Starting phenix.real_space_refine on Sat Aug 23 13:10:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpl_34932/08_2025/8hpl_34932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpl_34932/08_2025/8hpl_34932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hpl_34932/08_2025/8hpl_34932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpl_34932/08_2025/8hpl_34932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hpl_34932/08_2025/8hpl_34932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpl_34932/08_2025/8hpl_34932.map" } resolution = 4.29 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= 0.009 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 16 5.16 5 C 7576 2.51 5 N 2025 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12013 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1941 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 14, 'TRANS': 267} Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ARG:plan': 7, 'TYR:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1882 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 16, 'TRANS': 253} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2547 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 475 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 16, 'ASP:plan': 4, 'GLN:plan1': 5, 'ASN:plan1': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 209 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2554 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 18, 'GLN:plan1': 5, 'TYR:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 220 Chain: "E" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3004 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 31, 'TRANS': 405} Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TYR:plan': 4, 'ARG:plan': 15, 'GLN:plan1': 5, 'ASP:plan': 6, 'GLU:plan': 10, 'TRP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 219 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.52, per 1000 atoms: 0.21 Number of scatterers: 12013 At special positions: 0 Unit cell: (82.82, 95.94, 168.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 6 15.00 O 2390 8.00 N 2025 7.00 C 7576 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 Links applied ALPHA1-1 " GLC G 1 " - " GLC G 2 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 467.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3258 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 13 sheets defined 55.1% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 17 through 50 Proline residue: A 30 - end of helix removed outlier: 3.948A pdb=" N TYR A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 68 through 76 removed outlier: 3.940A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 111 removed outlier: 3.627A pdb=" N VAL A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.671A pdb=" N ALA A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 162 through 192 removed outlier: 3.509A pdb=" N ILE A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Proline residue: A 179 - end of helix removed outlier: 3.852A pdb=" N ALA A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 206 through 236 Proline residue: A 217 - end of helix Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.639A pdb=" N ASN A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 292 removed outlier: 3.697A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 35 Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.915A pdb=" N LYS B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 93 removed outlier: 3.699A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.878A pdb=" N LEU B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 132 removed outlier: 4.085A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 137 through 164 removed outlier: 3.812A pdb=" N LEU B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.989A pdb=" N LYS B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 208 removed outlier: 3.616A pdb=" N LYS B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Proline residue: B 189 - end of helix Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 242 through 273 Proline residue: B 255 - end of helix removed outlier: 3.886A pdb=" N ILE B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 71 through 75 removed outlier: 4.068A pdb=" N LYS C 75 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 127 through 132 removed outlier: 4.115A pdb=" N LEU C 132 " --> pdb=" O SER C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.649A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 165 through 169 removed outlier: 4.491A pdb=" N ASN C 168 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 189 removed outlier: 3.789A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 4.491A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 266 through 275 removed outlier: 3.582A pdb=" N LYS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 305 removed outlier: 4.185A pdb=" N ARG C 304 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 345 Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 77 through 80 Processing helix chain 'D' and resid 96 through 108 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.681A pdb=" N LEU D 139 " --> pdb=" O PRO D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 154 Processing helix chain 'D' and resid 170 through 189 Processing helix chain 'D' and resid 198 through 205 removed outlier: 4.476A pdb=" N ALA D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 266 through 275 Processing helix chain 'D' and resid 299 through 305 removed outlier: 4.179A pdb=" N ALA D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 374 through 377 Processing helix chain 'E' and resid 40 through 55 Processing helix chain 'E' and