Starting phenix.real_space_refine on Fri Aug 7 13:54:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fs8_29417/08_2026/8fs8_29417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs8_29417/08_2026/8fs8_29417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2026/8fs8_29417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2026/8fs8_29417.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2026/8fs8_29417.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2026/8fs8_29417.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2026/8fs8_29417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs8_29417/08_2026/8fs8_29417.map" } resolution = 3.04 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 68 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 13702 2.51 5 N 3764 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21906 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3489 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 317} Chain breaks: 2 Chain: "F" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2216 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain breaks: 7 Chain: "G" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2303 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 4, 'TRANS': 285} Chain breaks: 2 Chain: "H" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2296 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 5 Chain: "I" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "J" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.51, per 1000 atoms: 0.21 Number of scatterers: 21906 At special positions: 0 Unit cell: (122.544, 129.996, 139.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 114 16.00 P 68 15.00 Mg 4 11.99 O 4254 8.00 N 3764 7.00 C 13702 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: 1.82 Conformation dependent library (CDL) restraints added in 855.5 milliseconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 15 sheets defined 51.2% alpha, 14.3% beta 21 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.835A pdb=" N LYS A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 161 through 173 removed outlier: 4.162A pdb=" N PHE A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.502A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.143A pdb=" N LEU A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.105A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 6.081A pdb=" N ASN A 388 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 409 Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.654A pdb=" N LEU A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 497 Proline residue: A 489 - end of helix removed outlier: 4.479A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.861A pdb=" N VAL B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.912A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.287A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.507A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.534A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.598A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.971A pdb=" N ILE C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.838A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.753A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.596A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.522A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 240 through 253 Processing helix chain 'C' and resid 255 through 270 removed outlier: 3.862A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.301A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 4.133A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.716A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 removed outlier: 3.540A pdb=" N THR D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.074A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.823A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 151 Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.992A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 228 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.519A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 294 Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 335 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 20 through 32 removed outlier: 4.237A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.170A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.087A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.579A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 30 Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 96 through 113 Processing helix chain 'F' and resid 213 through 220 Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.323A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 425 removed outlier: 3.780A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 86 through 94 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 244 through 246 No H-bonds generated for 'chain 'G' and resid 244 through 246' Processing helix chain 'G' and resid 317 through 329 removed outlier: 4.175A pdb=" N GLN G 321 " --> pdb=" O ASP G 317 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 removed outlier: 3.521A pdb=" N GLN H 13 " --> pdb=" O GLU H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 98 through 102 Processing helix chain 'H' and resid 162 through 167 Processing helix chain 'H' and resid 234 through 244 Processing helix chain 'H' and resid 326 through 336 removed outlier: 3.522A pdb=" N ASN H 331 " --> pdb=" O LYS H 327 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 339 No H-bonds generated for 'chain 'H' and resid 337 through 339' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 removed outlier: 6.339A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.869A pdb=" N GLY A 109 " --> pdb=" O ILE A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114 removed outlier: 7.093A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 161 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 48 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.081A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.475A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 69 through 72 removed outlier: 4.078A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.559A pdb=" N PHE F 160 " --> pdb=" O HIS F 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.145A pdb=" N LYS F 206 " --> pdb=" O SER H 283 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER H 283 " --> pdb=" O LYS F 206 