Starting phenix.real_space_refine on Mon Oct 14 18:04:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/10_2024/7rtj_24682.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/10_2024/7rtj_24682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/10_2024/7rtj_24682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/10_2024/7rtj_24682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/10_2024/7rtj_24682.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/10_2024/7rtj_24682.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 13352 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 57 Restraints were copied for chains: C, D Time building chain proxies: 8.73, per 1000 atoms: 0.65 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: 3.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 12 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.824A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 4.146A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 222 removed outlier: 3.710A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.701A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 299 removed outlier: 6.158A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.557A pdb=" N LYS A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 306 through 314 removed outlier: 3.632A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.601A pdb=" N ALA A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.825A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.146A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 222 removed outlier: 3.711A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 removed outlier: 3.702A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 299 removed outlier: 6.159A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 removed outlier: 3.557A pdb=" N LYS B 303 " --> pdb=" O PRO B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 306 through 314 removed outlier: 3.632A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.601A pdb=" N ALA B 408 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 56 Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.825A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 removed outlier: 4.147A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 222 removed outlier: 3.710A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 removed outlier: 3.702A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 removed outlier: 6.159A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 303 removed outlier: 3.557A pdb=" N LYS C 303 " --> pdb=" O PRO C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 306 through 314 removed outlier: 3.632A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'C' and resid 404 through 420 removed outlier: 3.602A pdb=" N ALA C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 56 Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.373A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.825A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 removed outlier: 4.146A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.517A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 removed outlier: 3.725A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 222 removed outlier: 3.710A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 removed outlier: 3.701A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.874A pdb=" N VAL D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 299 removed outlier: 6.158A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 removed outlier: 3.556A pdb=" N LYS D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 306 through 314 removed outlier: 3.631A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 404 through 420 removed outlier: 3.601A pdb=" N ALA D 408 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR A 322 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 387 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 390 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 340 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 392 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 338 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 339 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 348 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR B 322 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 387 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 390 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 340 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 392 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 338 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 339 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 348 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR C 322 " --> pdb=" O CYS C 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C 387 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 390 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 340 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 392 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 338 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C 339 