0.8575 (p90) REVERT: D 394 LYS cc_start: 0.7634 (ttpp) cc_final: 0.7259 (tttp) outliers start: 68 outliers final: 40 residues processed: 321 average time/residue: 0.0999 time to fit residues: 48.9169 Evaluate side-chains 322 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 274 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 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 91 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.215110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.160530 restraints weight = 14603.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149217 restraints weight = 19739.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.149693 restraints weight = 16279.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.149421 restraints weight = 11645.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.147762 restraints weight = 13354.465| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13616 Z= 0.144 Angle : 0.689 9.706 18384 Z= 0.312 Chirality : 0.042 0.146 2140 Planarity : 0.005 0.067 2224 Dihedral : 9.042 60.876 2204 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.04 % Allowed : 25.73 % 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: 0.68 (0.23), residues: 1576 helix: 0.96 (0.17), residues: 1020 sheet: 0.09 (0.62), residues: 96 loop : -0.43 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 417 TYR 0.012 0.001 TYR A 175 PHE 0.006 0.001 PHE C 366 TRP 0.013 0.001 TRP D 264 HIS 0.003 0.001 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (13616) covalent geometry : angle 0.68912 / 0.31 (18384) hydrogen bonds : bond 0.03556 / 2.37 ( 732) hydrogen bonds : angle 3.96074 / 2.83 ( 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 351 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 282 time to evaluate : 0.435 Fit side-chains REVERT: A 270 TYR cc_start: 0.3512 (OUTLIER) cc_final: 0.2834 (m-80) REVERT: A 366 PHE cc_start: 0.8921 (p90) cc_final: 0.8653 (p90) REVERT: B 270 TYR cc_start: 0.3511 (OUTLIER) cc_final: 0.2802 (m-80) REVERT: B 366 PHE cc_start: 0.8880 (p90) cc_final: 0.8651 (p90) REVERT: B 394 LYS cc_start: 0.7827 (ttpp) cc_final: 0.7392 (tttp) REVERT: C 270 TYR cc_start: 0.3501 (OUTLIER) cc_final: 0.2796 (m-80) REVERT: C 394 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7390 (tttp) REVERT: D 270 TYR cc_start: 0.3525 (OUTLIER) cc_final: 0.2819 (m-80) REVERT: D 366 PHE cc_start: 0.8918 (p90) cc_final: 0.8650 (p90) REVERT: D 394 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7294 (tttp) outliers start: 69 outliers final: 46 residues processed: 310 average time/residue: 0.1031 time to fit residues: 48.6985 Evaluate side-chains 319 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.216898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.169346 restraints weight = 14628.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156457 restraints weight = 17667.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156402 restraints weight = 16473.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156371 restraints weight = 15388.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156413 restraints weight = 14080.402| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13616 Z= 0.122 Angle : 0.698 10.410 18384 Z= 0.309 Chirality : 0.042 0.145 2140 Planarity : 0.005 0.067 2224 Dihedral : 8.702 57.190 2204 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.46 % Allowed : 26.54 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1576 helix: 0.98 (0.17), residues: 1016 sheet: 0.09 (0.63), residues: 96 loop : -0.39 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 417 TYR 0.009 0.001 TYR A 175 PHE 0.006 0.001 PHE B 366 TRP 0.013 0.001 TRP C 264 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13616) covalent geometry : angle 0.69815 / 0.31 (18384) hydrogen bonds : bond 0.03320 / 2.22 ( 732) hydrogen bonds : angle 3.90905 / 2.79 ( 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 339 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 278 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3684 (OUTLIER) cc_final: 0.2946 (m-80) REVERT: B 270 TYR cc_start: 0.3678 (OUTLIER) cc_final: 0.2960 (m-80) REVERT: B 366 PHE cc_start: 0.8757 (p90) cc_final: 0.8526 (p90) REVERT: B 394 LYS cc_start: 0.7600 (ttpp) cc_final: 0.7370 (tttp) REVERT: C 270 TYR cc_start: 0.3699 (OUTLIER) cc_final: 0.2997 (m-80) REVERT: C 394 LYS cc_start: 0.7611 (ttpp) cc_final: 0.7335 (tttp) REVERT: D 270 TYR cc_start: 0.3680 (OUTLIER) cc_final: 0.2960 (m-80) outliers start: 61 outliers final: 38 residues processed: 310 average time/residue: 0.1020 time to fit residues: 48.4515 Evaluate side-chains 312 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 104 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 124 optimal weight: 0.0000 chunk 110 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.216711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166629 restraints weight = 14567.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.153137 restraints weight = 15426.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152657 restraints weight = 17655.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152777 restraints weight = 13958.