Starting phenix.real_space_refine on Wed Mar 4 09:49:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wdn_21642/03_2026/6wdn_21642.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wdn_21642/03_2026/6wdn_21642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wdn_21642/03_2026/6wdn_21642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wdn_21642/03_2026/6wdn_21642.map" model { file = "/net/cci-nas-00/data/ceres_data/6wdn_21642/03_2026/6wdn_21642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wdn_21642/03_2026/6wdn_21642.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8151 2.51 5 N 2129 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12612 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2539 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 308} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2833 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "C" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1453 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "D" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "G" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1463 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "H" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "I" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1354 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "J" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 354 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "E" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1462 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Time building chain proxies: 3.24, per 1000 atoms: 0.26 Number of scatterers: 12612 At special positions: 0 Unit cell: (84.8, 98.58, 185.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2264 8.00 N 2129 7.00 C 8151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS B 463 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 543.7 milliseconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2936 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 4 sheets defined 72.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.611A pdb=" N PHE A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 4.029A pdb=" N PHE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.505A pdb=" N ASP A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.504A pdb=" N THR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 4.016A pdb=" N HIS A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.869A pdb=" N PHE A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.582A pdb=" N MET A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 272 removed outlier: 3.559A pdb=" N GLU A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 288 removed outlier: 3.620A pdb=" N PHE A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 4.509A pdb=" N ASP A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 327 through 341 removed outlier: 3.589A pdb=" N ILE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.552A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 4.073A pdb=" N LEU A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.768A pdb=" N GLN A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TRP A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 415 " --> pdb=" O TRP A 411 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.834A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.566A pdb=" N PHE B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.836A pdb=" N PHE B 223 " --> pdb=" O PRO B 219 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.937A pdb=" N GLN B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 removed outlier: 6.575A pdb=" N MET B 256 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 278 through 284 Processing helix chain 'B' and resid 293 through 314 removed outlier: 3.504A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 323 through 333 Processing helix chain 'B' and resid 338 through 352 removed outlier: 3.709A pdb=" N GLN B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 372 removed outlier: 3.824A pdb=" N PHE B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 removed outlier: 4.920A pdb=" N THR B 379 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.661A pdb=" N GLN B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 4.134A pdb=" N PHE B 417 " --> pdb=" O CYS B 413 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.840A pdb=" N SER B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 4.304A pdb=" N ALA B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 70 Processing helix chain 'F' and resid 70 through 90 Proline residue: F 76 - end of helix removed outlier: 3.576A pdb=" N THR F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'C' and resid 174 through 190 removed outlier: 