resid 69 through 83 removed outlier: 3.514A pdb=" N LEU E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 127 through 134 Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.839A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 241 Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.982A pdb=" N GLN E 252 " --> pdb=" O SER E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 275 through 287 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'E' and resid 359 through 371 Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 404 through 414 Processing helix chain 'E' and resid 423 through 436 removed outlier: 3.585A pdb=" N THR E 434 " --> pdb=" O ARG E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 459 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 11 removed outlier: 4.383A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR C 10 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS C 25 " --> pdb=" O THR C 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.718A pdb=" N ALA C 83 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASP C 163 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C 85 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE C 160 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N VAL C 195 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 213 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 245 through 250 removed outlier: 3.940A pdb=" N PHE C 247 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 284 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 292 Processing sheet with id=AA5, first strand: chain 'C' and resid 314 through 316 Processing sheet with id=AA6, first strand: chain 'D' and resid 27 through 31 removed outlier: 7.046A pdb=" N MET D 29 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASP D 7 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE D 31 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL D 5 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 9 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER D 62 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 83 removed outlier: 6.767A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASP D 163 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE D 36 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL D 210 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 40 " --> pdb=" O MET D 212 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 263 through 264 removed outlier: 3.942A pdb=" N ILE D 282 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 291 through 292 Processing sheet with id=AB1, first strand: chain 'D' and resid 314 through 316 removed outlier: 3.665A pdb=" N ILE D 314 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 60 through 66 removed outlier: 11.033A pdb=" N ASP E 94 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY E 347 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR E 147 " --> pdb=" O GLY E 347 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 Processing sheet with id=AB4, first strand: chain 'E' and resid 184 through 186 removed outlier: 7.009A pdb=" N TRP E 184 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL E 271 " --> pdb=" O TRP E 184 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA E 186 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA E 268 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN E 272 " --> pdb=" O LEU E 151 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2216 1.31 - 1.44: 2864 1.44 - 1.57: 7124 1.57 - 1.69: 10 1.69 - 1.82: 28 Bond restraints: 12242 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.82e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.77e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C5 GLC G 1 " pdb=" O5 GLC G 1 " ideal model delta sigma weight residual 1.415 1.548 -0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 12237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 16325 3.90 - 7.80: 527 7.80 - 11.70: 11 11.70 - 15.60: 0 15.60 - 19.50: 4 Bond angle restraints: 16867 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.37 19.50 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.74 16.09 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C5 ATP D 501 " pdb=" C4 ATP D 501 " pdb=" N3 ATP D 501 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.62e+01 ... (remaining 16862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 6731 16.77 - 33.55: 426 33.55 - 50.32: 96 50.32 - 67.09: 13 67.09 - 83.87: 12 Dihedral angle restraints: 7278 sinusoidal: 2238 harmonic: 5040 Sorted by residual: dihedral pdb=" CA ARG E 64 " pdb=" C ARG E 64 " pdb=" N ASN E 65 " pdb=" CA ASN E 65 " ideal model delta harmonic sigma weight residual 180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ALA B 94 " pdb=" C ALA B 94 " pdb=" N VAL B 95 " pdb=" CA VAL B 95 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA TYR B 93 " pdb=" C TYR B 93 " pdb=" N ALA B 94 " pdb=" CA ALA B 94 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 7275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1433 0.087 - 0.173: 521 0.173 - 0.260: 103 0.260 - 0.346: 17 0.346 - 0.433: 2 Chirality restraints: 2076 Sorted by residual: chirality pdb=" C1 GLC G 1 " pdb=" C2 GLC G 1 " pdb=" O5 GLC G 1 " pdb=" O1 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.80e+01 chirality pdb=" CA THR A 178 " pdb=" N THR A 178 " pdb=" C THR A 178 " pdb=" CB THR A 178 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA SER C 309 " pdb=" N SER C 309 " pdb=" C SER C 309 " pdb=" CB SER C 309 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 2073 not shown) Planarity restraints: 2225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 79 " 0.188 2.00e-02 2.50e+03 9.58e-02 2.30e+02 pdb=" CG TRP