Starting phenix.real_space_refine on Wed Jun 11 01:48:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpl_34932/06_2025/8hpl_34932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpl_34932/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpl_34932/06_2025/8hpl_34932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpl_34932/06_2025/8hpl_34932.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpl_34932/06_2025/8hpl_34932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpl_34932/06_2025/8hpl_34932.cif" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 7} 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, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'ARG:plan': 3} 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: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 16} 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: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 18} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 15} 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: 8.07, per 1000 atoms: 0.67 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: 3.21 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.42 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: 3.76 Time building geometry restraints manager: 3.75 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 or \ resid 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 391 or resid 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: 2.340 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.110 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.188 0.020 TRP A 79 HIS 0.018 0.004 HIS D 325 PHE 0.064 0.013 PHE E 398 TYR 0.113 0.018 TYR E 424 ARG 0.003 0.001 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.16194 ( 693) hydrogen bonds : angle 7.92553 ( 1947) glycosidic custom : bond 0.02878 ( 1) glycosidic custom : angle 2.16030 ( 3) covalent geometry : bond 0.01172 (12242) covalent geometry : angle 1.77664 (16867) *********************** 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 : 1.322 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: 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: 0.8494 (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: 0.7096 (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: 0.8643 (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: 0.8497 (mt) REVERT: E 86 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8893 (mmmt) REVERT: E 198 TRP cc_start: 0.8989 (t60) cc_final: 0.8782 (t60) REVERT: E 259 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7609 (ptp-110) REVERT: E 276 VAL cc_start: 0.8331 (p) cc_final: 0.7901 (p) REVERT: E 388 VAL cc_start: 0.8774 (m) cc_final: 0.8555 (p) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2421 time to fit residues: 104.4882 Evaluate side-chains 200 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.0170 chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 0.0980 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 158 optimal weight: 30.0000 overall best weight: 3.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 261 ASN C 197 HIS D 218 GLN D 290 HIS D 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.082454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058308 restraints weight = 64094.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059838 restraints weight = 43901.