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 348 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 321 through 322 removed outlier: 3.556A pdb=" N TYR D 322 " --> pdb=" O CYS D 387 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS D 387 " --> pdb=" O TYR D 322 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 390 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 340 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 392 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 338 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR D 339 " --> pdb=" O PHE D 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.114A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 348 " --> pdb=" O ALA D 358 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2088 1.32 - 1.44: 3376 1.44 - 1.56: 8084 1.56 - 1.68: 20 1.68 - 1.81: 48 Bond restraints: 13616 Sorted by residual: bond pdb=" C10 PGW B 507 " pdb=" C9 PGW B 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW C 507 " pdb=" C9 PGW C 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW A 505 " pdb=" C9 PGW A 505 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW D 507 " pdb=" C9 PGW D 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 ... (remaining 13611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 18018 2.97 - 5.93: 274 5.93 - 8.90: 52 8.90 - 11.87: 24 11.87 - 14.84: 16 Bond angle restraints: 18384 Sorted by residual: angle pdb=" N LEU C 91 " pdb=" CA LEU C 91 " pdb=" C LEU C 91 " ideal model delta sigma weight residual 112.54 106.05 6.49 1.22e+00 6.72e-01 2.83e+01 angle pdb=" N LEU D 91 " pdb=" CA LEU D 91 " pdb=" C LEU D 91 " ideal model delta sigma weight residual 112.54 106.06 6.48 1.22e+00 6.72e-01 2.82e+01 angle pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 112.54 106.06 6.48 1.22e+00 6.72e-01 2.82e+01 angle pdb=" N LEU B 91 " pdb=" CA LEU B 91 " pdb=" C LEU B 91 " ideal model delta sigma weight residual 112.54 106.11 6.43 1.22e+00 6.72e-01 2.78e+01 angle pdb=" C10 PGW D 507 " pdb=" C9 PGW D 507 " pdb=" C8 PGW D 507 " ideal model delta sigma weight residual 127.02 112.18 14.84 3.00e+00 1.11e-01 2.45e+01 ... (remaining 18379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.75: 7824 31.75 - 63.50: 472 63.50 - 95.26: 20 95.26 - 127.01: 16 127.01 - 158.76: 12 Dihedral angle restraints: 8344 sinusoidal: 3664 harmonic: 4680 Sorted by residual: dihedral pdb=" C5' CMP D 503 " pdb=" O5' CMP D 503 " pdb=" P CMP D 503 " pdb=" O1P CMP D 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.67 -112.67 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' CMP B 503 " pdb=" O5' CMP B 503 " pdb=" P CMP B 503 " pdb=" O1P CMP B 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.64 -112.64 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" C5' CMP C 503 " pdb=" O5' CMP C 503 " pdb=" P CMP C 503 " pdb=" O1P CMP C 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.62 -112.62 1 2.00e+01 2.50e-03 3.32e+01 ... (remaining 8341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1560 0.052 - 0.104: 447 0.104 - 0.157: 113 0.157 - 0.209: 8 0.209 - 0.261: 12 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CA PRO C 405 " pdb=" N PRO C 405 " pdb=" C PRO C 405 " pdb=" CB PRO C 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO D 405 " pdb=" N PRO D 405 " pdb=" C PRO D 405 " pdb=" CB PRO D 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO B 405 " pdb=" N PRO B 405 " pdb=" C PRO B 405 " pdb=" CB PRO B 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2137 not shown) Planarity restraints: 2224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 504 " 0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW D 504 " -0.148 2.00e-02 2.50e+03 pdb=" C8 PGW D 504 " 0.142 2.00e-02 2.50e+03 pdb=" C9 PGW D 504 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 504 " -0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW B 504 " 0.148 2.00e-02 2.50e+03 pdb=" C8 PGW B 504 " -0.142 2.00e-02 2.50e+03 pdb=" C9 PGW B 504 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 502 " -0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW A 502 " 0.148 2.00e-02 2.50e+03 pdb=" C8 PGW A 502 " -0.142 2.00e-02 2.50e+03 pdb=" C9 PGW A 502 " 0.137 2.00e-02 2.50e+03 ... (remaining 2221 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2059 2.76 - 3.29: 12876 3.29 - 3.83: 21815 3.83 - 4.36: 23707 4.36 - 4.90: 42020 Nonbonded interactions: 102477 Sorted by model distance: nonbonded pdb=" O ARG D 417 " pdb=" NH1 ARG D 417 " model vdw 2.224 3.120 nonbonded pdb=" O ARG A 417 " pdb=" NH1 ARG A 417 " model vdw 2.224 3.120 nonbonded pdb=" O ARG C 417 " pdb=" NH1 ARG C 417 " model vdw 2.224 3.120 nonbonded pdb=" O ARG B 417 " pdb=" NH1 ARG B 417 " model vdw 2.225 3.120 nonbonded pdb=" O ILE C 178 " pdb=" OG1 THR C 182 " model vdw 2.253 3.040 ... (remaining 102472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or (resid 506 and (name C01 or name C02 or name C03 or name \ C1 or name C19 or name C2 or name C20 or name C3 or name C4 or name C5 or name C \ 6 or name O01 or name O02 or name O03 or name O04)) or (resid 508 and (name C01 \ or name C02 or name C03 or name C1 