3.648A pdb=" N THR C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 removed outlier: 3.690A pdb=" N HIS C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.566A pdb=" N ILE C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 215 through 220 removed outlier: 4.067A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 241 removed outlier: 3.764A pdb=" N ARG C 226 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 253 removed outlier: 4.163A pdb=" N PHE C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.877A pdb=" N ALA C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 286 Processing helix chain 'C' and resid 290 through 311 removed outlier: 3.860A pdb=" N ASP C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.714A pdb=" N GLN C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 75 through 93 removed outlier: 3.660A pdb=" N VAL D 80 " --> pdb=" O PRO D 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 190 removed outlier: 4.226A pdb=" N ASP G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL G 179 " --> pdb=" O THR G 175 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 228 removed outlier: 4.541A pdb=" N LEU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE G 204 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU G 208 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 210 " --> pdb=" O ARG G 206 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 4.324A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG G 226 " --> pdb=" O ILE G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 249 removed outlier: 3.664A pdb=" N MET G 243 " --> pdb=" O GLY G 239 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE G 247 " --> pdb=" O MET G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 256 removed outlier: 3.898A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 264 Processing helix chain 'G' and resid 265 through 270 Processing helix chain 'G' and resid 270 through 275 removed outlier: 3.662A pdb=" N ALA G 275 " --> pdb=" O THR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 285 Processing helix chain 'G' and resid 290 through 310 removed outlier: 4.462A pdb=" N ASP G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE G 302 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 310 " --> pdb=" O GLY G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 340 removed outlier: 3.652A pdb=" N ALA G 323 " --> pdb=" O GLN G 319 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU G 328 " --> pdb=" O ILE G 324 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP G 336 " --> pdb=" O LYS G 332 " (cutoff:3.500A) Proline residue: G 337 - end of helix Processing helix chain 'H' and resid 65 through 73 removed outlier: 3.501A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 93 removed outlier: 3.559A pdb=" N GLY H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 189 removed outlier: 3.788A pdb=" N LEU I 182 " --> pdb=" O ASP I 178 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL I 183 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN I 184 " --> pdb=" O LYS I 180 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 225 removed outlier: 3.570A pdb=" N LEU I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE I 204 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU I 205 " --> pdb=" O ARG I 201 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU I 210 " --> pdb=" O ARG I 206 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) Proline residue: I 216 - end of helix removed outlier: 4.287A pdb=" N VAL I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU I 223 " --> pdb=" O LYS I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 232 Processing helix chain 'I' and resid 233 through 254 removed outlier: 3.570A pdb=" N TRP I 237 " --> pdb=" O THR I 233 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE I 247 " --> pdb=" O MET I 243 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU I 250 " --> pdb=" O GLN I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 275 No H-bonds generated for 'chain 'I' and resid 273 through 275' Processing helix chain 'I' and resid 276 through 281 Processing helix chain 'I' and resid 281 through 286 Processing helix chain 'I' and resid 290 through 311 removed outlier: 3.782A pdb=" N GLN I 298 " --> pdb=" O ALA I 294 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS I 305 " --> pdb=" O LEU I 301 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS I 309 " --> pdb=" O LYS I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 330 removed outlier: 3.710A pdb=" N ALA I 323 " --> pdb=" O GLN I 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 74 through 79 Processing helix chain 'J' and resid 79 through 93 removed outlier: 3.999A pdb=" N SER J 85 " --> pdb=" O GLY J 