A 79 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 79 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 79 " -0.093 2.00e-02 2.50e+03 pdb=" NE1 TRP A 79 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TRP A 79 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 79 " -0.134 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 79 " 0.104 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 79 " -0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP A 79 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 207 " -0.116 2.00e-02 2.50e+03 5.55e-02 7.71e+01 pdb=" CG TRP B 207 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 207 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 207 " 0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP B 207 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP B 207 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 207 " 0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 207 " -0.055 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 207 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 207 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 424 " -0.113 2.00e-02 2.50e+03 6.11e-02 7.47e+01 pdb=" CG TYR E 424 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 424 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR E 424 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR E 424 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR E 424 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 424 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR E 424 " -0.093 2.00e-02 2.50e+03 ... (remaining 2222 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1749 2.80 - 3.32: 14270 3.32 - 3.85: 19949 3.85 - 4.37: 22593 4.37 - 4.90: 36453 Nonbonded interactions: 95014 Sorted by model distance: nonbonded pdb=" OG SER C 309 " pdb=" CG GLN C 367 " model vdw 2.269 3.440 nonbonded pdb=" O LEU A 51 " pdb=" N GLY A 66 " model vdw 2.320 3.120 nonbonded pdb=" CB LEU A 51 " pdb=" O GLY A 66 " model vdw 2.342 3.440 nonbonded pdb=" O ILE A 237 " pdb=" OG SER A 255 " model vdw 2.352 3.040 nonbonded pdb=" OD2 ASP C 313 " pdb=" NE2 HIS C 325 " model vdw 2.371 3.120 ... (remaining 95009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 36 or (resid 37 through 39 and (name N or name C \ A or name C or name O or name CB )) or resid 40 through 73 or (resid 74 through \ 76 and (name N or name CA or name C or name O or name CB )) or resid 77 through \ 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or resi \ d 86 through 88 or (resid 89 through 90 and (name N or name CA or name C or name \ O or name CB )) or resid 91 through 93 or (resid 94 and (name N or name CA or n \ ame C or name O or name CB )) or resid 95 through 132 or (resid 133 through 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 14 \ 4 or (resid 145 through 149 and (name N or name CA or name C or name O or name C \ B )) or resid 150 through 159 or (resid 160 and (name N or name CA or name C or \ name O or name CB )) or resid 161 through 193 or (resid 194 and (name N or name \ CA or name C or name O or name CB )) or resid 195 through 219 or (resid 220 and \ (name N or name CA or name C or name O or name CB )) or resid 221 through 274 or \ (resid 275 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 6 through 328 or (resid 329 and (name N or name CA or name C or name O or name C \ B )) or resid 330 through 362 or (resid 363 and (name N or name CA or name C or \ name O or name CB )) or resid 364 through 376 or (resid 377 and (name N or name \ CA or name C or name O or name CB )) or resid 378 through 386 or (resid 387 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 th \ rough 501)) selection = (chain 'D' and (resid 2 through 4 or (resid 5 through 6 and (name N or name CA o \ r name C or name O or name CB )) or resid 7 through 34 or (resid 35 through 39 a \ nd (name N or name CA or name C or name O or name CB )) or resid 40 through 63 o \ r (resid 64 through 67 and (name N or name CA or name C or name O or name CB )) \ or resid 68 through 69 or (resid 70 through 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 78 or (resid 79 through 81 and (name \ N or name CA or name C or name O or name CB )) or resid 82 through 106 or (resi \ d 107 through 109 and (name N or name CA or name C or name O or name CB )) or re \ sid 110 through 125 or (resid 126 and (name N or name CA or name C or name O or \ name CB )) or resid 127 through 130 or (resid 131 through 135 and (name N or nam \ e CA or name C or name O or name CB )) or resid 136 through 148 or (resid 149 an \ d (name N or name CA or name C or name O or name CB )) or (resid 150 through 153 \ and (name N or name CA or name C or name O or name CB )) or resid 154 through 1 \ 75 or (resid 176 through 179 and (name N or name CA or name C or name O or name \ CB )) or resid 180 through 195 or (resid 196 and (name N or name CA or name C or \ name O or name CB )) or resid 197 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 through 226 or (resid 227 and \ (name N or name CA or name C or name O or name CB )) or resid 228 through 299 o \ r (resid 300 through 301 and (name N or name CA or name C or name O or name CB ) \ ) or resid 302 through 379 or (resid 380 and (name N or name CA or name C or nam \ e O or name CB )) or resid 381 through 383 or (resid 384 and (name N or name CA \ or name C or name O or name CB )) or resid 385 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.640 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.012 0.133 12243 Z= 0.722 Angle : 1.777 19.500 16870 Z= 1.209 Chirality : 0.091 0.433 2076 Planarity : 0.012 0.096 2225 Dihedral : 12.898 83.868 4020 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Cbeta Deviations : 0.06 % 