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060870 restraints weight = 32878.453| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12243 Z= 0.219 Angle : 0.725 8.571 16870 Z= 0.390 Chirality : 0.046 0.184 2076 Planarity : 0.005 0.039 2225 Dihedral : 8.515 85.666 1927 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.19), residues: 1743 helix: 0.06 (0.16), residues: 877 sheet: -1.94 (0.36), residues: 166 loop : -1.35 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 207 HIS 0.008 0.002 HIS B 118 PHE 0.021 0.002 PHE E 317 TYR 0.022 0.002 TYR B 155 ARG 0.005 0.001 ARG E 343 Details of bonding type rmsd hydrogen bonds : bond 0.04967 ( 693) hydrogen bonds : angle 5.56443 ( 1947) glycosidic custom : bond 0.00107 ( 1) glycosidic custom : angle 0.61052 ( 3) covalent geometry : bond 0.00438 (12242) covalent geometry : angle 0.72494 (16867) *********************** 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 263 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ASN cc_start: 0.9194 (t0) cc_final: 0.8891 (t0) REVERT: A 270 LEU cc_start: 0.9592 (mt) cc_final: 0.9330 (mt) REVERT: A 287 PHE cc_start: 0.9429 (t80) cc_final: 0.9116 (t80) REVERT: A 288 ILE cc_start: 0.9428 (mm) cc_final: 0.9211 (mm) REVERT: B 185 LYS cc_start: 0.9221 (mttt) cc_final: 0.8851 (tppt) REVERT: C 170 ASP cc_start: 0.9028 (p0) cc_final: 0.8584 (p0) REVERT: C 172 LYS cc_start: 0.9544 (mttp) cc_final: 0.9265 (mppt) REVERT: C 234 PHE cc_start: 0.9272 (t80) cc_final: 0.8651 (t80) REVERT: C 284 VAL cc_start: 0.9122 (m) cc_final: 0.8875 (t) REVERT: C 318 LEU cc_start: 0.9574 (mp) cc_final: 0.9254 (mp) REVERT: D 8 ARG cc_start: 0.9638 (mmt90) cc_final: 0.9181 (mmm-85) REVERT: D 164 GLN cc_start: 0.8987 (mt0) cc_final: 0.8669 (mm110) REVERT: D 276 GLN cc_start: 0.8103 (mm110) cc_final: 0.7533 (mp10) REVERT: D 370 LEU cc_start: 0.9314 (mt) cc_final: 0.9114 (pp) REVERT: D 380 PHE cc_start: 0.9450 (m-80) cc_final: 0.9015 (m-80) REVERT: E 66 LEU cc_start: 0.8921 (mp) cc_final: 0.8718 (mp) REVERT: E 259 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7848 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2462 time to fit residues: 97.0504 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 : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 32 optimal weight: 0.0670 chunk 2 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 overall best weight: 1.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 HIS ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN E 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.082322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058780 restraints weight = 62903.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060334 restraints weight = 42379.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061433 restraints weight = 31935.552| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12243 Z= 0.154 Angle : 0.632 7.836 16870 Z= 0.335 Chirality : 0.043 0.186 2076 Planarity : 0.005 0.042 2225 Dihedral : 7.950 89.098 1927 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1743 helix: 0.55 (0.17), residues: 884 sheet: -1.62 (0.37), residues: 167 loop : -1.20 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 79 HIS 0.004 0.001 HIS C 325 PHE 0.025 0.002 PHE B 61 TYR 0.021 0.002 TYR B 57 ARG 0.003 0.000 ARG B 221 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 693) hydrogen bonds : angle 5.02867 ( 1947) glycosidic custom : bond 0.00111 ( 1) glycosidic custom : angle 0.64759 ( 3) covalent geometry : bond 0.00306 (12242) covalent geometry : angle 0.63203 (16867) *********************** 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 271 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8827 (t70) cc_final: 0.8552 (t0) REVERT: A 266 PHE cc_start: 0.9020 (m-80) cc_final: 0.8810 (m-80) REVERT: A 267 ASN cc_start: 0.9268 (t0) cc_final: 0.8918 (t0) REVERT: A 288 ILE cc_start: 0.9396 (mm) cc_final: 0.9192 (mm) REVERT: B 185 LYS cc_start: 0.9196 (mttt) cc_final: 0.8857 (tppt) REVERT: C 168 ASN cc_start: 0.9469 (t0) cc_final: 0.8511 (t0) REVERT: C 170 ASP cc_start: 0.9059 (p0) cc_final: 0.8637 (p0) REVERT: C 172 LYS cc_start: 0.9502 (mttp) cc_final: 0.9212 (mppt) REVERT: C 194 TYR cc_start: 0.8464 (t80) cc_final: 0.8102 (t80) REVERT: C 234 PHE cc_start: 0.9236 (t80) cc_final: 0.8600 (t80) REVERT: C 326 PHE cc_start: 0.9432 (p90) cc_final: 0.9198 (p90) REVERT: C 351 GLN cc_start: 0.9293 (mp10) cc_final: 0.9089 (mp10) REVERT: D 8 ARG cc_start: 0.9616 (mmt90) cc_final: 0.9112 (mmm-85) REVERT: D 