or name C15 or name C16 or name C17 or name C \ 18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or n \ ame C5 or name C6 or name O01 or name O02 or name O03 or name O04)) or resid 509 \ )) selection = (chain 'B' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) selection = (chain 'C' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) selection = (chain 'D' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.740 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.190 13616 Z= 0.529 Angle : 1.035 14.836 18384 Z= 0.510 Chirality : 0.053 0.261 2140 Planarity : 0.008 0.143 2224 Dihedral : 20.090 158.761 5320 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.17 % Allowed : 26.17 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP B 264 HIS 0.004 0.001 HIS D 149 PHE 0.009 0.002 PHE A 302 TYR 0.012 0.001 TYR B 175 ARG 0.004 0.001 ARG D 111 *********************** 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 fitting. rotamer outliers: 16 poor density : 284 time to evaluate : 1.353 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 288 average time/residue: 0.2479 time to fit residues: 105.0206 Evaluate side-chains 274 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13616 Z= 0.199 Angle : 0.651 8.602 18384 Z= 0.308 Chirality : 0.042 0.127 2140 Planarity : 0.005 0.064 2224 Dihedral : 17.229 162.433 2288 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.09 % Allowed : 25.37 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1576 helix: 0.77 (0.17), residues: 1020 sheet: 0.63 (0.65), residues: 96 loop : -0.56 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 264 HIS 0.002 0.001 HIS A 149 PHE 0.007 0.001 PHE A 366 TYR 0.009 0.001 TYR D 175 ARG 0.004 0.000 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 281 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 28 residues processed: 297 average time/residue: 0.2249 time to fit residues: 99.9746 Evaluate side-chains 287 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 259 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.0050 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13616 Z= 0.251 Angle : 0.671 9.375 18384 Z= 0.316 Chirality : 0.042 0.120 2140 Planarity : 0.005 0.065 2224 Dihedral : 16.359 145.500 2288 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.46 % Allowed : 25.58 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1576 helix: 0.80 (0.17), residues: 1020 sheet: 0.31 (0.61), residues: 96 loop : -0.58 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.004 0.001 HIS B 149 PHE 0.006 0.001 PHE A 366 TYR 0.014 0.001 TYR A 175 ARG 0.004 0.000 ARG A 403 *********************** 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 342 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 281 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7267 (tt) REVERT: A 270 TYR cc_start: 0.3891 (OUTLIER) cc_final: 0.3045 (m-80) REVERT: B 91 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7220 (tt) REVERT: B 270 TYR cc_start: 0.3875 (OUTLIER) cc_final: 0.2957 (m-80) REVERT: C 270 TYR cc_start: 0.3855 (OUTLIER) cc_final: 0.2913 (m-80) REVERT: D 270 TYR cc_start: 0.3871 (OUTLIER) cc_final: 0.2950 (m-80) outliers start: 61 outliers final: 32 residues processed: 305 average time/residue: 0.2385 time to fit residues: 107.0556 Evaluate side-chains 298 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 260 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 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 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 91 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 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 315 LEU 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 140 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13616 Z= 0.205 Angle : 0.651 9.689 18384 Z= 0.306 Chirality : 0.041 0.124 2140 Planarity : 0.005 0.065 2224 Dihedral : 15.301 137.297 2288 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.04 % Allowed : 25.88 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1576 helix: 0.93 (0.17), residues: 1016 sheet: 0.31 (0.61), residues: 96 loop : -0.51 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 264 HIS 0.002 0.001 HIS A 149 PHE 0.012 0.001 PHE B 26 TYR 0.010 0.001 TYR C 175 ARG 0.004 0.000 ARG C 417 *********************** 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 358 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 289 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.4022 (OUTLIER) cc_final: 0.3371 (m-80) REVERT: A 394 LYS cc_start: 0.7674 (ttpp) cc_final: 0.7383 (ttmm) REVERT: B 270 TYR cc_start: 0.4017 (OUTLIER) cc_final: 0.3070 (m-80) REVERT: C 270 TYR cc_start: 0.3999 (OUTLIER) cc_final: 0.3062 (m-80) REVERT: D 270 TYR cc_start: 0.4005 (OUTLIER) cc_final: 0.3072 (m-80) REVERT: D 394 LYS cc_start: 0.7619 (ttpp) cc_final: 0.7353 (tttp) outliers start: 69 outliers final: 40 residues processed: 326 average time/residue: 0.2311 time to fit residues: 112.3087 Evaluate side-chains 307 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 263 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13616 Z= 0.205 Angle : 0.653 9.816 18384 Z= 0.306 Chirality : 0.041 0.124 2140 Planarity : 0.005 0.067 2224 Dihedral : 14.274 135.236 2288 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.68 % Allowed : 26.