81 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE J 88 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU J 91 " --> pdb=" O ASN J 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 190 removed outlier: 3.557A pdb=" N THR E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 207 removed outlier: 4.186A pdb=" N LEU E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 199 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 219 removed outlier: 3.593A pdb=" N ALA E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 3.524A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 248 removed outlier: 3.864A pdb=" N ARG E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 259 through 264 removed outlier: 3.606A pdb=" N MET E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 285 Processing helix chain 'E' and resid 290 through 310 removed outlier: 3.536A pdb=" N ASP E 296 " --> pdb=" O PRO E 292 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 306 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 335 removed outlier: 4.143A pdb=" N ASP E 322 " --> pdb=" O ASN E 318 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.536A pdb=" N LYS B 174 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 237 through 238 609 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2038 1.31 - 1.44: 3504 1.44 - 1.57: 7215 1.57 - 1.71: 0 1.71 - 1.84: 123 Bond restraints: 12880 Sorted by residual: bond pdb=" C SER H 72 " pdb=" O SER H 72 " ideal model delta sigma weight residual 1.237 1.177 0.060 1.17e-02 7.31e+03 2.64e+01 bond pdb=" C PRO H 76 " pdb=" O PRO H 76 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.26e-02 6.30e+03 2.60e+01 bond pdb=" CA SER H 72 " pdb=" CB SER H 72 " ideal model delta sigma weight residual 1.528 1.462 0.066 1.56e-02 4.11e+03 1.81e+01 bond pdb=" C TYR H 79 " pdb=" O TYR H 79 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.19e-02 7.06e+03 1.80e+01 bond pdb=" C ARG B 259 " pdb=" O ARG B 259 " ideal model delta sigma weight residual 1.232 1.185 0.047 1.12e-02 7.97e+03 1.76e+01 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 17020 2.23 - 4.46: 258 4.46 - 6.68: 55 6.68 - 8.91: 5 8.91 - 11.14: 6 Bond angle restraints: 17344 Sorted by residual: angle pdb=" N VAL H 80 " pdb=" CA VAL H 80 " pdb=" C VAL H 80 " ideal model delta sigma weight residual 113.00 103.88 9.12 1.30e+00 5.92e-01 4.92e+01 angle pdb=" N ARG B 259 " pdb=" CA ARG B 259 " pdb=" C ARG B 259 " ideal model delta sigma weight residual 109.83 99.74 10.09 1.55e+00 4.16e-01 4.24e+01 angle pdb=" C PRO H 76 " pdb=" CA PRO H 76 " pdb=" CB PRO H 76 " ideal model delta sigma weight residual 112.62 102.28 10.34 1.65e+00 3.67e-01 3.92e+01 angle pdb=" CA PHE H 77 " pdb=" CB PHE H 77 " pdb=" CG PHE H 77 " ideal model delta sigma weight residual 113.80 107.75 6.05 1.00e+00 1.00e+00 3.66e+01 angle pdb=" C ARG B 259 " pdb=" N HIS B 260 " pdb=" CA HIS B 260 " ideal model delta sigma weight residual 121.87 111.03 10.84 1.83e+00 2.99e-01 3.51e+01 ... (remaining 17339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 6838 17.53 - 35.07: 735 35.07 - 52.60: 151 52.60 - 70.14: 22 70.14 - 87.67: 12 Dihedral angle restraints: 7758 sinusoidal: 3230 harmonic: 4528 Sorted by residual: dihedral pdb=" CB CYS A 413 " pdb=" SG CYS A 413 " pdb=" SG CYS B 463 " pdb=" CB CYS B 463 " ideal model delta sinusoidal sigma weight residual -86.00 -30.71 -55.29 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CD ARG B 261 " pdb=" NE ARG B 261 " pdb=" CZ ARG B 261 " pdb=" NH1 ARG B 261 " ideal model delta sinusoidal sigma weight residual 0.00 49.62 -49.62 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" C PRO H 76 " pdb=" N PRO H 76 " pdb=" CA PRO H 76 " pdb=" CB PRO H 76 " ideal model delta harmonic sigma weight residual -120.70 -107.65 -13.05 0 2.50e+00 1.60e-01 2.73e+01 ... (remaining 7755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1815 0.088 - 0.177: 76 0.177 - 0.265: 11 0.265 - 0.354: 4 0.354 - 0.442: 1 Chirality restraints: 1907 Sorted by residual: chirality pdb=" CA SER B 276 " pdb=" N SER B 276 " pdb=" C SER B 276 " pdb=" CB SER B 276 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA VAL H 70 " pdb=" N VAL H 70 " pdb=" C VAL H 70 " pdb=" CB VAL H 70 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ARG H 69 " pdb=" N ARG H 69 " pdb=" C ARG H 69 " pdb=" CB ARG H 69 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1904 not shown) Planarity restraints: 2185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 261 " 0.843 9.50e-02 1.11e+02 3.78e-01 8.67e+01 pdb=" NE ARG B 261 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 261 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 261 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 261 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 