164 GLN cc_start: 0.9067 (mt0) cc_final: 0.8550 (mm110) REVERT: D 276 GLN cc_start: 0.8107 (mm110) cc_final: 0.7604 (mp10) REVERT: D 370 LEU cc_start: 0.9346 (mt) cc_final: 0.9140 (pp) REVERT: D 380 PHE cc_start: 0.9343 (m-80) cc_final: 0.9001 (m-80) REVERT: E 259 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7826 (ptp-110) REVERT: E 319 ILE cc_start: 0.9539 (mt) cc_final: 0.9203 (tp) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2792 time to fit residues: 114.7992 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 : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN C 164 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.083422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060197 restraints weight = 62747.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061839 restraints weight = 41132.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.063050 restraints weight = 30442.454| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12243 Z= 0.129 Angle : 0.609 6.827 16870 Z= 0.318 Chirality : 0.043 0.182 2076 Planarity : 0.004 0.050 2225 Dihedral : 7.444 81.543 1927 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1743 helix: 0.65 (0.17), residues: 881 sheet: -1.43 (0.38), residues: 163 loop : -1.08 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 207 HIS 0.003 0.001 HIS C 94 PHE 0.018 0.001 PHE B 61 TYR 0.026 0.002 TYR C 89 ARG 0.004 0.000 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 693) hydrogen bonds : angle 4.79560 ( 1947) glycosidic custom : bond 0.00193 ( 1) glycosidic custom : angle 0.67794 ( 3) covalent geometry : bond 0.00268 (12242) covalent geometry : angle 0.60852 (16867) *********************** 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 273 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8941 (t70) cc_final: 0.8554 (t0) REVERT: A 266 PHE cc_start: 0.8951 (m-80) cc_final: 0.8722 (m-80) REVERT: B 185 LYS cc_start: 0.9199 (mttt) cc_final: 0.8884 (tppt) REVERT: B 237 GLN cc_start: 0.8834 (pm20) cc_final: 0.8535 (pm20) REVERT: B 259 PHE cc_start: 0.9213 (m-10) cc_final: 0.8930 (m-80) REVERT: C 168 ASN cc_start: 0.9367 (t0) cc_final: 0.8684 (t0) REVERT: C 172 LYS cc_start: 0.9500 (mttp) cc_final: 0.9218 (mppt) REVERT: C 234 PHE cc_start: 0.9291 (t80) cc_final: 0.8892 (t80) REVERT: C 351 GLN cc_start: 0.9286 (mp10) cc_final: 0.9015 (mp10) REVERT: D 8 ARG cc_start: 0.9609 (mmt90) cc_final: 0.9086 (mmm-85) REVERT: D 164 GLN cc_start: 0.8983 (mt0) cc_final: 0.8463 (mm-40) REVERT: D 276 GLN cc_start: 0.8207 (mm110) cc_final: 0.7558 (mp10) REVERT: D 380 PHE cc_start: 0.9251 (m-80) cc_final: 0.8912 (m-80) REVERT: E 159 MET cc_start: 0.6356 (ttp) cc_final: 0.5258 (tmm) REVERT: E 259 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7816 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.2087 time to fit residues: 85.5275 Evaluate side-chains 192 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 119 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** C 325 HIS ** 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 = 0.3572 r_free = 0.3572 target = 0.082100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.059664 restraints weight = 62924.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.061143 restraints weight = 42356.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.061995 restraints weight = 32224.799| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12243 Z= 0.200 Angle : 0.643 7.662 16870 Z= 0.338 Chirality : 0.043 0.170 2076 Planarity : 0.005 0.052 2225 Dihedral : 7.231 79.989 1927 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1743 helix: 0.61 (0.17), residues: 886 sheet: -1.42 (0.39), residues: 165 loop : -1.12 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 207 HIS 0.011 0.001 HIS B 118 PHE 0.024 0.002 PHE E 321 TYR 0.023 0.002 TYR C 89 ARG 0.002 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 693) hydrogen bonds : angle 4.90129 ( 1947) glycosidic custom : bond 