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 91 through 95 removed outlier: 3.913A pdb=" N ILE F 44 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS F 70 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 463 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET F 231 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 405 through 411 removed outlier: 3.521A pdb=" N ILE F 284 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 267 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 280 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU G 131 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG G 129 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE G 120 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU G 122 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 36 through 41 Processing sheet with id=AB3, first strand: chain 'G' and resid 45 through 52 removed outlier: 3.549A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 270 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 233 through 238 removed outlier: 3.959A pdb=" N GLU G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 78 through 79 removed outlier: 4.355A pdb=" N SER H 93 " --> pdb=" O ILE H 155 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 79 removed outlier: 7.338A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU H 38 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN H 363 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN H 365 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN H 348 " --> pdb=" O GLN H 365 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN H 228 " --> pdb=" O PHE H 353 " (cutoff:3.500A) 1074 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7083 1.36 - 1.51: 5957 1.51 - 1.65: 9184 1.65 - 1.80: 69 1.80 - 1.95: 100 Bond restraints: 22393 Sorted by residual: bond pdb=" C3' DT I 19 " pdb=" C2' DT I 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA J 9 " pdb=" C2' DA J 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.48e+00 bond pdb=" C3' DT I 21 " pdb=" C2' DT I 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DT I 23 " pdb=" C2' DT I 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.70e+00 bond pdb=" N ILE F 468 " pdb=" CA ILE F 468 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.44e+00 ... (remaining 22388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 29386 1.34 - 2.68: 959 2.68 - 4.01: 117 4.01 - 5.35: 26 5.35 - 6.69: 9 Bond angle restraints: 30497 Sorted by residual: angle pdb=" N GLU C 332 " pdb=" CA GLU C 332 " pdb=" C GLU C 332 " ideal model delta sigma weight residual 113.23 107.05 6.18 1.24e+00 6.50e-01 2.49e+01 angle pdb=" O4' DC I 20 " pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.28e+01 angle pdb=" CA GLY E 102 " pdb=" C GLY E 102 " pdb=" O GLY E 102 " ideal model delta sigma weight residual 121.18 117.19 3.99 8.80e-01 1.29e+00 2.05e+01 angle pdb=" N3 DT I 29 " pdb=" C4 DT I 29 " pdb=" O4 DT I 29 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT K 4 " pdb=" C4 DT K 4 " pdb=" O4 DT K 4 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 30492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 12698 23.25 - 46.50: 593 46.50 - 69.75: 200 69.75 - 93.00: 9 93.00 - 116.25: 1 Dihedral angle restraints: 13501 sinusoidal: 5921 harmonic: 7580 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -176.26 116.25 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" CA ASN C 180 " pdb=" CB ASN C 180 " pdb=" CG ASN C 180 " pdb=" OD1 ASN C 180 " ideal model delta sinusoidal sigma weight residual -90.00 -159.37 69.37 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" O1B AGS D 401 " pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " pdb=" PG AGS D 401 " ideal model delta sinusoidal sigma weight residual 68.91 157.20 -88.29 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 13498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2480 0.035 - 0.071: 737 0.071 - 0.106: 251 0.106 - 0.141: 56 0.141 - 0.177: 3 Chirality restraints: 3527 Sorted by residual: chirality pdb=" CB ILE G 137 " pdb=" CA ILE G 137 " pdb=" CG1 ILE G 137 " pdb=" CG2 ILE G 137 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA ASP E 100 " pdb=" N ASP E 100 " pdb=" C ASP E 100 " pdb=" CB ASP E 100 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 3524 not shown) Planarity restraints: 3643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 217 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C LEU D 217 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU D 217 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU D 218 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " -0.023 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" N9 DG I 28 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 131 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C MET B 131 " -0.030 2.00e-02 2.50e+03 pdb=" O MET B 131 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU B 132 " 0.010 2.00e-02 2.50e+03 ... (remaining 3640 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 206 2.58 - 3.16: 18227 3.16 - 3.74: 36468 3.74 - 4.32: 49106 4.32 - 4.90: 81377 Nonbonded interactions: 185384 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.050 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.065 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.218 2.170 nonbonded pdb=" O GLN A 207 " pdb=" OG SER A 211 " model vdw 2.236 3.040 ... (remaining 185379 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.790 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.003 0.039 22393 Z= 0.228 Angle : 0.561 6.692 30497 Z= 0.388 Chirality : 0.039 0.177 3527 Planarity : 0.003 0.044 3643 Dihedral : 14.133 116.254 8557 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.29 % Allowed : 7.31 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.18), residues: 2532 helix: 1.71 (0.16), residues: 1165 sheet: -0.66 (0.24), residues: 525 loop : -0.53 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 206 TYR 0.009 0.001 TYR A 67 PHE 0.010 0.001 PHE A 201 TRP 0.009 0.001 TRP E 259 HIS 0.004 0.000 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.23 (22393) covalent geometry : angle 0.56060 / 0.39 (30497) hydrogen bonds : bond 0.16803 / 11.00 ( 1118) hydrogen bonds : angle 6.76185 / 4.97 ( 3195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 554 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7846 (tt0) cc_final: 0.7187 (tm-30) REVERT: A 163 MET cc_start: 0.6551 (mtm) cc_final: 0.5838 (mtm) REVERT: A 174 