69 " 0.466 9.50e-02 1.11e+02 2.09e-01 2.66e+01 pdb=" NE ARG H 69 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG H 69 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG H 69 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 69 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 77 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C PHE H 77 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE H 77 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU H 78 " -0.025 2.00e-02 2.50e+03 ... (remaining 2182 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 599 2.71 - 3.26: 14288 3.26 - 3.81: 19900 3.81 - 4.35: 25722 4.35 - 4.90: 40353 Nonbonded interactions: 100862 Sorted by model distance: nonbonded pdb=" OG SER A 363 " pdb=" OD1 ASN A 365 " model vdw 2.166 3.040 nonbonded pdb=" OE2 GLU B 115 " pdb=" OH TYR B 130 " model vdw 2.172 3.040 nonbonded pdb=" OG SER C 225 " pdb=" OH TYR C 299 " model vdw 2.193 3.040 nonbonded pdb=" O GLN A 336 " pdb=" OG SER A 339 " model vdw 2.214 3.040 nonbonded pdb=" O ASP B 392 " pdb=" OG1 THR B 395 " model vdw 2.218 3.040 ... (remaining 100857 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 177 through 336) selection = (chain 'E' and resid 177 through 336) selection = (chain 'G' and resid 177 through 336) selection = chain 'I' } ncs_group { reference = (chain 'D' and resid 48 through 93) selection = (chain 'F' and resid 48 through 93) selection = (chain 'H' and resid 48 through 93) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.910 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.005 0.066 12881 Z= 0.278 Angle : 0.741 11.137 17346 Z= 0.462 Chirality : 0.048 0.442 1907 Planarity : 0.010 0.378 2185 Dihedral : 15.067 87.671 4819 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.52 % Allowed : 6.60 % Favored : 92.88 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.36 (0.16), residues: 1516 helix: -3.67 (0.11), residues: 1052 sheet: -4.70 (0.94), residues: 14 loop : -2.56 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 252 TYR 0.031 0.001 TYR H 79 PHE 0.015 0.001 PHE C 312 TRP 0.015 0.001 TRP C 256 HIS 0.016 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00519 (12880) covalent geometry : angle 0.74060 (17344) SS BOND : bond 0.00441 ( 1) SS BOND : angle 2.89888 ( 2) hydrogen bonds : bond 0.28994 ( 609) hydrogen bonds : angle 10.22425 ( 1788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 261 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8265 (mtp) cc_final: 0.8050 (mtp) REVERT: A 103 TYR cc_start: 0.7299 (m-80) cc_final: 0.6424 (m-80) REVERT: A 189 ASN cc_start: 0.8940 (t0) cc_final: 0.8489 (p0) REVERT: A 295 ASN cc_start: 0.9094 (t0) cc_final: 0.8763 (t0) REVERT: B 463 CYS cc_start: 0.6990 (t) cc_final: 0.6633 (t) REVERT: C 257 GLU cc_start: 0.8353 (tp30) cc_final: 0.7981 (tp30) REVERT: C 329 MET cc_start: 0.8640 (tpt) cc_final: 0.8349 (tpp) REVERT: I 329 MET cc_start: 0.8234 (tmm) cc_final: 0.8023 (tmm) REVERT: J 86 LYS cc_start: 0.8011 (tmmt) cc_final: 0.7754 (ttmt) REVERT: E 329 MET cc_start: 0.8735 (tmm) cc_final: 0.8485 (tpp) outliers start: 7 outliers final: 5 residues processed: 267 average time/residue: 0.1075 time to fit residues: 40.9709 Evaluate side-chains 190 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 185 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain H residue 76 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 260 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 408 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN C 287 GLN G 196 GLN I 304 HIS E 213 GLN E 287 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.098601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.070366 restraints weight = 30718.348| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.95 r_work: 0.3182 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12881 Z= 0.144 Angle : 0.641 8.892 17346 Z= 0.335 Chirality : 0.042 0.189 1907 Planarity : 0.004 0.058 2185 Dihedral : 5.245 33.585 1694 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.71 % Allowed : 14.76 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.19), residues: 1516 helix: -2.30 (0.13), residues: 1078 sheet: -3.76 (1.27), residues: 14 loop : -2.03 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 261 TYR 0.013 0.001 TYR E 258 PHE 0.025 0.001 PHE G 247 TRP 0.012 0.001 TRP C 256 HIS 0.005 0.001 HIS E 304 Details of bonding type rmsd covalent geometry : bond 0.00310 (12880) covalent geometry : angle 0.64081 (17344) SS BOND : bond 0.00579 ( 1) SS BOND : angle 2.37714 ( 2) hydrogen bonds : bond 0.05056 ( 609) hydrogen bonds : angle 5.43871 ( 1788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7328 (m-80) cc_final: 0.6539 (m-80) REVERT: A 191 MET cc_start: 0.8047 (mtp) cc_final: 0.7186 (mtp) REVERT: A 295 ASN cc_start: 0.9032 (t0) cc_final: 0.8701 (t0) REVERT: A 323 HIS cc_start: 0.9045 (t70) cc_final: 0.8789 (t-170) REVERT: B 384 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8301 (t80) REVERT: B 413 CYS cc_start: 0.8813 (m) cc_final: 0.8325 (m) REVERT: B 463 CYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7785 (t) REVERT: C 257 GLU cc_start: 0.8780 (tp30) cc_final: 0.8467 (tp30) REVERT: C 313 ASP cc_start: 0.8663 (t0) cc_final: 0.7076 (t0) REVERT: G 187 TYR cc_start: 0.8711 (t80) cc_final: 0.8248 (t80) REVERT: G 212 GLU cc_start: 0.8886 (pp20) cc_final: 0.8623 (pp20) REVERT: G 222 ILE cc_start: 0.9121 (tp) cc_final: 0.8812 (tp) REVERT: G 243 MET cc_start: 0.8445 (ttm) cc_final: 0.8098 (ttm) REVERT: G 253 LEU cc_start: 0.9163 (tp) cc_final: 0.8934 (tt) REVERT: G 270 ILE cc_start: 0.8917 (mm) cc_final: 0.8698 (mt) REVERT: G 322 ASP cc_start: 0.8789 (p0) cc_final: 0.8533 (p0) REVERT: G 329 MET cc_start: 0.8680 (ppp) cc_final: 0.8307 (ppp) REVERT: G 330 ASP cc_start: 0.8077 (m-30) cc_final: 0.7854 (m-30) REVERT: I 246 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8622 (tm-30) REVERT: I 293 GLU cc_start: 0.8539 (mp0) cc_final: 0.8201 (mp0) REVERT: J 86 LYS cc_start: 0.8209 (tmmt) cc_final: 0.8002 (ttpt) outliers start: 23 outliers final: 10 residues processed: 239 average time/residue: 0.0967 time to fit residues: 34.7905 Evaluate side-chains 205 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 35 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 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 = 0.3781 r_free = 0.3781 target = 0.097345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068487 restraints weight = 31241.935| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.02 r_work: 0.3125 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12881 Z= 0.167 Angle : 0.620 6.971 17346 Z= 0.323 Chirality : 0.042 0.204 1907 Planarity : 0.004 0.055 2185 Dihedral : 5.074 35.792 1687 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.74 % Allowed : 18.18 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.20), residues: 1516 helix: -1.71 (0.14), residues: 1083 sheet: -3.58 (1.29), residues: 14 loop : -1.89 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 311 TYR 0.014 0.001 TYR E 299 PHE 0.025 0.001 PHE E 312 TRP 0.011 0.001 TRP E 255 HIS 0.006 0.001 HIS E 304 Details of bonding type rmsd covalent geometry : bond 0.00381 (12880) covalent geometry : angle 0.61921 (17344) SS BOND : bond 0.00399 ( 1) SS BOND : angle 2.21405 ( 2) hydrogen bonds : bond 0.04356 ( 609) hydrogen bonds : angle 4.95500 ( 1788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7363 (m-80) cc_final: 0.6640 (m-80) REVERT: A 183 MET cc_start: 0.8772 (ptm) cc_final: 0.8527 (ptm) REVERT: A 295 ASN cc_start: 0.9109 (t0) cc_final: 0.8764 (t0) REVERT: B 311 GLU cc_start: 0.8456 (tt0) cc_final: 0.8031 (tm-30) REVERT: B 384 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8214 (t80) REVERT: B 413 CYS cc_start: 0.8700 (m) cc_final: 0.8221 (m) REVERT: B 463 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7929 (t) REVERT: C 194 GLN cc_start: 0.8634 (mm110) cc_final: 0.8321 (tm-30) REVERT: C 213 GLN cc_start: 0.8537 (mp10) cc_final: 0.8240 (mp10) REVERT: C 246 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8474 (tm-30) REVERT: C 257 GLU cc_start: 0.8772 (tp30) cc_final: 0.8289 (tp30) REVERT: C 284 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8297 (mtp) REVERT: G 176 LEU cc_start: 0.8693 (pp) cc_final: 0.8485 (mp) REVERT: G 222 ILE cc_start: 0.9130 (tp) cc_final: 0.8882 (tp) REVERT: G 243 MET cc_start: 0.8599 (ttm) cc_final: 0.8211 (ttm) REVERT: G 270 ILE cc_start: 0.8886 (mm) cc_final: 0.8647 (mt) REVERT: G 322 ASP cc_start: 0.8843 (p0) cc_final: 0.8643 (p0) REVERT: H 94 GLU cc_start: 0.8316 (tp30) cc_final: 0.7894 (tm-30) REVERT: I 212 GLU cc_start: 0.9119 (tp30) cc_final: 0.8613 (tm-30) REVERT: I 246 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8641 (tm-30) REVERT: I 293 GLU cc_start: 0.8602 (mp0) cc_final: 0.8229 (mp0) REVERT: I 311 ARG cc_start: 0.8351 (tpp80) cc_final: 0.7951 (mmm160) outliers start: 37 outliers final: 25 residues processed: 237 average time/residue: 0.0908 time to fit residues: 32.5317 Evaluate side-chains 227 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 276 MET Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** 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 = 0.3811 r_free = 0.3811 target = 0.099132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.070474 restraints weight = 30819.317| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.01 r_work: 0.3154 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12881 Z= 0.127 Angle : 0.589 6.668 17346 Z= 0.305 Chirality : 0.041 0.222 1907 Planarity : 0.004 