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.153086 restraints weight = 12797.861| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13616 Z= 0.128 Angle : 0.698 9.942 18384 Z= 0.312 Chirality : 0.042 0.145 2140 Planarity : 0.005 0.069 2224 Dihedral : 8.625 57.256 2204 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.58 % Allowed : 27.49 % 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: 0.74 (0.23), residues: 1576 helix: 1.00 (0.17), residues: 1016 sheet: 0.10 (0.63), residues: 96 loop : -0.38 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 417 TYR 0.009 0.001 TYR A 175 PHE 0.011 0.001 PHE A 26 TRP 0.013 0.001 TRP C 264 HIS 0.002 0.001 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13616) covalent geometry : angle 0.69778 / 0.31 (18384) hydrogen bonds : bond 0.03371 / 2.24 ( 732) hydrogen bonds : angle 3.92794 / 2.80 ( 2148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3598 (OUTLIER) cc_final: 0.2902 (m-80) REVERT: B 270 TYR cc_start: 0.3635 (OUTLIER) cc_final: 0.2939 (m-80) REVERT: B 366 PHE cc_start: 0.8820 (p90) cc_final: 0.8573 (p90) REVERT: B 394 LYS cc_start: 0.7607 (ttpp) cc_final: 0.7257 (tttp) REVERT: C 270 TYR cc_start: 0.3615 (OUTLIER) cc_final: 0.2937 (m-80) REVERT: C 394 LYS cc_start: 0.7620 (ttpp) cc_final: 0.7255 (tttp) REVERT: D 270 TYR cc_start: 0.3635 (OUTLIER) cc_final: 0.2949 (m-80) outliers start: 49 outliers final: 37 residues processed: 302 average time/residue: 0.1031 time to fit residues: 47.3231 Evaluate side-chains 311 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 62 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 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 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 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 54 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 121 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 342 ASN C 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.216833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.165331 restraints weight = 14529.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155637 restraints weight = 18431.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.155227 restraints weight = 15092.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155333 restraints weight = 13391.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.155115 restraints weight = 13289.677| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 0.052 13616 Z= 0.126 Angle : 0.708 10.064 18384 Z= 0.316 Chirality : 0.042 0.150 2140 Planarity : 0.005 0.071 2224 Dihedral : 8.523 57.166 2204 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.95 % Allowed : 26.83 % 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: 1012 sheet: 0.12 (0.64), residues: 96 loop : -0.35 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 417 TYR 0.009 0.001 TYR A 175 PHE 0.005 0.001 PHE B 366 TRP 0.013 0.001 TRP D 264 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13616) covalent geometry : angle 0.70762 / 0.32 (18384) hydrogen bonds : bond 0.03380 / 2.24 ( 732) hydrogen bonds : angle 3.92845 / 2.80 ( 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 329 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3678 (OUTLIER) cc_final: 0.3025 (m-80) REVERT: B 270 TYR cc_start: 0.3663 (OUTLIER) cc_final: 0.3014 (m-80) REVERT: B 366 PHE cc_start: 0.8736 (p90) cc_final: 0.8492 (p90) REVERT: B 394 LYS cc_start: 0.7615 (ttpp) cc_final: 0.7321 (tttp) REVERT: C 270 TYR cc_start: 0.3650 (OUTLIER) cc_final: 0.3012 (m-80) REVERT: C 364 GLN cc_start: 0.8448 (pm20) cc_final: 0.8153 (pm20) REVERT: D 270 TYR cc_start: 0.3658 (OUTLIER) cc_final: 0.3014 (m-80) outliers start: 54 outliers final: 36 residues processed: 299 average time/residue: 0.1068 time to fit residues: 48.4033 Evaluate side-chains 310 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 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 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 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 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 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: 1.9990 chunk 113 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.211614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.166597 restraints weight = 14754.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.155001 restraints weight = 19148.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.153717 restraints weight = 21037.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.153912 restraints weight = 17753.