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.5957 (ptm160) REVERT: A 196 ASP cc_start: 0.7677 (t0) cc_final: 0.7439 (t0) REVERT: A 225 GLU cc_start: 0.7597 (tt0) cc_final: 0.6986 (mp0) REVERT: A 289 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6540 (mtmm) REVERT: A 374 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6511 (tp30) REVERT: A 436 HIS cc_start: 0.4305 (m-70) cc_final: 0.3830 (m-70) REVERT: A 443 PHE cc_start: 0.7430 (t80) cc_final: 0.7158 (t80) REVERT: B 38 LYS cc_start: 0.7533 (tmmm) cc_final: 0.7069 (mtmt) REVERT: B 146 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7184 (mt0) REVERT: B 152 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7275 (mt-10) REVERT: B 272 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7508 (mmm160) REVERT: C 250 SER cc_start: 0.7262 (m) cc_final: 0.6947 (p) REVERT: C 256 TRP cc_start: 0.8091 (OUTLIER) cc_final: 0.6405 (t60) REVERT: D 83 TYR cc_start: 0.7239 (m-80) cc_final: 0.6940 (m-80) REVERT: E 19 ASN cc_start: 0.6100 (m110) cc_final: 0.5824 (m-40) REVERT: E 32 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6421 (mp10) REVERT: E 34 ARG cc_start: 0.7177 (ptp90) cc_final: 0.6107 (ptm160) REVERT: E 68 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7142 (tm) REVERT: E 221 ARG cc_start: 0.6469 (mtp180) cc_final: 0.6129 (mtp-110) REVERT: E 329 ASP cc_start: 0.8077 (p0) cc_final: 0.7867 (p0) REVERT: F 109 ARG cc_start: 0.7665 (mpt90) cc_final: 0.7442 (mmt180) REVERT: F 120 THR cc_start: 0.6685 (OUTLIER) cc_final: 0.6259 (m) REVERT: F 162 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6173 (tm-30) REVERT: F 293 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6872 (tt0) REVERT: F 422 TYR cc_start: 0.7459 (t80) cc_final: 0.7185 (t80) REVERT: F 461 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5475 (ptm160) REVERT: G 40 PHE cc_start: 0.7072 (m-80) cc_final: 0.6499 (m-80) REVERT: G 188 ASP cc_start: 0.7642 (m-30) cc_final: 0.7349 (m-30) REVERT: G 270 LEU cc_start: 0.6031 (tt) cc_final: 0.5573 (mp) REVERT: G 321 GLN cc_start: 0.8006 (tt0) cc_final: 0.7619 (mp10) REVERT: H 158 ASP cc_start: 0.7336 (p0) cc_final: 0.7094 (p0) REVERT: H 282 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6316 (mm) REVERT: H 320 LYS cc_start: 0.7100 (mmtm) cc_final: 0.6797 (mmtm) REVERT: H 364 MET cc_start: 0.7705 (ptm) cc_final: 0.7301 (ptt) outliers start: 77 outliers final: 24 residues processed: 600 average time/residue: 0.1673 time to fit residues: 154.6171 Evaluate side-chains 391 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 358 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 282 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0170 chunk 111 optimal weight: 0.7980 chunk 258 optimal weight: 50.0000 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS A 355 ASN A 368 ASN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 436 HIS ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 96 GLN C 333 ASN D 345 ASN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN G 9 ASN ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN H 132 ASN H 295 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.185186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148669 restraints weight = 27309.998| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.27 r_work: 0.3770 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22393 Z= 0.132 Angle : 0.559 7.531 30497 Z= 0.301 Chirality : 0.041 0.190 3527 Planarity : 0.004 0.078 3643 Dihedral : 16.266 98.515 3473 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.38 % Allowed : 11.46 % Favored : 85.16 % 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: 0.57 (0.18), residues: 2532 helix: 1.53 (0.15), residues: 1210 sheet: -0.61 (0.24), residues: 516 loop : -0.60 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 297 TYR 0.024 0.001 TYR A 67 PHE 0.024 0.001 PHE B 96 TRP 0.013 0.001 TRP H 42 HIS 0.013 0.001 HIS F 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (22393) covalent geometry : angle 0.55892 / 0.30 (30497) hydrogen bonds : bond 0.04631 / 3.00 ( 1118) hydrogen bonds : angle 5.28261 / 3.86 ( 3195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 379 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7905 (tt0) cc_final: 0.7243 (tm-30) REVERT: A 163 MET cc_start: 0.6763 (mtm) cc_final: 0.6071 (mtm) REVERT: A 178 MET cc_start: 0.7103 (mpp) cc_final: 0.6822 (mpp) REVERT: A 196 ASP cc_start: 0.7935 (t0) cc_final: 0.7620 (t0) REVERT: A 225 GLU cc_start: 0.7864 (tt0) cc_final: 0.7042 (mp0) REVERT: A 289 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6672 (mtmm) REVERT: A 306 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7434 (mt0) REVERT: A 374 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6541 (tp30) REVERT: B 38 LYS cc_start: 0.7581 (tmmm) cc_final: 0.7157 (mtmt) REVERT: B 272 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7638 (mmm160) REVERT: C 250 SER cc_start: 0.7178 (m) cc_final: 0.6940 (p) REVERT: C 256 TRP cc_start: 0.8082 (OUTLIER) cc_final: 0.6567 (t-100) REVERT: D 227 ASP cc_start: 0.8011 (t0) cc_final: 0.7485 (t70) REVERT: E 19 ASN cc_start: 0.5979 (m110) cc_final: 0.5776 (m-40) REVERT: E 32 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6588 (mp10) REVERT: E 34 ARG cc_start: 0.7413 (ptp90) cc_final: 0.6316 (ptm160) REVERT: E 221 ARG cc_start: 0.6621 (mtp180) cc_final: 0.6274 (mtp-110) REVERT: F 111 MET cc_start: 0.5369 (mmm) cc_final: 0.5102 (mmt) REVERT: F 293 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6863 (tt0) REVERT: F 461 ARG cc_start: 0.5739 (OUTLIER) cc_final: 0.5520 (ptm160) REVERT: G 40 PHE cc_start: 0.6902 (m-80) cc_final: 0.6634 (m-80) REVERT: G 66 LEU cc_start: 0.8387 (tp) cc_final: 0.8102 (tp) REVERT: G 188 ASP cc_start: 0.7594 (m-30) cc_final: 0.7325 (m-30) REVERT: G 270 LEU cc_start: 0.6127 (tt) cc_final: 0.5563 (mp) REVERT: H 158 ASP cc_start: 0.7297 (p0) cc_final: 0.7046 (p0) REVERT: H 253 LYS cc_start: 0.8199 (tmtm) cc_final: 0.7975 (tptt) REVERT: H 320 LYS cc_start: 0.7226 (mmtm) cc_final: 0.6989 (mmtm) REVERT: H 364 MET cc_start: 0.7720 (ptm) cc_final: 0.7248 (ptt) REVERT: H 375 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6782 (mt-10) outliers start: 79 outliers final: 48 residues processed: 431 average time/residue: 0.1537 time to fit residues: 104.2020 Evaluate side-chains 384 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 215 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN A 409 ASN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN G 218 GLN G 321 GLN