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1576 helix: 1.00 (0.17), residues: 1016 sheet: 0.32 (0.61), residues: 96 loop : -0.48 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 264 HIS 0.002 0.001 HIS B 149 PHE 0.005 0.001 PHE B 40 TYR 0.010 0.001 TYR D 175 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 275 time to evaluate : 1.323 Fit side-chains REVERT: A 270 TYR cc_start: 0.3914 (OUTLIER) cc_final: 0.3170 (m-80) REVERT: B 270 TYR cc_start: 0.3778 (OUTLIER) cc_final: 0.3108 (m-80) REVERT: B 394 LYS cc_start: 0.7781 (ttpp) cc_final: 0.7510 (tttp) REVERT: C 270 TYR cc_start: 0.3843 (OUTLIER) cc_final: 0.3159 (m-80) REVERT: C 394 LYS cc_start: 0.7762 (ttpp) cc_final: 0.7485 (tttp) REVERT: D 270 TYR cc_start: 0.3860 (OUTLIER) cc_final: 0.3141 (m-80) outliers start: 64 outliers final: 37 residues processed: 304 average time/residue: 0.2445 time to fit residues: 111.0405 Evaluate side-chains 304 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 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 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 50 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13616 Z= 0.206 Angle : 0.679 10.175 18384 Z= 0.314 Chirality : 0.041 0.124 2140 Planarity : 0.005 0.068 2224 Dihedral : 13.485 134.252 2288 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.46 % Allowed : 26.83 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1576 helix: 0.98 (0.17), residues: 1020 sheet: 0.27 (0.62), residues: 96 loop : -0.40 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 264 HIS 0.002 0.001 HIS D 149 PHE 0.005 0.001 PHE B 40 TYR 0.011 0.001 TYR D 175 ARG 0.004 0.000 ARG C 417 *********************** 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 340 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 279 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3871 (OUTLIER) cc_final: 0.3096 (m-80) REVERT: B 270 TYR cc_start: 0.3857 (OUTLIER) cc_final: 0.3107 (m-80) REVERT: B 394 LYS cc_start: 0.7760 (ttpp) cc_final: 0.7543 (tttp) REVERT: C 270 TYR cc_start: 0.3853 (OUTLIER) cc_final: 0.3105 (m-80) REVERT: D 270 TYR cc_start: 0.3867 (OUTLIER) cc_final: 0.3099 (m-80) outliers start: 61 outliers final: 44 residues processed: 313 average time/residue: 0.2378 time to fit residues: 110.5471 Evaluate side-chains 319 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 271 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 PHE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 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 94 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 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 145 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 20.0000 chunk 127 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13616 Z= 0.202 Angle : 0.677 9.939 18384 Z= 0.315 Chirality : 0.041 0.125 2140 Planarity : 0.005 0.069 2224 Dihedral : 13.175 133.471 2288 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.73 % Allowed : 27.70 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1576 helix: 1.02 (0.17), residues: 1012 sheet: 0.22 (0.63), residues: 96 loop : -0.36 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 264 HIS 0.002 0.001 HIS B 149 PHE 0.010 0.001 PHE A 26 TYR 0.009 0.001 TYR D 175 ARG 0.008 0.000 ARG A 403 *********************** 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 335 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 284 time to evaluate : 1.544 Fit side-chains REVERT: A 270 TYR cc_start: 0.3848 (OUTLIER) cc_final: 0.3078 (m-80) REVERT: B 270 TYR cc_start: 0.3846 (OUTLIER) cc_final: 0.3106 (m-80) REVERT: C 178 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8706 (mm) REVERT: C 270 TYR cc_start: 0.3832 (OUTLIER) cc_final: 0.3102 (m-80) REVERT: C 394 LYS cc_start: 0.7625 (ttpp) cc_final: 0.7382 (tttp) REVERT: D 178 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8709 (mm) REVERT: D 270 TYR cc_start: 0.3847 (OUTLIER) cc_final: 0.3101 (m-80) outliers start: 51 outliers final: 34 residues processed: 309 average time/residue: 0.2280 time to fit residues: 105.0458 Evaluate side-chains 308 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 268 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 178 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR 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 178 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13616 Z= 0.240 Angle : 0.699 9.858 18384 Z= 0.327 Chirality : 0.043 0.197 2140 Planarity : 0.005 0.072 2224 Dihedral : 13.140 133.749 2288 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.39 % Allowed : 27.70 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1576 helix: 0.98 (0.17), residues: 1020 sheet: 0.05 (0.63), residues: 96 loop : -0.39 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 264 HIS 0.003 0.001 HIS D 149 PHE 0.005 0.001 PHE C 40 TYR 0.012 0.001 TYR B 175 ARG 0.006 0.000 ARG C 417 *********************** 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 