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.153710 restraints weight = 16097.387| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13616 Z= 0.164 Angle : 0.742 9.944 18384 Z= 0.334 Chirality : 0.043 0.145 2140 Planarity : 0.005 0.076 2224 Dihedral : 9.023 63.394 2204 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.80 % Allowed : 27.19 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1576 helix: 1.01 (0.17), residues: 1020 sheet: 0.07 (0.63), residues: 96 loop : -0.41 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 417 TYR 0.014 0.001 TYR A 175 PHE 0.006 0.001 PHE D 366 TRP 0.014 0.002 TRP D 264 HIS 0.004 0.001 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (13616) covalent geometry : angle 0.74240 / 0.33 (18384) hydrogen bonds : bond 0.03690 / 2.46 ( 732) hydrogen bonds : angle 4.02307 / 2.88 ( 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 320 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.472 Fit side-chains REVERT: A 270 TYR cc_start: 0.3636 (OUTLIER) cc_final: 0.3102 (m-80) REVERT: A 366 PHE cc_start: 0.8809 (p90) cc_final: 0.8551 (p90) REVERT: B 270 TYR cc_start: 0.3610 (OUTLIER) cc_final: 0.3083 (m-80) REVERT: B 366 PHE cc_start: 0.8797 (p90) cc_final: 0.8563 (p90) REVERT: B 394 LYS cc_start: 0.7657 (ttpp) cc_final: 0.7330 (tttp) REVERT: C 270 TYR cc_start: 0.3610 (OUTLIER) cc_final: 0.3084 (m-80) REVERT: D 270 TYR cc_start: 0.3609 (OUTLIER) cc_final: 0.3084 (m-80) REVERT: D 394 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7320 (tttp) outliers start: 52 outliers final: 41 residues processed: 291 average time/residue: 0.0982 time to fit residues: 43.7006 Evaluate side-chains 313 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 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 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 46 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 318 GLU 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: 4.9990 chunk 101 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.213084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161157 restraints weight = 14634.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.152120 restraints weight = 18658.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150871 restraints weight = 17298.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.150819 restraints weight = 14506.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150924 restraints weight = 13270.023| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13616 Z= 0.151 Angle : 0.737 10.120 18384 Z= 0.330 Chirality : 0.043 0.147 2140 Planarity : 0.005 0.077 2224 Dihedral : 8.987 59.914 2204 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.02 % Allowed : 26.97 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1576 helix: 1.00 (0.17), residues: 1020 sheet: 0.12 (0.65), residues: 96 loop : -0.42 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 417 TYR 0.012 0.001 TYR A 175 PHE 0.006 0.001 PHE D 366 TRP 0.013 0.001 TRP C 264 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (13616) covalent geometry : angle 0.73682 / 0.33 (18384) hydrogen bonds : bond 0.03561 / 2.37 ( 732) hydrogen bonds : angle 3.98190 / 2.82 ( 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 330 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 275 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3519 (OUTLIER) cc_final: 0.2988 (m-80) REVERT: B 270 TYR cc_start: 0.3498 (OUTLIER) cc_final: 0.3003 (m-80) REVERT: B 366 PHE cc_start: 0.8804 (p90) cc_final: 0.8577 (p90) REVERT: C 270 TYR cc_start: 0.3492 (OUTLIER) cc_final: 0.3005 (m-80) REVERT: C 394 LYS cc_start: 0.7678 (ttpp) cc_final: 0.7420 (ttmm) REVERT: D 270 TYR cc_start: 0.3497 (OUTLIER) cc_final: 0.2966 (m-80) REVERT: D 394 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7489 (ttmm) outliers start: 55 outliers final: 41 residues processed: 298 average time/residue: 0.1005 time to fit residues: 45.7164 Evaluate side-chains 317 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 203 ILE 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 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 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 152 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 134 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 108 optimal weight: 0.0770 chunk 5 optimal weight: 5.9990 chunk 59 optimal weight: 0.0060 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.217071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.165927 restraints weight = 14626.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.154793 restraints weight = 18190.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154449 restraints weight = 15699.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154496 restraints weight = 13227.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154915 restraints weight = 11695.788| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13616 Z= 0.124 Angle : 0.727 10.117 18384 Z= 0.323 Chirality : 0.042 0.148 2140 Planarity : 0.005 0.076 2224 Dihedral : 8.490 56.166 2204 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.07 % Allowed : 28.14 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.23), residues: 1576 helix: 1.06 (0.17), residues: 1012 sheet: 0.17 (0.65), residues: 96 loop : -0.35 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 417 TYR 0.007 0.001 TYR C 175 PHE 0.008 0.001 PHE D 26 TRP 0.011 0.001 TRP C 264 HIS 0.001 0.000 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13616) covalent geometry : angle 0.72687 / 0.32 (18384) hydrogen bonds : bond 0.03290 / 2.19 ( 732) hydrogen bonds : angle 3.91742 / 2.78 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2521.56 seconds wall clock time: 44 minutes 11.98 seconds (2651.98 seconds total)