H 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.177956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140207 restraints weight = 27645.744| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.30 r_work: 0.3670 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22393 Z= 0.190 Angle : 0.608 8.398 30497 Z= 0.323 Chirality : 0.043 0.161 3527 Planarity : 0.004 0.050 3643 Dihedral : 16.342 97.380 3468 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.19 % Allowed : 12.78 % Favored : 83.03 % 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: 0.14 (0.17), residues: 2532 helix: 1.13 (0.15), residues: 1210 sheet: -0.83 (0.23), residues: 529 loop : -0.67 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 106 TYR 0.024 0.002 TYR A 67 PHE 0.048 0.002 PHE A 443 TRP 0.014 0.002 TRP H 42 HIS 0.007 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (22393) covalent geometry : angle 0.60815 / 0.32 (30497) hydrogen bonds : bond 0.04463 / 2.88 ( 1118) hydrogen bonds : angle 5.00891 / 3.66 ( 3195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 359 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6967 (mtm) cc_final: 0.6239 (mtm) REVERT: A 178 MET cc_start: 0.7279 (mpp) cc_final: 0.6993 (mpp) REVERT: A 196 ASP cc_start: 0.8070 (t0) cc_final: 0.7630 (t0) REVERT: A 223 ILE cc_start: 0.8717 (mt) cc_final: 0.8431 (mt) REVERT: A 225 GLU cc_start: 0.8036 (tt0) cc_final: 0.7067 (mp0) REVERT: A 289 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6752 (mtmm) REVERT: A 290 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8041 (pt0) REVERT: A 456 PHE cc_start: 0.7516 (t80) cc_final: 0.7300 (t80) REVERT: B 38 LYS cc_start: 0.7601 (tmmm) cc_final: 0.7021 (mtmt) REVERT: B 87 ASP cc_start: 0.8274 (t70) cc_final: 0.8065 (p0) REVERT: B 272 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7803 (mmm160) REVERT: C 250 SER cc_start: 0.7352 (m) cc_final: 0.6913 (p) REVERT: D 207 GLN cc_start: 0.7917 (tp40) cc_final: 0.7353 (tp40) REVERT: D 353 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7611 (mp) REVERT: E 32 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6569 (mp10) REVERT: E 34 ARG cc_start: 0.7619 (ptp90) cc_final: 0.6477 (ptm160) REVERT: E 52 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.5432 (mpt90) REVERT: E 210 ARG cc_start: 0.6315 (tpp80) cc_final: 0.5801 (mmt180) REVERT: E 221 ARG cc_start: 0.7006 (mtp180) cc_final: 0.6524 (mtp-110) REVERT: E 240 MET cc_start: 0.6863 (mtt) cc_final: 0.6645 (mtp) REVERT: E 311 GLU cc_start: 0.7478 (mp0) cc_final: 0.7082 (tp30) REVERT: F 293 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7041 (tt0) REVERT: F 461 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.5596 (ptm160) REVERT: F 472 LYS cc_start: 0.7378 (mtmm) cc_final: 0.7149 (mtmm) REVERT: G 9 ASN cc_start: 0.8463 (m-40) cc_final: 0.8256 (m-40) REVERT: G 188 ASP cc_start: 0.7668 (m-30) cc_final: 0.7393 (m-30) REVERT: G 206 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8089 (tttm) REVERT: G 325 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8701 (mp0) REVERT: H 158 ASP cc_start: 0.7562 (p0) cc_final: 0.7320 (p0) REVERT: H 274 ASN cc_start: 0.7769 (t0) cc_final: 0.7547 (t0) REVERT: H 320 LYS cc_start: 0.7213 (mmtm) cc_final: 0.6896 (mmtm) REVERT: H 375 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7267 (mt-10) outliers start: 98 outliers final: 64 residues processed: 428 average time/residue: 0.1556 time to fit residues: 104.3308 Evaluate side-chains 390 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 321 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 47 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 32 optimal weight: 0.0970 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 156 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN C 12 ASN D 128 ASN E 224 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN F 263 HIS ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN H 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.178358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140747 restraints weight = 27638.657| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.28 r_work: 0.3679 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22393 Z= 0.149 Angle : 0.556 7.871 30497 Z= 0.297 Chirality : 0.042 0.161 3527 Planarity : 0.004 0.133 3643 Dihedral : 16.284 96.331 3462 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.45 % Allowed : 13.55 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2532 helix: 1.12 (0.15), residues: 1213 sheet: -0.98 (0.23), residues: 527 loop : -0.67 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 331 TYR 0.028 0.001 TYR B 15 PHE 0.030 0.002 PHE H 353 TRP 0.013 0.001 TRP H 42 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (22393) covalent geometry : angle 0.55639 / 0.30 (30497) hydrogen bonds : bond 0.04025 / 2.61 ( 1118) hydrogen bonds : angle 4.87757 / 3.56 ( 3195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 342 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7055 (mtm) cc_final: 0.6309 (mtm) REVERT: A 184 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7797 (mt) REVERT: A 196 ASP cc_start: 0.7957 (t0) cc_final: 0.7501 (t0) REVERT: A 223 ILE cc_start: 0.8740 (mt) cc_final: 0.8522 (mt) REVERT: A 225 GLU cc_start: 0.8031 (tt0) cc_final: 0.7165 (mp0) REVERT: A 306 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7405 (mt0) REVERT: B 38 LYS cc_start: 0.7648 (tmmm) cc_final: 0.7037 (mtmt) REVERT: B 129 ARG cc_start: 0.7816 (tpt170) cc_final: 0.7505 (tpp80) REVERT: B 272 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7704 (mmm160) REVERT: C 250 SER cc_start: 0.7364 (m) cc_final: 0.6916 (p) REVERT: D 207 GLN cc_start: 0.7875 (tp40) cc_final: 0.7307 (tp40) REVERT: E 32 GLN cc_start: 0.7307 (mm-40) cc_final: 0.6601 (mp10) REVERT: E 34 ARG cc_start: 0.7606 (ptp90) cc_final: 0.6445 (ptm160) REVERT: E 52 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.5231 (mpt90) REVERT: E 210 ARG cc_start: 0.6285 (tpp80) cc_final: 0.5804 (mmt180) REVERT: E 221 ARG cc_start: 0.7001 (mtp180) cc_final: 0.6529 (mtp-110) REVERT: E 311 GLU cc_start: 0.7399 (mp0) cc_final: 0.7067 (tp30) REVERT: F 111 MET cc_start: 0.5508 (mmm) cc_final: 0.5131 (mmt) REVERT: F 293 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7033 (tt0) REVERT: F 461 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5536 (ptm160) REVERT: F 472 LYS cc_start: 0.7467 (mtmm) cc_final: 0.7199 (mtmm) REVERT: G 9 ASN cc_start: 0.8496 (m-40) cc_final: 0.8271 (m-40) REVERT: G 96 MET cc_start: 0.6987 (tpt) cc_final: 0.6685 (tpt) REVERT: G 188 ASP cc_start: 0.7674 (m-30) cc_final: 0.7403 (m-30) REVERT: G 206 LYS cc_start: 0.8349 (mtpp) cc_final: 0.8046 (tttm) REVERT: G 325 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8734 (mp0) REVERT: H 158 ASP cc_start: 0.7574 (p0) cc_final: 0.7340 (p0) REVERT: H 375 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7312 (mt-10) outliers start: 104 outliers final: 78 residues processed: 410 average time/residue: 0.1447 time to fit residues: 92.9369 Evaluate side-chains 407 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 325 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 chunk 131 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 345 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.179175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141342 restraints weight = 27302.294| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.27 r_work: 0.3684 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22393 Z= 0.124 Angle : 0.533 8.372 30497 Z= 0.283 Chirality : 0.041 0.152 3527 Planarity : 0.004 0.100 3643 Dihedral : 16.226 96.928 3462 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.06 % Allowed : 14.45 % Favored : 81.49 % 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: 0.15 (0.17), residues: 2532 helix: 1.16 (0.15), residues: 1215 sheet: -0.92 (0.23), residues: 527 loop : -0.66 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.022 0.001 TYR A 67 PHE 0.032 0.002 PHE H 353 TRP 0.010 0.001 TRP H 42 HIS 0.006 0.001 HIS F 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (22393) covalent geometry : angle 0.53262 / 0.28 (30497) hydrogen bonds : bond 0.03690 / 2.40 ( 1118) hydrogen bonds : angle 4.74763 / 3.46 ( 3195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 343 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6944 (mtm) cc_final: 0.6226 (mtm) REVERT: A 178 MET cc_start: 0.7163 (mpp) cc_final: 0.6875 (mpp) REVERT: A 184 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7811 (mt) REVERT: A 196 ASP cc_start: 0.7957 (t0) cc_final: 0.7490 (t0) REVERT: A 225 GLU cc_start: 0.8060 (tt0) cc_final: 0.7325 (mt-10) REVERT: B 38 LYS cc_start: 0.7661 (tmmm) cc_final: 0.7040 (mtmt) REVERT: B 129 ARG cc_start: 0.7818 (tpt170) cc_final: 0.7508 (tpp80) REVERT: B 272 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7741 (mmm160) REVERT: C 250 SER cc_start: 0.7306 (m) cc_final: 0.6885 (p) REVERT: D 207 GLN cc_start: 0.7833 (tp40) cc_final: 0.7283 (tp40) REVERT: E 32 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6694 (mt0) REVERT: E 34 ARG cc_start: 0.7737 (ptp90) cc_final: 0.6590 (ptm160) REVERT: E 52 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5197 (mpt90) REVERT: E 104 ASN cc_start: 0.6420 (p0) cc_final: 0.5846 (t0) REVERT: E 210 ARG cc_start: 0.6275 (tpp80) cc_final: 0.5836 (mmt180) REVERT: E 221 ARG cc_start: 0.7083 (mtp180) cc_final: 0.6591 (mtp-110) REVERT: E 240 MET cc_start: 0.6692 (mtt) cc_final: 0.6474 (mtp) REVERT: E 311 GLU cc_start: 0.7351 (mp0) cc_final: 0.7062 (tp30) REVERT: F 111 MET cc_start: 0.5503 (mmm) cc_final: 0.5284 (mmt) REVERT: F 228 ILE cc_start: 0.6017 (OUTLIER) cc_final: 0.5757 (tp) REVERT: F 293 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7041 (tt0) REVERT: F 461 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.5481 (ptm160) REVERT: G 9 ASN cc_start: 0.8540 (m-40) cc_final: 0.8333 (m-40) REVERT: G 125 PHE cc_start: 0.7163 (m-10) cc_final: 0.6819 (m-10) REVERT: G 188 ASP cc_start: 0.7617 (m-30) cc_final: 0.7355 (m-30) REVERT: G 206 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8143 (tttm) REVERT: H 158 ASP cc_start: 0.7508 (p0) cc_final: 0.7261 (p0) REVERT: H 320 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7573 (mttp) REVERT: H 322 ILE cc_start: 0.8374 (tp) cc_final: 0.8038 (tt) REVERT: H 375 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7265 (mt-10) outliers start: 95 outliers final: 69 residues processed: 409 average time/residue: 0.1340 time to fit residues: 86.7192 Evaluate side-chains 395 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 320 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 2 optimal weight: 0.6980 chunk 240 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 0.0670 chunk 178 optimal weight: 4.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 260 ASN H 27 GLN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.181802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.147527 restraints weight = 27226.948| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.00 r_work: 0.3738 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22393 Z= 0.119 Angle : 0.524 7.767 30497 Z= 0.279 Chirality : 0.040 0.145 3527 Planarity : 0.004 0.084 3643 Dihedral : 16.177 97.578 3462 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.68 % Allowed : 15.52 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2532 helix: 1.28 (0.15), residues: 1207 sheet: -0.84 (0.23), residues: 522 loop : -0.65 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.020 0.001 TYR A 67 PHE 0.033 0.001 PHE H 353 TRP 0.010 0.001 TRP F 415 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (22393) covalent geometry : angle 0.52411 / 0.28 (30497) hydrogen bonds : bond 0.03559 / 2.31 ( 1118) hydrogen bonds : angle 4.66728 / 3.40 ( 3195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 329 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7012 (mtm) cc_final: 0.6270 (mtm) REVERT: A 178 MET cc_start: 0.7047 (mpp) cc_final: 0.6762 (mpp) REVERT: A 184 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7857 (mt) REVERT: A 196 ASP cc_start: 0.8014 (t0) cc_final: 0.7527 (t0) REVERT: A 225 GLU cc_start: 0.8119 (tt0) cc_final: 0.7197 (mp0) REVERT: A 306 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7409 (mt0) REVERT: B 38 LYS cc_start: 0.7662 (tmmm) cc_final: 0.7077 (mtmt) REVERT: B 119 MET cc_start: 0.8859 (ttp) cc_final: 0.8641 (ttp) REVERT: B 129 ARG cc_start: 0.7806 (tpt170) cc_final: 0.7523 (tpp80) REVERT: B 272 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7792 (mmm160) REVERT: C 250 SER cc_start: 0.7297 (m) cc_final: 0.6895 (p) REVERT: D 207 GLN cc_start: 0.7894 (tp40) cc_final: 0.7381 (tp40) REVERT: D 353 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7568 (mp) REVERT: E 32 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6662 (mt0) REVERT: E 34 ARG cc_start: 0.7750 (ptp90) cc_final: 0.6646 (ptm160) REVERT: E 52 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.5355 (mpt90) REVERT: E 104 ASN cc_start: 