328 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 268 time to evaluate : 1.415 Fit side-chains REVERT: A 270 TYR cc_start: 0.3863 (OUTLIER) cc_final: 0.3162 (m-80) REVERT: A 366 PHE cc_start: 0.8386 (p90) cc_final: 0.8154 (p90) REVERT: B 270 TYR cc_start: 0.3833 (OUTLIER) cc_final: 0.3165 (m-80) REVERT: C 270 TYR cc_start: 0.3810 (OUTLIER) cc_final: 0.3151 (m-80) REVERT: D 270 TYR cc_start: 0.3860 (OUTLIER) cc_final: 0.3164 (m-80) outliers start: 60 outliers final: 45 residues processed: 297 average time/residue: 0.2225 time to fit residues: 100.2151 Evaluate side-chains 311 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 262 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 178 ILE 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 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 178 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 ILE 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 338 VAL 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 131 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13616 Z= 0.213 Angle : 0.697 9.865 18384 Z= 0.326 Chirality : 0.042 0.183 2140 Planarity : 0.005 0.074 2224 Dihedral : 12.744 133.304 2288 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.87 % Allowed : 28.73 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1576 helix: 1.02 (0.17), residues: 1012 sheet: 0.04 (0.63), residues: 96 loop : -0.36 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 264 HIS 0.002 0.001 HIS D 149 PHE 0.007 0.001 PHE C 366 TYR 0.010 0.001 TYR B 175 ARG 0.007 0.000 ARG C 417 *********************** 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 313 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 260 time to evaluate : 1.554 Fit side-chains REVERT: A 178 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8752 (mm) REVERT: A 270 TYR cc_start: 0.3873 (OUTLIER) cc_final: 0.3188 (m-80) REVERT: B 178 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8746 (mm) REVERT: B 270 TYR cc_start: 0.3912 (OUTLIER) cc_final: 0.3228 (m-80) REVERT: C 178 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8744 (mm) REVERT: C 270 TYR cc_start: 0.3890 (OUTLIER) cc_final: 0.3210 (m-80) REVERT: D 178 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8745 (mm) REVERT: D 270 TYR cc_start: 0.3905 (OUTLIER) cc_final: 0.3218 (m-80) outliers start: 53 outliers final: 30 residues processed: 287 average time/residue: 0.2226 time to fit residues: 97.3104 Evaluate side-chains 295 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 257 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR 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 177 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 338 VAL 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 148 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1858 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= 0.192 Angle : 0.696 10.150 18384 Z= 0.323 Chirality : 0.042 0.175 2140 Planarity : 0.005 0.076 2224 Dihedral : 12.309 133.029 2288 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.85 % Allowed : 29.53 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1576 helix: 1.12 (0.17), residues: 1012 sheet: 0.14 (0.64), residues: 96 loop : -0.34 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 264 HIS 0.002 0.001 HIS C 316 PHE 0.011 0.001 PHE A 366 TYR 0.008 0.001 TYR B 175 ARG 0.007 0.000 ARG C 417 ********************** 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 312 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 273 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.3757 (OUTLIER) cc_final: 0.3090 (m-80) REVERT: B 270 TYR cc_start: 0.3742 (OUTLIER) cc_final: 0.3078 (m-80) REVERT: C 270 TYR cc_start: 0.3752 (OUTLIER) cc_final: 0.3088 (m-80) REVERT: D 270 TYR cc_start: 0.3757 (OUTLIER) cc_final: 0.3083 (m-80) outliers start: 39 outliers final: 26 residues processed: 293 average time/residue: 0.2432 time to fit residues: 105.8422 Evaluate side-chains 296 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 108 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.216380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.164728 restraints weight = 14433.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.155936 restraints weight = 18502.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.155181 restraints weight = 16362.891| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1898 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= 0.202 Angle : 0.705 10.193 18384 Z= 0.327 Chirality : 0.042 0.172 2140 Planarity : 0.005 0.076 2224 Dihedral : 12.222 133.252 2288 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.92 % Allowed : 29.90 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.23), residues: 1576 helix: 1.08 (0.17), residues: 1012 sheet: 0.18 (0.64), residues: 96 loop : -0.33 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 264 HIS 0.002 0.001 HIS B 149 PHE 0.009 0.001 PHE B 366 TYR 0.009 0.001 TYR B 175 ARG 0.008 0.000 ARG C 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.58 seconds wall clock time: 50 minutes 42.32 seconds (3042.32 seconds total)