0.055 2185 Dihedral : 4.870 35.410 1687 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.97 % Allowed : 20.40 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.21), residues: 1516 helix: -1.33 (0.15), residues: 1084 sheet: -3.36 (1.31), residues: 14 loop : -1.69 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 304 TYR 0.025 0.001 TYR A 410 PHE 0.024 0.001 PHE G 247 TRP 0.011 0.001 TRP C 256 HIS 0.006 0.001 HIS E 304 Details of bonding type rmsd covalent geometry : bond 0.00282 (12880) covalent geometry : angle 0.58877 (17344) SS BOND : bond 0.00412 ( 1) SS BOND : angle 2.11570 ( 2) hydrogen bonds : bond 0.03753 ( 609) hydrogen bonds : angle 4.62816 ( 1788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7292 (m-80) cc_final: 0.6631 (m-80) REVERT: A 295 ASN cc_start: 0.9101 (t0) cc_final: 0.8733 (t0) REVERT: B 271 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7744 (mtmm) REVERT: B 311 GLU cc_start: 0.8347 (tt0) cc_final: 0.7959 (tm-30) REVERT: B 384 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8280 (t80) REVERT: B 413 CYS cc_start: 0.8693 (m) cc_final: 0.8220 (m) REVERT: B 442 MET cc_start: 0.8846 (ptp) cc_final: 0.8612 (pmm) REVERT: B 463 CYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7967 (t) REVERT: C 194 GLN cc_start: 0.8686 (mm110) cc_final: 0.8357 (tm-30) REVERT: C 213 GLN cc_start: 0.8673 (mp10) cc_final: 0.8364 (mp10) REVERT: C 246 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8438 (tm-30) REVERT: C 257 GLU cc_start: 0.8740 (tp30) cc_final: 0.8371 (tp30) REVERT: C 284 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8192 (mtp) REVERT: C 319 GLN cc_start: 0.9393 (tm-30) cc_final: 0.8992 (pt0) REVERT: G 222 ILE cc_start: 0.9094 (tp) cc_final: 0.8853 (tp) REVERT: G 270 ILE cc_start: 0.8923 (mm) cc_final: 0.8700 (mt) REVERT: G 322 ASP cc_start: 0.8855 (p0) cc_final: 0.8602 (p0) REVERT: H 94 GLU cc_start: 0.8243 (tp30) cc_final: 0.7783 (tm-30) REVERT: I 212 GLU cc_start: 0.9155 (tp30) cc_final: 0.8719 (tm-30) REVERT: I 246 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8597 (tm-30) REVERT: I 293 GLU cc_start: 0.8582 (mp0) cc_final: 0.8216 (mp0) REVERT: I 311 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7965 (mmm160) REVERT: J 73 ILE cc_start: 0.8570 (tp) cc_final: 0.8241 (tp) outliers start: 40 outliers final: 24 residues processed: 234 average time/residue: 0.0906 time to fit residues: 31.8897 Evaluate side-chains 222 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 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 = 0.3808 r_free = 0.3808 target = 0.098914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.070199 restraints weight = 31381.784| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.04 r_work: 0.3148 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12881 Z= 0.139 Angle : 0.605 11.452 17346 Z= 0.309 Chirality : 0.042 0.227 1907 Planarity : 0.004 0.051 2185 Dihedral : 4.797 36.460 1687 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.04 % Allowed : 21.74 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.21), residues: 1516 helix: -1.08 (0.15), residues: 1095 sheet: -3.24 (1.32), residues: 14 loop : -1.62 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 52 TYR 0.012 0.001 TYR E 299 PHE 0.023 0.001 PHE G 247 TRP 0.011 0.001 TRP E 255 HIS 0.006 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00320 (12880) covalent geometry : angle 0.60484 (17344) SS BOND : bond 0.00402 ( 1) SS BOND : angle 2.11431 ( 2) hydrogen bonds : bond 0.03619 ( 609) hydrogen bonds : angle 4.49835 ( 1788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7353 (m-80) cc_final: 0.6676 (m-80) REVERT: A 183 MET cc_start: 0.8693 (ptm) cc_final: 0.8456 (ptm) REVERT: A 189 ASN cc_start: 0.8782 (t0) cc_final: 0.8564 (t0) REVERT: A 295 ASN cc_start: 0.9076 (t0) cc_final: 0.8691 (t0) REVERT: B 271 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7747 (mtmm) REVERT: B 311 GLU cc_start: 0.8370 (tt0) cc_final: 0.7996 (tm-30) REVERT: B 384 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.8165 (t80) REVERT: B 413 CYS cc_start: 0.8664 (m) cc_final: 0.8196 (m) REVERT: B 455 ARG cc_start: 0.8678 (mtm110) cc_final: 0.8058 (mtm110) REVERT: B 463 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8030 (t) REVERT: C 194 GLN cc_start: 0.8712 (mm110) cc_final: 0.8311 (tm-30) REVERT: C 213 GLN cc_start: 0.8675 (mp10) cc_final: 0.8347 (mp10) REVERT: C 246 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8568 (tm-30) REVERT: C 257 GLU cc_start: 0.8714 (tp30) cc_final: 0.8292 (tp30) REVERT: C 284 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8373 (mtp) REVERT: C 319 GLN cc_start: 0.9380 (tm-30) cc_final: 0.8992 (pt0) REVERT: G 222 ILE cc_start: 0.9086 (tp) cc_final: 0.8833 (tp) REVERT: G 270 ILE cc_start: 0.8885 (mm) cc_final: 0.8633 (mt) REVERT: G 322 ASP cc_start: 0.8854 (p0) cc_final: 0.8587 (p0) REVERT: G 340 VAL cc_start: 0.9123 (p) cc_final: 0.8921 (m) REVERT: H 94 GLU cc_start: 0.8284 (tp30) cc_final: 0.7808 (tm-30) REVERT: I 212 GLU cc_start: 0.9182 (tp30) cc_final: 0.8771 (tm-30) REVERT: I 246 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8570 (tm-30) REVERT: I 293 GLU cc_start: 0.8582 (mp0) cc_final: 0.8207 (mp0) REVERT: I 311 ARG cc_start: 0.8384 (tpp80) cc_final: 0.8031 (mmm160) REVERT: J 73 ILE cc_start: 0.8564 (tp) cc_final: 0.8229 (tp) outliers start: 41 outliers final: 35 residues processed: 231 average time/residue: 0.0883 time to fit residues: 31.2558 Evaluate side-chains 239 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 0.0020 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN G 184 GLN ** I 184 GLN ** 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 = 0.3819 r_free = 0.3819 target = 0.099442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.070721 restraints weight = 31089.103| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.04 r_work: 0.3158 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12881 Z= 0.134 Angle : 0.609 13.451 17346 Z= 0.307 Chirality : 0.042 0.197 1907 Planarity : 0.003 0.053 2185 Dihedral : 4.738 36.611 1687 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.56 % Allowed : 22.18 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1516 helix: -0.83 (0.16), residues: 1095 sheet: -3.14 (1.32), residues: 14 loop : -1.57 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 52 TYR 0.018 0.001 TYR G 187 PHE 0.020 0.001 PHE E 312 TRP 0.012 0.001 TRP E 255 HIS 0.005 0.001 HIS E 304 Details of bonding type rmsd covalent geometry : bond 0.00307 (12880) covalent geometry : angle 0.60883 (17344) SS BOND : bond 0.00343 ( 1) SS BOND : angle 1.99261 ( 2) hydrogen bonds : bond 0.03450 ( 609) hydrogen bonds : angle 4.37548 ( 1788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7312 (m-80) cc_final: 0.6672 (m-80) REVERT: A 183 MET cc_start: 0.8735 (ptm) cc_final: 0.8514 (ptm) REVERT: A 191 MET cc_start: 0.8104 (tpp) cc_final: 0.7268 (tpp) REVERT: A 295 ASN cc_start: 0.9074 (t0) cc_final: 0.8706 (t0) REVERT: A 338 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8966 (m-80) REVERT: B 212 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9178 (mp) REVERT: B 271 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7757 (mtmm) REVERT: B 311 GLU cc_start: 0.8479 (tt0) cc_final: 0.8111 (tm-30) REVERT: B 384 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 442 MET cc_start: 0.8947 (ptp) cc_final: 0.8655 (pmm) REVERT: B 463 CYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8081 (t) REVERT: C 194 GLN cc_start: 0.8690 (mm110) cc_final: 0.8273 (tm-30) REVERT: C 213 GLN cc_start: 0.8641 (mp10) cc_final: 0.8332 (mt0) REVERT: C 246 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 257 GLU cc_start: 0.8699 (tp30) cc_final: 0.8323 (tp30) REVERT: C 319 GLN cc_start: 0.9343 (tm-30) cc_final: 0.8952 (pt0) REVERT: G 207 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8225 (tt) REVERT: G 222 ILE cc_start: 0.9039 (tp) cc_final: 0.8799 (tp) REVERT: G 322 ASP cc_start: 0.8845 (p0) cc_final: 0.8590 (p0) REVERT: H 94 GLU cc_start: 0.8363 (tp30) cc_final: 0.7796 (tm-30) REVERT: I 196 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: I 212 GLU cc_start: 0.9168 (tp30) cc_final: 0.8758 (tm-30) REVERT: I 246 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8546 (tm-30) REVERT: I 293 GLU cc_start: 0.8586 (mp0) cc_final: 0.8172 (mp0) REVERT: I 311 ARG cc_start: 0.8446 (tpp80) cc_final: 0.8077 (mmm160) REVERT: I 332 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8380 (mmtm) REVERT: J 57 LEU cc_start: 0.8902 (mp) cc_final: 0.8652 (mp) REVERT: J 73 ILE cc_start: 0.8549 (tp) cc_final: 0.8223 (tp) REVERT: E 312 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6403 (p90) outliers start: 48 outliers final: 34 residues processed: 241 average time/residue: 0.0873 time to fit residues: 32.1180 Evaluate side-chains 238 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 38 optimal weight: 0.0270 chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.097491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068645 restraints weight = 31210.650| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.03 r_work: 0.3116 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12881 Z= 0.195 Angle : 0.667 13.463 17346 Z= 0.334 Chirality : 0.044 0.236 1907 Planarity : 0.004 0.050 2185 Dihedral : 4.859 38.113 1687 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.30 % Allowed : 22.70 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.21), residues: 1516 helix: -0.79 (0.16), residues: 1101 sheet: -2.94 (1.87), residues: 10 loop : -1.50 