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 aren not related in a simple way. whole: -2.47 (0.18), residues: 1743 helix: -1.29 (0.15), residues: 847 sheet: -1.83 (0.43), residues: 127 loop : -1.90 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 183 TYR 0.113 0.018 TYR E 424 PHE 0.064 0.013 PHE E 398 TRP 0.188 0.020 TRP A 79 HIS 0.018 0.004 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.01172 (12242) covalent geometry : angle 1.77664 (16867) hydrogen bonds : bond 0.16194 ( 693) hydrogen bonds : angle 7.92553 ( 1947) glycosidic custom : bond 0.02878 ( 1) glycosidic custom : angle 2.16030 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.288 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8278 (tpt) cc_final: 0.8023 (tpt) REVERT: A 267 ASN cc_start: 0.9095 (t0) cc_final: 0.8879 (t0) REVERT: A 287 PHE cc_start: 0.9358 (t80) cc_final: 0.9114 (t80) REVERT: B 185 LYS cc_start: 0.9232 (mttt) cc_final: 0.8727 (tppt) REVERT: C 170 ASP cc_start: 0.9022 (p0) cc_final: 0.8495 (p0) REVERT: C 172 LYS cc_start: 0.9453 (mttp) cc_final: 0.9101 (mppt) REVERT: C 194 TYR cc_start: 0.8182 (t80) cc_final: 0.7975 (t80) REVERT: C 218 GLN cc_start: 0.8770 (mm110) cc_final: 0.8272 (mm-40) REVERT: C 284 VAL cc_start: 0.9108 (m) cc_final: 0.8543 (t) REVERT: C 326 PHE cc_start: 0.9539 (p90) cc_final: 0.9143 (p90) REVERT: D 139 LEU cc_start: 0.7995 (mt) cc_final: 0.7095 (tp) REVERT: D 164 GLN cc_start: 0.8974 (mt0) cc_final: 0.8625 (mm-40) REVERT: D 177 MET cc_start: 0.9446 (mtp) cc_final: 0.9178 (ttm) REVERT: D 195 VAL cc_start: 0.7767 (p) cc_final: 0.7383 (t) REVERT: D 218 GLN cc_start: 0.9176 (mm110) cc_final: 0.8644 (mp10) REVERT: D 276 GLN cc_start: 0.8262 (mm110) cc_final: 0.7869 (mm-40) REVERT: D 316 GLU cc_start: 0.9497 (pm20) cc_final: 0.9276 (pm20) REVERT: D 353 ILE cc_start: 0.8707 (mt) cc_final: 0.8496 (mt) REVERT: E 86 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8894 (mmmt) REVERT: E 198 TRP cc_start: 0.8989 (t60) cc_final: 0.8781 (t60) REVERT: E 259 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7618 (ptp-110) REVERT: E 276 VAL cc_start: 0.8331 (p) cc_final: 0.7924 (p) REVERT: E 388 VAL cc_start: 0.8774 (m) cc_final: 0.8556 (p) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.0919 time to fit residues: 40.1030 Evaluate side-chains 201 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 261 ASN C 197 HIS D 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060297 restraints weight = 62935.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.061809 restraints weight = 42316.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.062922 restraints weight = 32054.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063678 restraints weight = 25600.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.064057 restraints weight = 21812.416| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12243 Z= 0.158 Angle : 0.695 7.640 16870 Z= 0.377 Chirality : 0.045 0.190 2076 Planarity : 0.005 0.037 2225 Dihedral : 8.470 87.900 1927 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.12 % 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 aren not related in a simple way. whole: -0.91 (0.19), residues: 1743 helix: 0.28 (0.17), residues: 871 sheet: -1.77 (0.36), residues: 165 loop : -1.34 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 251 TYR 0.020 0.002 TYR B 155 PHE 0.023 0.002 PHE E 317 TRP 0.020 0.002 TRP B 207 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00311 (12242) covalent geometry : angle 0.69514 (16867) hydrogen bonds : bond 0.05147 ( 693) hydrogen bonds : angle 5.43357 ( 1947) glycosidic custom : bond 0.00958 ( 1) glycosidic custom : angle 0.58253 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 PHE cc_start: 0.9071 (m-80) cc_final: 0.8849 (m-80) REVERT: A 287 PHE cc_start: 0.9410 (t80) cc_final: 0.9114 (t80) REVERT: A 288 ILE cc_start: 0.9404 (mm) cc_final: 0.9191 (mm) REVERT: B 116 PHE cc_start: 0.8914 (t80) cc_final: 0.8110 (t80) REVERT: B 185 LYS cc_start: 0.9220 (mttt) cc_final: 0.8809 (tppt) REVERT: C 170 ASP cc_start: 0.9017 (p0) cc_final: 0.8665 (p0) REVERT: C 172 LYS cc_start: 0.9482 (mttp) cc_final: 0.9161 (mppt) REVERT: C 218 GLN cc_start: 0.8642 (mm110) cc_final: 0.8151 (mm-40) REVERT: C 234 PHE cc_start: 0.9283 (t80) cc_final: 0.8662 (t80) REVERT: C 284 VAL cc_start: 0.9171 (m) cc_final: 0.8884 (t) REVERT: C 318 LEU cc_start: 0.9498 (mp) cc_final: 0.9200 (mp) REVERT: D 8 ARG cc_start: 0.9629 (mmt90) cc_final: 0.9204 (mmm-85) REVERT: D 164 GLN cc_start: 0.8900 (mt0) cc_final: 0.8554 (mm110) REVERT: D 276 GLN cc_start: 0.8120 (mm110) cc_final: 0.7515 (mp10) REVERT: D 380 PHE cc_start: 0.9473 (m-80) cc_final: 0.9025 (m-80) REVERT: E 66 LEU cc_start: 0.9089 (mp) cc_final: 0.8741 (mp) REVERT: E 198 TRP cc_start: 0.8995 (t60) cc_final: 0.8783 (t60) REVERT: E 259 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7483 (ptt180) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.0760 time to fit residues: 31.6606 Evaluate side-chains 190 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 16 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 117 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 HIS D 218 GLN D 337 GLN E 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.082431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.058581 restraints weight = 62564.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060210 restraints weight = 41918.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061305 restraints weight = 31082.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.062080 restraints weight = 24924.