0.00478 ( 1) glycosidic custom : angle 1.17989 ( 3) covalent geometry : bond 0.00406 (12242) covalent geometry : angle 0.64263 (16867) *********************** 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 252 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ASN cc_start: 0.9220 (t0) cc_final: 0.8875 (t0) REVERT: A 270 LEU cc_start: 0.9541 (mt) cc_final: 0.9338 (mt) REVERT: A 288 ILE cc_start: 0.9373 (mm) cc_final: 0.9157 (mm) REVERT: B 90 MET cc_start: 0.8699 (ppp) cc_final: 0.7922 (mmt) REVERT: B 145 TYR cc_start: 0.8987 (m-80) cc_final: 0.8712 (m-80) REVERT: B 160 PHE cc_start: 0.9144 (m-80) cc_final: 0.8748 (m-80) REVERT: B 185 LYS cc_start: 0.9193 (mttt) cc_final: 0.8882 (tppt) REVERT: C 168 ASN cc_start: 0.9422 (t0) cc_final: 0.8808 (t0) REVERT: C 172 LYS cc_start: 0.9518 (mttp) cc_final: 0.9241 (mppt) REVERT: C 234 PHE cc_start: 0.9448 (t80) cc_final: 0.8828 (t80) REVERT: C 318 LEU cc_start: 0.9591 (mp) cc_final: 0.9257 (mp) REVERT: C 340 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8546 (pt0) REVERT: D 164 GLN cc_start: 0.9016 (mt0) cc_final: 0.8438 (mm110) REVERT: D 276 GLN cc_start: 0.8264 (mm110) cc_final: 0.7616 (mp10) REVERT: D 380 PHE cc_start: 0.9170 (m-80) cc_final: 0.8810 (m-80) REVERT: E 40 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8571 (mm-30) REVERT: E 159 MET cc_start: 0.6716 (ttp) cc_final: 0.5623 (tmm) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.2071 time to fit residues: 79.9332 Evaluate side-chains 181 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 96 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 99 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 89 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 HIS D 337 GLN E 358 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.078748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.055322 restraints weight = 65015.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056823 restraints weight = 43035.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057876 restraints weight = 31844.399| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12243 Z= 0.272 Angle : 0.727 10.214 16870 Z= 0.382 Chirality : 0.046 0.192 2076 Planarity : 0.005 0.045 2225 Dihedral : 7.538 77.732 1927 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1743 helix: 0.33 (0.17), residues: 883 sheet: -1.63 (0.39), residues: 165 loop : -1.38 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 79 HIS 0.010 0.002 HIS B 118 PHE 0.021 0.002 PHE A 113 TYR 0.023 0.002 TYR A 135 ARG 0.010 0.001 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 693) hydrogen bonds : angle 5.29007 ( 1947) glycosidic custom : bond 0.00843 ( 1) glycosidic custom : angle 1.91182 ( 3) covalent geometry : bond 0.00543 (12242) covalent geometry : angle 0.72686 (16867) *********************** 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 222 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.9166 (t70) cc_final: 0.8552 (p0) REVERT: A 267 ASN cc_start: 0.9223 (t0) cc_final: 0.8871 (t0) REVERT: A 270 LEU cc_start: 0.9625 (mt) cc_final: 0.9308 (mt) REVERT: B 145 TYR cc_start: 0.8973 (m-80) cc_final: 0.8757 (m-80) REVERT: B 185 LYS cc_start: 0.9169 (mttt) cc_final: 0.8818 (tppt) REVERT: C 172 LYS cc_start: 0.9539 (mttp) cc_final: 0.9242 (mppt) REVERT: C 234 PHE cc_start: 0.9464 (t80) cc_final: 0.8982 (t80) REVERT: C 318 LEU cc_start: 0.9611 (mp) cc_final: 0.9257 (mp) REVERT: D 164 GLN cc_start: 0.9091 (mt0) cc_final: 0.8458 (mm110) REVERT: D 276 GLN cc_start: 0.8254 (mm110) cc_final: 0.7876 (mp10) REVERT: D 380 PHE cc_start: 0.9077 (m-80) cc_final: 0.8775 (m-80) REVERT: E 159 MET cc_start: 0.6808 (ttp) cc_final: 0.5803 (tmm) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1895 time to fit residues: 65.2555 Evaluate side-chains 161 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** D 337 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 = 0.3553 r_free = 0.3553 target = 0.079945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.057431 restraints weight = 63950.