0.6541 (p0) cc_final: 0.5964 (t0) REVERT: E 210 ARG cc_start: 0.6298 (tpp80) cc_final: 0.5888 (mmt180) REVERT: E 221 ARG cc_start: 0.7179 (mtp180) cc_final: 0.6715 (mtp-110) REVERT: E 240 MET cc_start: 0.6708 (mtt) cc_final: 0.6498 (mtp) REVERT: E 311 GLU cc_start: 0.7361 (mp0) cc_final: 0.7081 (tp30) REVERT: F 119 MET cc_start: 0.6003 (tmm) cc_final: 0.5559 (tmm) REVERT: F 228 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5744 (tp) REVERT: F 293 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7106 (tt0) REVERT: F 461 ARG cc_start: 0.5999 (OUTLIER) cc_final: 0.5441 (ptm160) REVERT: F 472 LYS cc_start: 0.7547 (mtmm) cc_final: 0.7335 (mtmm) REVERT: G 168 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7838 (ttpt) REVERT: G 188 ASP cc_start: 0.7584 (m-30) cc_final: 0.7326 (m-30) REVERT: H 158 ASP cc_start: 0.7487 (p0) cc_final: 0.7243 (p0) REVERT: H 320 LYS cc_start: 0.7876 (mmtm) cc_final: 0.7582 (mttp) REVERT: H 322 ILE cc_start: 0.8408 (tp) cc_final: 0.8075 (tt) REVERT: H 375 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7156 (mt-10) outliers start: 86 outliers final: 70 residues processed: 388 average time/residue: 0.1392 time to fit residues: 85.0655 Evaluate side-chains 383 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 307 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 237 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 115 optimal weight: 0.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 260 ASN H 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.179607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142368 restraints weight = 27509.833| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.24 r_work: 0.3677 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22393 Z= 0.119 Angle : 0.523 8.120 30497 Z= 0.278 Chirality : 0.041 0.150 3527 Planarity : 0.004 0.067 3643 Dihedral : 16.090 97.836 3458 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.15 % Allowed : 15.65 % Favored : 80.21 % 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: 0.32 (0.17), residues: 2532 helix: 1.30 (0.15), residues: 1207 sheet: -0.76 (0.23), residues: 529 loop : -0.62 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 106 TYR 0.020 0.001 TYR A 67 PHE 0.030 0.001 PHE H 353 TRP 0.011 0.001 TRP F 415 HIS 0.010 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (22393) covalent geometry : angle 0.52349 / 0.28 (30497) hydrogen bonds : bond 0.03507 / 2.29 ( 1118) hydrogen bonds : angle 4.61968 / 3.37 ( 3195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 334 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: A 163 MET cc_start: 0.6806 (mtm) cc_final: 0.5821 (mtm) REVERT: A 164 GLU cc_start: 0.7206 (mp0) cc_final: 0.6917 (tp30) REVERT: A 178 MET cc_start: 0.6996 (mpp) cc_final: 0.6708 (mpp) REVERT: A 184 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7735 (mt) REVERT: A 196 ASP cc_start: 0.7936 (t0) cc_final: 0.7439 (t0) REVERT: A 302 ASP cc_start: 0.7398 (m-30) cc_final: 0.6889 (m-30) REVERT: A 306 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7436 (mt0) REVERT: B 13 GLU cc_start: 0.6644 (tp30) cc_final: 0.6232 (tp30) REVERT: B 38 LYS cc_start: 0.7679 (tmmm) cc_final: 0.7097 (mtmt) REVERT: B 67 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6070 (mm) REVERT: B 129 ARG cc_start: 0.7645 (tpt170) cc_final: 0.7292 (tpp80) REVERT: B 132 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7065 (mm-30) REVERT: B 272 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7626 (mmm160) REVERT: C 98 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7634 (ttpt) REVERT: C 250 SER cc_start: 0.7221 (m) cc_final: 0.6819 (p) REVERT: D 207 GLN cc_start: 0.7730 (tp40) cc_final: 0.7213 (tp40) REVERT: E 32 GLN cc_start: 0.7082 (mm-40) cc_final: 0.6536 (mt0) REVERT: E 34 ARG cc_start: 0.7665 (ptp90) cc_final: 0.5929 (ptm160) REVERT: E 104 ASN cc_start: 0.6611 (p0) cc_final: 0.5913 (t0) REVERT: E 135 TYR cc_start: 0.5031 (OUTLIER) cc_final: 0.4347 (m-80) REVERT: E 210 ARG cc_start: 0.6224 (tpp80) cc_final: 0.5826 (mmt180) REVERT: E 221 ARG cc_start: 0.7014 (mtp180) cc_final: 0.6553 (mtp-110) REVERT: E 240 MET cc_start: 0.6690 (mtt) cc_final: 0.6487 (mtp) REVERT: F 111 MET cc_start: 0.5909 (mmt) cc_final: 0.5681 (mmt) REVERT: F 119 MET cc_start: 0.5881 (tmm) cc_final: 0.5610 (tmm) REVERT: F 228 ILE cc_start: 0.5963 (OUTLIER) cc_final: 0.5668 (tp) REVERT: F 246 PHE cc_start: 0.7094 (t80) cc_final: 0.6665 (t80) REVERT: F 293 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6976 (tt0) REVERT: F 413 LYS cc_start: 0.7873 (mptt) cc_final: 0.7576 (mtpp) REVERT: F 461 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5282 (ptm160) REVERT: F 472 LYS cc_start: 0.7503 (mtmm) cc_final: 0.7263 (mtmm) REVERT: G 9 ASN cc_start: 0.8584 (m-40) cc_final: 0.8304 (m-40) REVERT: G 168 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7669 (ttpt) REVERT: G 188 ASP cc_start: 0.7612 (m-30) cc_final: 0.7370 (m-30) REVERT: H 158 ASP cc_start: 0.7313 (p0) cc_final: 0.7095 (p0) REVERT: H 320 LYS cc_start: 0.7770 (mmtm) cc_final: 0.7428 (mttp) REVERT: H 322 ILE cc_start: 0.8322 (tp) cc_final: 0.8002 (tt) REVERT: H 375 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7068 (mt-10) outliers start: 97 outliers final: 74 residues processed: 401 average time/residue: 0.1467 time to fit residues: 92.8606 Evaluate side-chains 391 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 310 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 148 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 HIS ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 HIS ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.177893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139842 restraints weight = 27551.912| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.28 r_work: 0.3665 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22393 Z= 0.143 Angle : 0.550 8.142 30497 Z= 0.290 Chirality : 0.041 0.145 3527 Planarity : 0.004 0.051 3643 Dihedral : 16.083 97.893 3458 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.76 % Allowed : 16.42 % Favored : 79.82 % 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: 0.26 (0.17), residues: 2532 helix: 1.23 (0.15), residues: 1209 sheet: -0.74 (0.23), residues: 529 loop : -0.65 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 149 TYR 0.017 0.001 TYR A 67 PHE 0.033 0.002 PHE H 353 TRP 0.012 0.001 TRP F 69 HIS 0.008 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (22393) covalent geometry : angle 0.54956 / 0.29 (30497) hydrogen