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.062609 restraints weight = 21245.300| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12243 Z= 0.164 Angle : 0.644 7.669 16870 Z= 0.340 Chirality : 0.043 0.184 2076 Planarity : 0.005 0.044 2225 Dihedral : 7.884 89.006 1927 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.12 % 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 aren not related in a simple way. whole: -0.61 (0.20), residues: 1743 helix: 0.51 (0.17), residues: 888 sheet: -1.53 (0.38), residues: 164 loop : -1.23 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 311 TYR 0.024 0.002 TYR E 275 PHE 0.018 0.002 PHE E 317 TRP 0.015 0.002 TRP B 207 HIS 0.008 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00334 (12242) covalent geometry : angle 0.64372 (16867) hydrogen bonds : bond 0.04291 ( 693) hydrogen bonds : angle 5.04027 ( 1947) glycosidic custom : bond 0.00001 ( 1) glycosidic custom : angle 0.91500 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.546 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: symmetry clash REVERT: A 267 ASN cc_start: 0.9141 (t0) cc_final: 0.8719 (t0) REVERT: A 288 ILE cc_start: 0.9397 (mm) cc_final: 0.9193 (mm) REVERT: B 185 LYS cc_start: 0.9196 (mttt) cc_final: 0.8861 (tppt) REVERT: C 168 ASN cc_start: 0.9463 (t0) cc_final: 0.9026 (t0) REVERT: C 170 ASP cc_start: 0.9055 (p0) cc_final: 0.8612 (p0) REVERT: C 172 LYS cc_start: 0.9516 (mttp) cc_final: 0.9186 (mppt) REVERT: C 234 PHE cc_start: 0.9248 (t80) cc_final: 0.8587 (t80) REVERT: D 8 ARG cc_start: 0.9615 (mmt90) cc_final: 0.9172 (mmm-85) REVERT: D 164 GLN cc_start: 0.9053 (mt0) cc_final: 0.8545 (mm110) REVERT: D 276 GLN cc_start: 0.8135 (mm110) cc_final: 0.7591 (mp10) REVERT: D 380 PHE cc_start: 0.9381 (m-80) cc_final: 0.9048 (m-80) REVERT: E 35 TYR cc_start: 0.8249 (m-80) cc_final: 0.7347 (m-80) REVERT: E 259 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7592 (ptt180) REVERT: E 275 TYR cc_start: 0.8550 (p90) cc_final: 0.8061 (p90) REVERT: E 319 ILE cc_start: 0.9556 (mt) cc_final: 0.9328 (tp) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.0764 time to fit residues: 30.0801 Evaluate side-chains 187 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.0470 chunk 100 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 HIS ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.083601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060569 restraints weight = 62873.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.062275 restraints weight = 41374.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.063412 restraints weight = 30222.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.064194 restraints weight = 23805.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.064764 restraints weight = 20065.485| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12243 Z= 0.142 Angle : 0.607 6.928 16870 Z= 0.317 Chirality : 0.043 0.173 2076 Planarity : 0.004 0.043 2225 Dihedral : 7.371 81.669 1927 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.10 % Allowed : 2.23 % Favored : 97.67 % 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 aren not related in a simple way. whole: -0.36 (0.20), residues: 1743 helix: 0.73 (0.17), residues: 887 sheet: -1.40 (0.38), residues: 161 loop : -1.15 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.021 0.002 TYR C 323 PHE 0.016 0.001 PHE B 61 TRP 0.010 0.001 TRP B 207 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00292 (12242) covalent geometry : angle 0.60663 (16867) hydrogen bonds : bond 0.03877 ( 693) hydrogen bonds : angle 4.73658 ( 1947) glycosidic custom : bond 0.00033 ( 1) glycosidic custom : angle 0.78442 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 ILE cc_start: 0.9382 (mm) cc_final: 0.9161 (mm) REVERT: B 136 ASP cc_start: 0.8315 (p0) cc_final: 0.8104 (m-30) REVERT: B 185 LYS cc_start: 0.9220 (mttt) cc_final: 0.8897 (tppt) REVERT: C 168 ASN cc_start: 0.9499 (t0) cc_final: 0.9033 (t0) REVERT: C 172 LYS cc_start: 0.9505 (mttp) cc_final: 0.9221 (mppt) REVERT: C 197 HIS cc_start: 0.8564 (t-90) cc_final: 0.8346 (t70) REVERT: C 234 PHE cc_start: 0.9283 (t80) cc_final: 0.8640 (t80) REVERT: D 8 ARG cc_start: 0.9601 (mmt90) cc_final: 0.9158 (mmm-85) REVERT: D 164 GLN cc_start: 0.8960 (mt0) cc_final: 0.8441 (mm110) REVERT: D 276 GLN cc_start: 0.8222 (mm110) cc_final: 0.7558 (mp10) REVERT: D 380 PHE cc_start: 0.9258 (m-80) cc_final: 0.8911 (m-80) REVERT: E 259 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7538 (ptt180) outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.0721 time to fit residues: 28.4385 Evaluate side-chains 185 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 21 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 52 optimal weight: 0.0980 chunk 94 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN C 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060350 restraints weight = 62833.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062102 restraints weight = 40990.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.063279 restraints weight = 29817.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064105 restraints weight = 23679.