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058849 restraints weight = 42508.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059879 restraints weight = 31383.754| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12243 Z= 0.204 Angle : 0.656 9.339 16870 Z= 0.345 Chirality : 0.044 0.199 2076 Planarity : 0.005 0.042 2225 Dihedral : 7.347 78.166 1927 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1743 helix: 0.47 (0.17), residues: 885 sheet: -1.67 (0.38), residues: 165 loop : -1.37 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 79 HIS 0.005 0.001 HIS C 325 PHE 0.019 0.002 PHE E 321 TYR 0.023 0.002 TYR B 57 ARG 0.004 0.000 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 693) hydrogen bonds : angle 5.07828 ( 1947) glycosidic custom : bond 0.00276 ( 1) glycosidic custom : angle 1.58411 ( 3) covalent geometry : bond 0.00417 (12242) covalent geometry : angle 0.65598 (16867) *********************** 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 223 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ASN cc_start: 0.9197 (t0) cc_final: 0.8815 (t0) REVERT: A 270 LEU cc_start: 0.9599 (mt) cc_final: 0.9281 (mt) REVERT: B 145 TYR cc_start: 0.8958 (m-80) cc_final: 0.8715 (m-80) REVERT: B 185 LYS cc_start: 0.9129 (mttt) cc_final: 0.8750 (tppt) REVERT: C 95 MET cc_start: 0.7585 (ppp) cc_final: 0.6874 (ppp) REVERT: C 172 LYS cc_start: 0.9539 (mttp) cc_final: 0.9246 (mppt) REVERT: C 234 PHE cc_start: 0.9296 (t80) cc_final: 0.8928 (t80) REVERT: C 318 LEU cc_start: 0.9619 (mp) cc_final: 0.9265 (mp) REVERT: C 351 GLN cc_start: 0.9340 (mp10) cc_final: 0.9132 (mp10) REVERT: D 164 GLN cc_start: 0.9077 (mt0) cc_final: 0.8544 (mm110) REVERT: D 276 GLN cc_start: 0.8192 (mm110) cc_final: 0.7878 (mp10) REVERT: D 380 PHE cc_start: 0.8994 (m-80) cc_final: 0.8706 (m-80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2151 time to fit residues: 74.6382 Evaluate side-chains 163 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 337 GLN D 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.080831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.058117 restraints weight = 63134.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.059515 restraints weight = 42293.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060648 restraints weight = 30969.754| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12243 Z= 0.161 Angle : 0.622 8.150 16870 Z= 0.322 Chirality : 0.043 0.202 2076 Planarity : 0.004 0.041 2225 Dihedral : 6.938 79.031 1927 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1743 helix: 0.67 (0.18), residues: 881 sheet: -1.60 (0.38), residues: 165 loop : -1.23 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 79 HIS 0.003 0.001 HIS B 118 PHE 0.020 0.002 PHE B 61 TYR 0.023 0.002 TYR B 57 ARG 0.004 0.000 ARG D 278 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 693) hydrogen bonds : angle 4.85930 ( 1947) glycosidic custom : bond 0.00048 ( 1) glycosidic custom : angle 1.38654 ( 3) covalent geometry : bond 0.00335 (12242) covalent geometry : angle 0.62155 (16867) *********************** 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 235 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.287 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: A 78 TYR cc_start: 0.8750 (t80) cc_final: 0.8485 (t80) REVERT: A 264 LYS cc_start: 0.9533 (ptpp) cc_final: 0.8916 (tptt) REVERT: A 267 ASN cc_start: 0.9204 (t0) cc_final: 0.8781 (t0) REVERT: A 270 LEU cc_start: 0.9602 (mt) cc_final: 0.9278 (mm) REVERT: B 145 TYR cc_start: 0.8965 (m-80) cc_final: 0.8695 (m-80) REVERT: B 185 LYS cc_start: 0.9133 (mttt) cc_final: 0.8769 (tppt) REVERT: C 95 MET cc_start: 0.7647 (ppp) cc_final: 0.7178 (ppp) REVERT: C 168 ASN cc_start: 0.9336 (t0) cc_final: 0.8481 (t0) REVERT: C 172 LYS cc_start: 0.9539 (mttp) cc_final: 0.9243 (mppt) REVERT: C 234 PHE cc_start: 0.9382 (t80) cc_final: 0.8928 (t80) REVERT: C 318 LEU cc_start: 0.9621 (mp) cc_final: 0.9265 (mp) REVERT: C 351 GLN cc_start: 0.9361 (mp10) cc_final: 0.9140 (mp10) REVERT: C 359 ASP cc_start: 0.8971 (m-30) cc_final: 0.8764 (m-30) REVERT: D 164 GLN cc_start: 0.9081 (mt0) cc_final: 0.8542 (mm110) REVERT: D 276 GLN cc_start: 0.8241 (mm110) cc_final: 0.7838 (mp10) REVERT: D 380 PHE cc_start: 0.9008 (m-80) cc_final: 0.8668 (m-80) REVERT: E 159 MET cc_start: 0.6856 (ttp) cc_final: 0.6053 (tmm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2125 time to fit residues: 74.0140 Evaluate side-chains 178 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 158 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN D 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.082412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058830 restraints weight = 65454.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.060428 restraints weight = 42907.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061376 restraints weight = 31302.895| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12243 Z= 0.125 Angle : 0.613 9.878 16870 Z= 0.313 Chirality : 0.043 0.207 2076 Planarity : 0.004 0.044 2225 Dihedral : 6.537 80.653 1927 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1743 helix: 0.75 (0.18), residues: 889 sheet: -1.46 (0.38), residues: 167 loop : -1.09 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 79 HIS 0.003 0.001 HIS C 268 PHE 0.024 0.001 PHE A 235 TYR 0.022 0.002 TYR B 57 ARG 0.004 0.000 ARG D 278 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 693) hydrogen bonds : angle 4.65658 ( 1947) glycosidic custom : bond 0.00175 ( 1) glycosidic custom : angle 0.96478 ( 3) covalent geometry : bond 0.00264 (12242) covalent geometry : angle 0.61249 (16867) *********************** 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 260 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.310 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 180 PHE cc_start: 0.9276 (t80) cc_final: 0.9046 (t80) REVERT: A 233 ASP cc_start: 0.8971 (t70) cc_final: 0.8501 (t0) REVERT: A 264 LYS cc_start: 0.9482 (ptpp) cc_final: 0.8885 (tptt) REVERT: A 267 ASN cc_start: 0.9176 (t0) cc_final: 0.8769 (t0) REVERT: A 270 LEU cc_start: 0.9567 (mt) cc_final: 0.9323 (mt) REVERT: A 288 ILE cc_start: 0.9324 (mm) cc_final: 0.9104 (mm) REVERT: B 116 PHE cc_start: 0.9285 (t80) cc_final: 0.8600 (t80) REVERT: B 169 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8481 (tm-30) REVERT: B 185 LYS cc_start: 0.9135 (mttt) cc_final: 0.8769 (tppt) REVERT: B 259 PHE cc_start: 0.9279 (m-10) cc_final: 0.8979 (m-80) REVERT: C 164 GLN cc_start: 0.9040 (tp40) cc_final: 0.8833 (tp-100) REVERT: C 168 ASN cc_start: 0.9278 (t0) cc_final: 0.8465 (t0) REVERT: C 172 LYS cc_start: 0.9531 (mttp) cc_final: 0.9222 (mppt) REVERT: C 234 PHE cc_start: 0.9424 (t80) cc_final: 0.8990 (t80) REVERT: C 318 LEU cc_start: 0.9648 (mp) cc_final: 0.9299 (mp) REVERT: C 323 TYR cc_start: 0.9563 (m-10) cc_final: 0.9353 (m-10) REVERT: C 351 GLN cc_start: 0.9363 (mp10) cc_final: 0.9118 (mp10) REVERT: C 359 ASP cc_start: 0.8980 (m-30) cc_final: 0.8779 (m-30) REVERT: D 276 GLN cc_start: 0.8203 (mm110) cc_final: 0.7826 (mp10) REVERT: D 380 PHE cc_start: 0.9115 (m-80) cc_final: 0.8822 (m-80) REVERT: E 159 MET cc_start: 0.6697 (ttp) cc_final: 0.5850 (tmm) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2250 time to fit residues: 88.0393 Evaluate side-chains 189 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 68 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 0.1980 chunk 172 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 123 optimal weight: 0.0000 chunk 88 optimal weight: 9.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 56 ASN D 337 GLN 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 = 0.083457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060056 restraints weight = 63961.