bonds : bond 0.03673 / 2.39 ( 1118) hydrogen bonds : angle 4.59077 / 3.35 ( 3195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 331 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: A 163 MET cc_start: 0.7026 (mtm) cc_final: 0.6048 (mtm) REVERT: A 164 GLU cc_start: 0.7287 (mp0) cc_final: 0.6947 (tp30) REVERT: A 178 MET cc_start: 0.7069 (mpp) cc_final: 0.6732 (mpp) REVERT: A 184 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7839 (mt) REVERT: A 196 ASP cc_start: 0.8043 (t0) cc_final: 0.7591 (t0) REVERT: A 306 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7499 (mt0) REVERT: B 38 LYS cc_start: 0.7631 (tmmm) cc_final: 0.7050 (mtmt) REVERT: B 67 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6306 (mm) REVERT: B 129 ARG cc_start: 0.7860 (tpt170) cc_final: 0.7506 (tpp80) REVERT: B 243 SER cc_start: 0.8792 (m) cc_final: 0.8580 (p) REVERT: B 272 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7821 (mmm160) REVERT: C 98 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7751 (ttpt) REVERT: C 250 SER cc_start: 0.7360 (m) cc_final: 0.6883 (p) REVERT: D 207 GLN cc_start: 0.7885 (tp40) cc_final: 0.7344 (tp40) REVERT: D 255 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7826 (mt0) REVERT: D 318 PHE cc_start: 0.7090 (t80) cc_final: 0.6796 (t80) REVERT: E 32 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6214 (mt0) REVERT: E 34 ARG cc_start: 0.7759 (ptp90) cc_final: 0.5952 (ptm160) REVERT: E 52 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5130 (mpt90) REVERT: E 104 ASN cc_start: 0.6566 (p0) cc_final: 0.5920 (t0) REVERT: E 135 TYR cc_start: 0.5479 (OUTLIER) cc_final: 0.4660 (m-80) REVERT: E 197 GLU cc_start: 0.6425 (mt-10) cc_final: 0.6165 (mp0) REVERT: E 221 ARG cc_start: 0.7200 (mtp180) cc_final: 0.6694 (mtp-110) REVERT: E 240 MET cc_start: 0.6809 (mtt) cc_final: 0.6589 (mtp) REVERT: F 228 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5627 (tp) REVERT: F 246 PHE cc_start: 0.7145 (t80) cc_final: 0.6730 (t80) REVERT: F 293 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7101 (tt0) REVERT: F 413 LYS cc_start: 0.7912 (mptt) cc_final: 0.7624 (mtpp) REVERT: F 461 ARG cc_start: 0.5997 (OUTLIER) cc_final: 0.5184 (ptm160) REVERT: G 9 ASN cc_start: 0.8752 (m-40) cc_final: 0.8530 (m-40) REVERT: G 168 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7772 (ttpt) REVERT: G 188 ASP cc_start: 0.7627 (m-30) cc_final: 0.7374 (m-30) REVERT: G 321 GLN cc_start: 0.7903 (pm20) cc_final: 0.7572 (pm20) REVERT: H 158 ASP cc_start: 0.7543 (p0) cc_final: 0.7263 (p0) REVERT: H 320 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7466 (mttp) REVERT: H 322 ILE cc_start: 0.8425 (tp) cc_final: 0.8104 (tt) REVERT: H 375 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7253 (mt-10) outliers start: 88 outliers final: 69 residues processed: 389 average time/residue: 0.1503 time to fit residues: 92.2674 Evaluate side-chains 390 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 313 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 40 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 144 optimal weight: 0.0970 chunk 203 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 156 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 HIS ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.179151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141354 restraints weight = 27511.079| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.26 r_work: 0.3681 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22393 Z= 0.118 Angle : 0.541 13.357 30497 Z= 0.284 Chirality : 0.041 0.145 3527 Planarity : 0.004 0.052 3643 Dihedral : 16.030 96.848 3455 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.51 % Allowed : 16.80 % Favored : 79.69 % 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: 0.33 (0.17), residues: 2532 helix: 1.27 (0.15), residues: 1215 sheet: -0.71 (0.23), residues: 530 loop : -0.62 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 450 TYR 0.019 0.001 TYR A 67 PHE 0.032 0.001 PHE H 353 TRP 0.017 0.001 TRP F 290 HIS 0.011 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (22393) covalent geometry : angle 0.54111 / 0.28 (30497) hydrogen bonds : bond 0.03468 / 2.26 ( 1118) hydrogen bonds : angle 4.53267 / 3.31 ( 3195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 323 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6997 (mtm) cc_final: 0.6374 (ttp) REVERT: A 164 GLU cc_start: 0.7322 (mp0) cc_final: 0.7028 (tp30) REVERT: A 178 MET cc_start: 0.7036 (mpp) cc_final: 0.6694 (mpp) REVERT: A 184 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7853 (mt) REVERT: A 196 ASP cc_start: 0.8028 (t0) cc_final: 0.7660 (t0) REVERT: A 306 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7450 (mt0) REVERT: B 38 LYS cc_start: 0.7608 (tmmm) cc_final: 0.7042 (mtmt) REVERT: B 67 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6291 (mm) REVERT: B 129 ARG cc_start: 0.7849 (tpt170) cc_final: 0.7544 (tpp80) REVERT: B 243 SER cc_start: 0.8809 (m) cc_final: 0.8596 (p) REVERT: B 272 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7807 (mmm160) REVERT: B 321 ASN cc_start: 0.7674 (m110) cc_final: 0.7347 (m-40) REVERT: C 98 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7714 (ttpt) REVERT: C 250 SER cc_start: 0.7361 (m) cc_final: 0.6910 (p) REVERT: D 207 GLN cc_start: 0.7872 (tp40) cc_final: 0.7342 (tp40) REVERT: D 318 PHE cc_start: 0.7070 (t80) cc_final: 0.6801 (t80) REVERT: E 32 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6307 (mt0) REVERT: E 34 ARG cc_start: 0.7746 (ptp90) cc_final: 0.5933 (ptm160) REVERT: E 52 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.5130 (mpt90) REVERT: E 104 ASN cc_start: 0.6582 (p0) cc_final: 0.5868 (t0) REVERT: E 135 TYR cc_start: 0.5395 (OUTLIER) cc_final: 0.4603 (m-80) REVERT: E 210 ARG cc_start: 0.6353 (tpp80) cc_final: 0.5932 (mmt180) REVERT: E 221 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6738 (mtp-110) REVERT: E 240 MET cc_start: 0.6785 (mtt) cc_final: 0.6580 (mtp) REVERT: F 8 ASN cc_start: 0.6891 (t0) cc_final: 0.6671 (t0) REVERT: F 111 MET cc_start: 0.5692 (mmt) cc_final: 0.5279 (mmt) REVERT: F 228 ILE cc_start: 0.5897 (OUTLIER) cc_final: 0.5553 (tp) REVERT: F 246 PHE cc_start: 0.7124 (t80) cc_final: 0.6682 (t80) REVERT: F 293 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6964 (tt0) REVERT: F 461 ARG cc_start: 0.5952 (OUTLIER) cc_final: 0.5086 (ptm160) REVERT: F 472 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7708 (mtmm) REVERT: G 9 ASN cc_start: 0.8750 (m-40) cc_final: 