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.064702 restraints weight = 19991.279| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12243 Z= 0.123 Angle : 0.586 6.148 16870 Z= 0.303 Chirality : 0.042 0.175 2076 Planarity : 0.004 0.050 2225 Dihedral : 6.872 78.763 1927 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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 aren not related in a simple way. whole: -0.17 (0.20), residues: 1743 helix: 0.86 (0.18), residues: 881 sheet: -1.27 (0.39), residues: 163 loop : -1.01 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 236 TYR 0.023 0.002 TYR B 145 PHE 0.023 0.001 PHE A 235 TRP 0.014 0.001 TRP B 207 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00253 (12242) covalent geometry : angle 0.58590 (16867) hydrogen bonds : bond 0.03602 ( 693) hydrogen bonds : angle 4.55912 ( 1947) glycosidic custom : bond 0.00080 ( 1) glycosidic custom : angle 0.67458 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 PHE cc_start: 0.9117 (t80) cc_final: 0.8907 (t80) REVERT: B 185 LYS cc_start: 0.9229 (mttt) cc_final: 0.8883 (tppt) REVERT: B 259 PHE cc_start: 0.9199 (m-10) cc_final: 0.8918 (m-80) REVERT: C 168 ASN cc_start: 0.9473 (t0) cc_final: 0.9036 (t0) REVERT: C 172 LYS cc_start: 0.9511 (mttp) cc_final: 0.9192 (mppt) REVERT: C 234 PHE cc_start: 0.9329 (t80) cc_final: 0.8984 (t80) REVERT: C 318 LEU cc_start: 0.9598 (mp) cc_final: 0.9305 (mp) REVERT: D 8 ARG cc_start: 0.9587 (mmt90) cc_final: 0.9131 (mmm-85) REVERT: D 164 GLN cc_start: 0.8968 (mt0) cc_final: 0.8425 (mm110) REVERT: D 276 GLN cc_start: 0.8253 (mm110) cc_final: 0.7593 (mp10) REVERT: D 323 TYR cc_start: 0.7115 (m-80) cc_final: 0.6749 (m-80) REVERT: D 380 PHE cc_start: 0.9238 (m-80) cc_final: 0.8901 (m-80) REVERT: E 159 MET cc_start: 0.6671 (ttp) cc_final: 0.5548 (tmm) REVERT: E 259 ARG cc_start: 0.8444 (ttp80) cc_final: 0.7680 (ptp-170) REVERT: E 275 TYR cc_start: 0.8529 (p90) cc_final: 0.7321 (p90) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.0748 time to fit residues: 30.6943 Evaluate side-chains 198 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 173 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 125 optimal weight: 40.0000 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.082730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059270 restraints weight = 64197.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.061005 restraints weight = 41656.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.062200 restraints weight = 30398.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.062879 restraints weight = 23963.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063581 restraints weight = 20581.784| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12243 Z= 0.144 Angle : 0.588 6.160 16870 Z= 0.304 Chirality : 0.042 0.170 2076 Planarity : 0.004 0.047 2225 Dihedral : 6.599 78.049 1927 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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 aren not related in a simple way. whole: -0.09 (0.21), residues: 1743 helix: 0.90 (0.18), residues: 893 sheet: -1.20 (0.40), residues: 163 loop : -0.98 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 221 TYR 0.021 0.002 TYR A 78 PHE 0.015 0.002 PHE A 235 TRP 0.021 0.001 TRP A 79 HIS 0.004 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00297 (12242) covalent geometry : angle 0.58770 (16867) hydrogen bonds : bond 0.03499 ( 693) hydrogen bonds : angle 4.51347 ( 1947) glycosidic custom : bond 0.00078 ( 1) glycosidic custom : angle 0.91247 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.9357 (ptpp) cc_final: 0.9040 (tptt) REVERT: A 267 ASN cc_start: 0.9211 (t0) cc_final: 0.8829 (t0) REVERT: A 288 ILE cc_start: 0.9302 (mm) cc_final: 0.9087 (mm) REVERT: B 90 MET cc_start: 0.8639 (ppp) cc_final: 0.7808 (mmt) REVERT: B 116 PHE cc_start: 0.9171 (t80) cc_final: 0.8911 (t80) REVERT: B 185 LYS cc_start: 0.9198 (mttt) cc_final: 0.8840 (tppt) REVERT: B 259 PHE cc_start: 0.9228 (m-10) cc_final: 0.8948 (m-80) REVERT: C 124 LYS cc_start: 0.9555 (mtmm) cc_final: 0.9342 (pttt) REVERT: C 168 ASN cc_start: 0.9490 (t0) cc_final: 0.9012 (t0) REVERT: C 172 LYS cc_start: 0.9493 (mttp) cc_final: 0.9214 (mppt) REVERT: C 234 PHE cc_start: 0.9507 (t80) cc_final: 0.8923 (t80) REVERT: C 318 LEU cc_start: 0.9592 (mp) cc_final: 0.9244 (mp) REVERT: C 340 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8618 (pt0) REVERT: C 351 GLN cc_start: 0.9322 (mp10) cc_final: 0.9083 (mp10) REVERT: D 8 ARG cc_start: 0.9585 (mmt90) cc_final: 0.9125 (mmm-85) REVERT: D 164 GLN cc_start: 0.9012 (mt0) cc_final: 0.8421 (mm110) REVERT: D 276 GLN cc_start: 0.8152 (mm110) cc_final: 0.7909 (mp10) REVERT: D 380 PHE cc_start: 0.9204 (m-80) cc_final: 0.8862 (m-80) REVERT: E 159 MET cc_start: 0.6696 (ttp) cc_final: 0.5625 (tmm) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.0772 time to fit residues: 30.9338 Evaluate side-chains 190 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 118 optimal weight: 30.0000 chunk 32 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 48 optimal weight: 0.0970 chunk 3 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN C 197 HIS C 367 GLN E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.084743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061308 restraints weight = 63332.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063000 restraints weight = 41695.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064151 restraints weight = 30535.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.065013 restraints weight = 24220.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.065606 restraints weight = 20371.899| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12243 Z= 0.114 Angle : 0.593 10.120 16870 Z= 0.300 Chirality : 0.042 0.172 2076 Planarity : 0.004 0.045 2225 Dihedral : 6.262 78.852 1927 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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 aren not related in a simple way. whole: -0.04 (0.21), residues: 1743 helix: 0.93 (0.18), residues: 894 sheet: -1.15 (0.40), residues: 163 loop : -0.95 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 259 TYR 0.018 0.001 TYR B 155 PHE 0.024 0.001 PHE A 235 TRP 0.020 0.001 TRP A 79 HIS 0.003 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00235 (12242) covalent geometry : angle 0.59255 (16867) hydrogen bonds : bond 0.03312 ( 693) hydrogen bonds : angle 4.33558 ( 1947) glycosidic custom : bond 0.00388 ( 1) glycosidic