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.061681 restraints weight = 42468.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.062805 restraints weight = 31182.832| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4863 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= 0.120 Angle : 0.628 9.445 16870 Z= 0.318 Chirality : 0.043 0.196 2076 Planarity : 0.004 0.056 2225 Dihedral : 6.302 82.627 1927 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1743 helix: 0.71 (0.18), residues: 890 sheet: -1.39 (0.38), residues: 167 loop : -1.07 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 79 HIS 0.003 0.001 HIS C 94 PHE 0.028 0.002 PHE E 44 TYR 0.021 0.001 TYR B 57 ARG 0.003 0.000 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 693) hydrogen bonds : angle 4.60877 ( 1947) glycosidic custom : bond 0.00238 ( 1) glycosidic custom : angle 0.70697 ( 3) covalent geometry : bond 0.00250 (12242) covalent geometry : angle 0.62814 (16867) ********************** 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 263 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.341 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: A 233 ASP cc_start: 0.8946 (t70) cc_final: 0.8618 (t0) REVERT: A 264 LYS cc_start: 0.9486 (ptpp) cc_final: 0.8787 (tptt) REVERT: A 267 ASN cc_start: 0.9202 (t0) cc_final: 0.8803 (t0) REVERT: A 270 LEU cc_start: 0.9563 (mt) cc_final: 0.9266 (mt) REVERT: A 288 ILE cc_start: 0.9288 (mm) cc_final: 0.9063 (mm) REVERT: B 93 TYR cc_start: 0.9134 (t80) cc_final: 0.8884 (t80) REVERT: B 116 PHE cc_start: 0.9275 (t80) cc_final: 0.8552 (t80) REVERT: B 169 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8470 (tm-30) REVERT: B 185 LYS cc_start: 0.9146 (mttt) cc_final: 0.8818 (tppt) REVERT: B 259 PHE cc_start: 0.9250 (m-10) cc_final: 0.8941 (m-80) REVERT: C 95 MET cc_start: 0.7587 (ppp) cc_final: 0.7151 (ppp) REVERT: C 168 ASN cc_start: 0.9334 (t0) cc_final: 0.8641 (t0) REVERT: C 172 LYS cc_start: 0.9512 (mttp) cc_final: 0.9203 (mppt) REVERT: C 194 TYR cc_start: 0.8607 (t80) cc_final: 0.8101 (t80) REVERT: C 234 PHE cc_start: 0.9424 (t80) cc_final: 0.9006 (t80) REVERT: C 318 LEU cc_start: 0.9630 (mp) cc_final: 0.9304 (mp) REVERT: C 351 GLN cc_start: 0.9363 (mp10) cc_final: 0.9117 (mp10) REVERT: D 276 GLN cc_start: 0.8108 (mm110) cc_final: 0.7725 (mp10) REVERT: D 380 PHE cc_start: 0.9140 (m-80) cc_final: 0.8838 (m-80) REVERT: E 75 LEU cc_start: 0.9230 (mm) cc_final: 0.8847 (mm) REVERT: E 159 MET cc_start: 0.6549 (ttp) cc_final: 0.5662 (tmm) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2040 time to fit residues: 80.3302 Evaluate side-chains 195 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 1 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 0.0010 chunk 166 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.084239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060630 restraints weight = 61910.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.062312 restraints weight = 40832.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.063499 restraints weight = 29854.376| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5031 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 : 0.605 10.160 16870 Z= 0.305 Chirality : 0.043 0.196 2076 Planarity : 0.004 0.045 2225 Dihedral : 6.045 83.388 1927 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1743 helix: 0.83 (0.18), residues: 888 sheet: -1.24 (0.39), residues: 171 loop : -1.01 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 79 HIS 0.003 0.001 HIS D 268 PHE 0.015 0.001 PHE B 61 TYR 0.019 0.001 TYR B 57 ARG 0.006 0.000 ARG E 418 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 693) hydrogen bonds : angle 4.44485 ( 1947) glycosidic custom : bond 0.00270 ( 1) glycosidic custom : angle 0.78449 ( 3) covalent geometry : bond 0.00236 (12242) covalent geometry : angle 0.60499 (16867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4471.73 seconds wall clock time: 79 minutes 58.95 seconds (4798.95 seconds total)