0.8534 (m-40) REVERT: G 168 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7754 (ttpt) REVERT: G 188 ASP cc_start: 0.7623 (m-30) cc_final: 0.7372 (m-30) REVERT: G 223 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7441 (p0) REVERT: G 321 GLN cc_start: 0.7847 (pm20) cc_final: 0.7522 (pm20) REVERT: H 158 ASP cc_start: 0.7524 (p0) cc_final: 0.7248 (p0) REVERT: H 320 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7324 (mttp) REVERT: H 322 ILE cc_start: 0.8419 (tp) cc_final: 0.8103 (tt) REVERT: H 375 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7226 (mt-10) outliers start: 82 outliers final: 69 residues processed: 377 average time/residue: 0.1497 time to fit residues: 88.3858 Evaluate side-chains 392 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 315 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 202 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 176 optimal weight: 7.9990 chunk 231 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 218 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 HIS ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 180 ASN D 255 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.178914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140838 restraints weight = 27621.380| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.30 r_work: 0.3678 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22393 Z= 0.123 Angle : 0.542 13.166 30497 Z= 0.285 Chirality : 0.041 0.148 3527 Planarity : 0.004 0.050 3643 Dihedral : 16.011 96.980 3455 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.42 % Allowed : 16.80 % Favored : 79.78 % 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: 0.35 (0.17), residues: 2532 helix: 1.28 (0.15), residues: 1214 sheet: -0.66 (0.23), residues: 532 loop : -0.62 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 450 TYR 0.018 0.001 TYR A 67 PHE 0.030 0.001 PHE H 353 TRP 0.016 0.001 TRP F 69 HIS 0.007 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (22393) covalent geometry : angle 0.54203 / 0.29 (30497) hydrogen bonds : bond 0.03475 / 2.27 ( 1118) hydrogen bonds : angle 4.50570 / 3.29 ( 3195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 329 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6934 (mtm) cc_final: 0.6306 (ttp) REVERT: A 164 GLU cc_start: 0.7234 (mp0) cc_final: 0.6932 (tp30) REVERT: A 184 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7840 (mp) REVERT: A 196 ASP cc_start: 0.8014 (t0) cc_final: 0.7637 (t0) REVERT: A 302 ASP cc_start: 0.7404 (m-30) cc_final: 0.6883 (m-30) REVERT: A 306 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7383 (mt0) REVERT: B 38 LYS cc_start: 0.7533 (tmmm) cc_final: 0.6994 (mtmt) REVERT: B 67 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6206 (mm) REVERT: B 129 ARG cc_start: 0.7813 (tpt170) cc_final: 0.7482 (tpp80) REVERT: B 243 SER cc_start: 0.8867 (m) cc_final: 0.8641 (p) REVERT: B 272 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7778 (mmm160) REVERT: B 321 ASN cc_start: 0.7688 (m110) cc_final: 0.7348 (m-40) REVERT: C 98 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7603 (ttpt) REVERT: C 250 SER cc_start: 0.7294 (m) cc_final: 0.6827 (p) REVERT: D 207 GLN cc_start: 0.7891 (tp40) cc_final: 0.7331 (tp40) REVERT: D 318 PHE cc_start: 0.7131 (t80) cc_final: 0.6864 (t80) REVERT: E 32 GLN cc_start: 0.6905 (mm-40) cc_final: 0.6161 (mt0) REVERT: E 34 ARG cc_start: 0.7753 (ptp90) cc_final: 0.5939 (ptm160) REVERT: E 52 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.4970 (mpt90) REVERT: E 104 ASN cc_start: 0.6466 (p0) cc_final: 0.5749 (t0) REVERT: E 135 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.4541 (m-80) REVERT: E 221 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6487 (mtp-110) REVERT: E 240 MET cc_start: 0.6588 (mtt) cc_final: 0.6385 (mtp) REVERT: F 8 ASN cc_start: 0.6848 (t0) cc_final: 0.6621 (t0) REVERT: F 111 MET cc_start: 0.5694 (mmt) cc_final: 0.5336 (mmt) REVERT: F 228 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5617 (tp) REVERT: F 246 PHE cc_start: 0.7141 (t80) cc_final: 0.6711 (t80) REVERT: F 293 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7076 (tt0) REVERT: F 413 LYS cc_start: 0.7885 (mptt) cc_final: 0.7588 (mtpp) REVERT: F 461 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5003 (ptm160) REVERT: F 472 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7698 (mtmm) REVERT: G 9 ASN cc_start: 0.8712 (m-40) cc_final: 0.8511 (m-40) REVERT: G 168 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7662 (ttpt) REVERT: G 188 ASP cc_start: 0.7662 (m-30) cc_final: 0.7420 (m-30) REVERT: G 223 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7397 (p0) REVERT: G 321 GLN cc_start: 0.7900 (pm20) cc_final: 0.7562 (pm20) REVERT: H 158 ASP cc_start: 0.7541 (p0) cc_final: 0.7235 (p0) REVERT: H 322 ILE cc_start: 0.8426 (tp) cc_final: 0.8092 (tt) REVERT: H 375 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7293 (mt-10) outliers start: 80 outliers final: 67 residues processed: 382 average time/residue: 0.1561 time to fit residues: 93.7969 Evaluate side-chains 389 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 314 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 112 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 109 optimal weight: 0.0040 chunk 172 optimal weight: 8.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS A 368 ASN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.179188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141992 restraints weight = 27560.354| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.24 r_work: 0.3674 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22393 Z= 0.120 Angle : 0.546 13.141 30497 Z= 0.286 Chirality : 0.041 0.153 3527 Planarity : 0.004 0.050 3643 Dihedral : 15.988 96.069 3455 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.38 % Allowed : 16.93 % Favored : 79.69 % 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: 0.39 (0.17), residues: 2532 helix: 1.30 (0.15), residues: 1214 sheet: -0.62 (0.23), residues: 531 loop : -0.59 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 450 TYR 0.019 0.001 TYR A 67 PHE 0.031 0.001 PHE H 353 TRP 0.018 0.001 TRP F 69 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22393) covalent geometry : angle 0.54589 / 0.29 (30497) hydrogen bonds : bond 0.03414 / 2.23 ( 1118) hydrogen bonds : angle 4.46456 / 3.26 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6072.31 seconds wall clock time: 104 minutes 55.98 seconds (6295.98 seconds total)