custom : angle 0.66117 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.9169 (t80) cc_final: 0.8889 (t80) REVERT: A 180 PHE cc_start: 0.9290 (t80) cc_final: 0.9052 (t80) REVERT: A 229 PHE cc_start: 0.8818 (t80) cc_final: 0.8588 (t80) REVERT: A 264 LYS cc_start: 0.9350 (ptpp) cc_final: 0.8956 (tptt) REVERT: A 288 ILE cc_start: 0.9248 (mm) cc_final: 0.9011 (mm) REVERT: B 116 PHE cc_start: 0.9132 (t80) cc_final: 0.8818 (t80) REVERT: B 185 LYS cc_start: 0.9229 (mttt) cc_final: 0.8934 (tppt) REVERT: B 259 PHE cc_start: 0.9166 (m-10) cc_final: 0.8932 (m-80) REVERT: C 124 LYS cc_start: 0.9537 (mtmm) cc_final: 0.9304 (pttt) REVERT: C 164 GLN cc_start: 0.8950 (tp40) cc_final: 0.8743 (tp-100) REVERT: C 168 ASN cc_start: 0.9441 (t0) cc_final: 0.8901 (t0) REVERT: C 172 LYS cc_start: 0.9480 (mttp) cc_final: 0.9167 (mppt) REVERT: C 234 PHE cc_start: 0.9520 (t80) cc_final: 0.8964 (t80) REVERT: C 318 LEU cc_start: 0.9606 (mp) cc_final: 0.9270 (mp) REVERT: C 323 TYR cc_start: 0.9581 (m-10) cc_final: 0.9377 (m-10) REVERT: C 351 GLN cc_start: 0.9352 (mp10) cc_final: 0.9101 (mp10) REVERT: D 8 ARG cc_start: 0.9566 (mmt90) cc_final: 0.9090 (mmm-85) REVERT: D 276 GLN cc_start: 0.8232 (mm110) cc_final: 0.7900 (mp10) REVERT: D 380 PHE cc_start: 0.9228 (m-80) cc_final: 0.8890 (m-80) REVERT: E 159 MET cc_start: 0.6734 (ttp) cc_final: 0.5665 (tmm) REVERT: E 193 GLU cc_start: 0.8917 (mp0) cc_final: 0.8575 (mm-30) REVERT: E 325 LYS cc_start: 0.8818 (pttt) cc_final: 0.8560 (pttm) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.0770 time to fit residues: 33.1909 Evaluate side-chains 193 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 169 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 116 optimal weight: 0.0870 chunk 140 optimal weight: 3.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN C 197 HIS E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.084314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.060968 restraints weight = 63960.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062659 restraints weight = 41883.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063840 restraints weight = 30636.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064699 restraints weight = 24252.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065295 restraints weight = 20290.780| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12243 Z= 0.111 Angle : 0.585 7.612 16870 Z= 0.294 Chirality : 0.042 0.205 2076 Planarity : 0.004 0.040 2225 Dihedral : 6.069 79.151 1927 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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 aren not related in a simple way. whole: 0.03 (0.21), residues: 1743 helix: 0.99 (0.18), residues: 895 sheet: -1.18 (0.39), residues: 166 loop : -0.90 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 418 TYR 0.026 0.002 TYR B 145 PHE 0.024 0.002 PHE A 235 TRP 0.019 0.001 TRP A 79 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00229 (12242) covalent geometry : angle 0.58470 (16867) hydrogen bonds : bond 0.03175 ( 693) hydrogen bonds : angle 4.32750 ( 1947) glycosidic custom : bond 0.00123 ( 1) glycosidic custom : angle 0.66032 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.365 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 264 LYS cc_start: 0.9419 (ptpp) cc_final: 0.9081 (tptt) REVERT: A 288 ILE cc_start: 0.9248 (mm) cc_final: 0.9013 (mm) REVERT: B 90 MET cc_start: 0.8686 (ppp) cc_final: 0.7679 (mmt) REVERT: B 116 PHE cc_start: 0.9126 (t80) cc_final: 0.8792 (t80) REVERT: B 185 LYS cc_start: 0.9221 (mttt) cc_final: 0.8874 (tppt) REVERT: B 259 PHE cc_start: 0.9152 (m-10) cc_final: 0.8913 (m-80) REVERT: C 124 LYS cc_start: 0.9531 (mtmm) cc_final: 0.9296 (pttt) REVERT: C 168 ASN cc_start: 0.9431 (t0) cc_final: 0.8853 (t0) REVERT: C 172 LYS cc_start: 0.9462 (mttp) cc_final: 0.9174 (mppt) REVERT: C 234 PHE cc_start: 0.9344 (t80) cc_final: 0.8982 (t80) REVERT: C 318 LEU cc_start: 0.9594 (mp) cc_final: 0.9259 (mp) REVERT: C 351 GLN cc_start: 0.9358 (mp10) cc_final: 0.9113 (mp10) REVERT: D 8 ARG cc_start: 0.9565 (mmt90) cc_final: 0.9086 (mmm-85) REVERT: D 276 GLN cc_start: 0.8219 (mm110) cc_final: 0.7871 (mp10) REVERT: D 380 PHE cc_start: 0.9253 (m-80) cc_final: 0.8928 (m-80) REVERT: E 159 MET cc_start: 0.6714 (ttp) cc_final: 0.5640 (tmm) REVERT: E 193 GLU cc_start: 0.8921 (mp0) cc_final: 0.8565 (mm-30) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.0740 time to fit residues: 30.6348 Evaluate side-chains 201 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 62 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN C 197 HIS D 337 GLN E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.082741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059730 restraints weight = 65552.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061294 restraints weight = 44093.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.062384 restraints weight = 32413.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.063149 restraints weight = 25743.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063677 restraints weight = 21871.932| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12243 Z= 0.155 Angle : 0.598 6.191 16870 Z= 0.308 Chirality : 0.043 0.186 2076 Planarity : 0.004 0.045 2225 Dihedral : 6.092 80.877 1927 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.21), residues: 1743 helix: 1.05 (0.18), residues: 895 sheet: -1.10 (0.39), residues: 161 loop : -0.91 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 418 TYR 0.013 0.002 TYR E 275 PHE 0.027 0.002 PHE A 235 TRP 0.025 0.001 TRP A 79 HIS 0.003 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00321 (12242) covalent geometry : angle 0.59758 (16867) hydrogen bonds : bond 0.03411 ( 693) hydrogen bonds : angle 4.43033 ( 1947) glycosidic custom : bond 0.00361 ( 1) glycosidic custom : angle 1.00584 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.9464 (ptpp) cc_final: 0.8874 (tptt) REVERT: A 267 ASN cc_start: 0.9172 (t0) cc_final: 0.8778 (t0) REVERT: A 288 ILE cc_start: 0.9281 (mm) cc_final: 0.9052 (mm) REVERT: B 116 PHE cc_start: 0.9207 (t80) cc_final: 0.8882 (t80) REVERT: B 145 TYR cc_start: 0.9003 (m-80) cc_final: 0.8774 (m-80) REVERT: B 185 LYS cc_start: 0.9268 (mttt) cc_final: 0.8911 (tppt) REVERT: B 259 PHE cc_start: 0.9198 (m-10) cc_final: 0.8941 (m-80) REVERT: C 162 MET cc_start: 0.9084 (mmp) cc_final: 0.8844 (mmp) REVERT: C 168 ASN cc_start: 0.9450 (t0) cc_final: 0.8815 (t0) REVERT: C 172 LYS cc_start: 0.9502 (mttp) cc_final: 0.9206 (mppt) REVERT: C 194 TYR cc_start: 0.8501 (t80) cc_final: 0.7950 (t80) REVERT: C 234 PHE cc_start: 0.9430 (t80) cc_final: 0.8954 (t80) REVERT: C 318 LEU cc_start: 0.9583 (mp) cc_final: 0.9221 (mp) REVERT: C 351 GLN cc_start: 0.9309 (mp10) cc_final: 0.9069 (mp10) REVERT: D 8 ARG cc_start: 0.9572 (mmt90) cc_final: 0.9088 (mmm-85) REVERT: D 164 GLN cc_start: 0.8803 (mt0) cc_final: 0.8099 (mm110) REVERT: D 276 GLN cc_start: 0.8199 (mm110) cc_final: 0.7839 (mp10) REVERT: D 380 PHE cc_start: 0.9233 (m-80) cc_final: 0.8911 (m-80) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.0776 time to fit residues: 31.1733 Evaluate side-chains 193 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 140 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 92 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN C 367 GLN E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.059715 restraints weight = 64631.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061367 restraints weight = 42602.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.062526 restraints weight = 31065.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.063369 restraints weight = 24541.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.063843 restraints weight = 20538.781| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12243 Z= 0.129 Angle : 0.593 10.696 16870 Z= 0.301 Chirality : 0.043 0.198 2076 Planarity : 0.004 0.036 2225 Dihedral : 6.066 81.817 1927 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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 aren not related in a simple way. whole: 0.12 (0.21), residues: 1743 helix: 1.08 (0.18), residues: 894 sheet: -1.14 (0.39), residues: 162 loop : -0.89 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 418 TYR 0.018 0.002 TYR A 135 PHE 0.028 0.002 PHE A 235 TRP 0.026 0.001 TRP A 79 HIS 0.002 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00271 (12242) covalent geometry : angle 0.59318 (16867) hydrogen bonds : bond 0.03319 ( 693) hydrogen bonds : angle 4.37856 ( 1947) glycosidic custom : bond 0.00028 ( 1) glycosidic custom : angle 0.92990 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.9416 (ptpp) cc_final: 0.8837 (tptt) REVERT: A 267 ASN cc_start: 0.9124 (t0) cc_final: 0.8758 (t0) REVERT: A 288 ILE cc_start: 0.9256 (mm) cc_final: 0.9028 (mm) REVERT: B 116 PHE cc_start: 0.9191 (t80) cc_final: 0.8870 (t80) REVERT: B 138 TRP cc_start: 0.8788 (m100) cc_final: 0.8516 (m100) REVERT: B 185 LYS cc_start: 0.9223 (mttt) cc_final: 0.8887 (tppt) REVERT: B 240 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8023 (mp0) REVERT: B 259 PHE cc_start: 0.9186 (m-10) cc_final: 0.8917 (m-80) REVERT: C 95 MET cc_start: 0.7623 (ppp) cc_final: 0.7029 (ppp) REVERT: C 164 GLN cc_start: 0.8971 (tp40) cc_final: 0.8750 (tp-100) REVERT: C 168 ASN cc_start: 0.9423 (t0) cc_final: 0.8782 (t0) REVERT: C 172 LYS cc_start: 0.9489 (mttp) cc_final: 0.9172 (mppt) REVERT: C 234 PHE cc_start: 0.9431 (t80) cc_final: 0.8957 (t80) REVERT: C 318 LEU cc_start: 0.9595 (mp) cc_final: 0.9231 (mp) REVERT: C 351 GLN cc_start: 0.9321 (mp10) cc_final: 0.9092 (mp10) REVERT: D 8 ARG cc_start: 0.9561 (mmt90) cc_final: 0.9065 (mmm-85) REVERT: D 164 GLN cc_start: 0.8823 (mt0) cc_final: 0.8111 (mm110) REVERT: D 276 GLN cc_start: 0.8242 (mm110) cc_final: 0.7847 (mp10) REVERT: D 380 PHE cc_start: 0.9232 (m-80) cc_final: 0.8914 (m-80) REVERT: E 159 MET cc_start: 0.6799 (ttp) cc_final: 0.5731 (tmm) REVERT: E 351 LEU cc_start: 0.8953 (mt) cc_final: 0.8698 (mt) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.0773 time to fit residues: 30.4948 Evaluate side-chains 191 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 165 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059288 restraints weight = 64264.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.060905 restraints weight = 41994.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062041 restraints weight = 30742.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062853 restraints weight = 24422.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063365 restraints weight = 20570.384| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12243 Z= 0.138 Angle : 0.597 6.519 16870 Z= 0.306 Chirality : 0.042 0.180 2076 Planarity : 0.004 0.037 2225 Dihedral : 6.051 81.970 1927 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.13 (0.21), residues: 1743 helix: 1.08 (0.18), residues: 894 sheet: -1.16 (0.38), residues: 162 loop : -0.85 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 418 TYR 0.020 0.002 TYR A 135 PHE 0.031 0.002 PHE D 246 TRP 0.028 0.001 TRP A 79 HIS 0.003 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00291 (12242) covalent geometry : angle 0.59693 (16867) hydrogen bonds : bond 0.03392 ( 693) hydrogen bonds : angle 4.43488 ( 1947) glycosidic custom : bond 0.00227 ( 1) glycosidic custom : angle 1.03727 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.86 seconds wall clock time: 34 minutes 44.15 seconds (2084.15 seconds total)