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 52 TYR 0.020 0.001 TYR G 187 PHE 0.019 0.001 PHE G 247 TRP 0.013 0.001 TRP E 255 HIS 0.005 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00458 (12880) covalent geometry : angle 0.66621 (17344) SS BOND : bond 0.00286 ( 1) SS BOND : angle 1.95816 ( 2) hydrogen bonds : bond 0.03675 ( 609) hydrogen bonds : angle 4.52740 ( 1788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7314 (m-80) cc_final: 0.6598 (m-80) REVERT: A 114 MET cc_start: 0.8511 (mtp) cc_final: 0.8253 (mtp) REVERT: A 191 MET cc_start: 0.8266 (tpp) cc_final: 0.7477 (tpp) REVERT: A 295 ASN cc_start: 0.9082 (t0) cc_final: 0.8719 (t0) REVERT: A 338 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8949 (m-80) REVERT: B 212 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9172 (mp) REVERT: B 311 GLU cc_start: 0.8523 (tt0) cc_final: 0.8167 (tm-30) REVERT: B 384 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8149 (t80) REVERT: B 413 CYS cc_start: 0.8656 (m) cc_final: 0.8178 (m) REVERT: B 442 MET cc_start: 0.8936 (ptp) cc_final: 0.8642 (pmm) REVERT: B 455 ARG cc_start: 0.8717 (mtm110) cc_final: 0.8085 (mtm110) REVERT: B 463 CYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8113 (t) REVERT: F 52 ARG cc_start: 0.8909 (tpp80) cc_final: 0.8679 (tpp80) REVERT: C 194 GLN cc_start: 0.8730 (mm110) cc_final: 0.8354 (tm-30) REVERT: C 246 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8569 (tm-30) REVERT: C 257 GLU cc_start: 0.8679 (tp30) cc_final: 0.8373 (tp30) REVERT: C 319 GLN cc_start: 0.9358 (tm-30) cc_final: 0.8951 (pt0) REVERT: G 222 ILE cc_start: 0.9068 (tp) cc_final: 0.8822 (tp) REVERT: G 301 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8505 (mm) REVERT: G 322 ASP cc_start: 0.8805 (p0) cc_final: 0.8553 (p0) REVERT: H 94 GLU cc_start: 0.8326 (tp30) cc_final: 0.7803 (tm-30) REVERT: I 196 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: I 212 GLU cc_start: 0.9108 (tp30) cc_final: 0.8758 (tm-30) REVERT: I 293 GLU cc_start: 0.8576 (mp0) cc_final: 0.8226 (mp0) REVERT: I 311 ARG cc_start: 0.8453 (tpp80) cc_final: 0.8094 (mmm160) REVERT: I 332 LYS cc_start: 0.8678 (mmtm) cc_final: 0.8426 (mmtm) REVERT: J 73 ILE cc_start: 0.8703 (tp) cc_final: 0.8355 (tp) REVERT: E 312 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6573 (p90) outliers start: 58 outliers final: 42 residues processed: 242 average time/residue: 0.0865 time to fit residues: 32.2671 Evaluate side-chains 247 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 135 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN ** I 184 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 = 0.3807 r_free = 0.3807 target = 0.098939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070208 restraints weight = 30623.683| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.00 r_work: 0.3146 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12881 Z= 0.142 Angle : 0.646 14.045 17346 Z= 0.319 Chirality : 0.042 0.203 1907 Planarity : 0.004 0.054 2185 Dihedral : 4.741 35.783 1687 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.78 % Allowed : 23.44 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.22), residues: 1516 helix: -0.61 (0.16), residues: 1097 sheet: -2.65 (1.43), residues: 14 loop : -1.45 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 52 TYR 0.023 0.001 TYR G 187 PHE 0.021 0.001 PHE E 312 TRP 0.012 0.001 TRP E 255 HIS 0.006 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00330 (12880) covalent geometry : angle 0.64568 (17344) SS BOND : bond 0.00283 ( 1) SS BOND : angle 1.81540 ( 2) hydrogen bonds : bond 0.03406 ( 609) hydrogen bonds : angle 4.37986 ( 1788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7187 (m-80) cc_final: 0.6526 (m-80) REVERT: A 183 MET cc_start: 0.8693 (ptm) cc_final: 0.8482 (ptm) REVERT: A 191 MET cc_start: 0.8362 (tpp) cc_final: 0.7777 (tpp) REVERT: A 295 ASN cc_start: 0.9078 (t0) cc_final: 0.8746 (t0) REVERT: A 338 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8947 (m-80) REVERT: B 212 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9144 (mp) REVERT: B 311 GLU cc_start: 0.8532 (tt0) cc_final: 0.8235 (tm-30) REVERT: B 384 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.8028 (t80) REVERT: B 413 CYS cc_start: 0.8602 (m) cc_final: 0.8127 (m) REVERT: B 442 MET cc_start: 0.8925 (ptp) cc_final: 0.8642 (pmm) REVERT: B 455 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8072 (mtm110) REVERT: B 463 CYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8182 (t) REVERT: F 52 ARG cc_start: 0.8907 (tpp80) cc_final: 0.8652 (tpp80) REVERT: C 194 GLN cc_start: 0.8691 (mm110) cc_final: 0.8318 (tm-30) REVERT: C 246 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8502 (tm-30) REVERT: C 257 GLU cc_start: 0.8659 (tp30) cc_final: 0.8355 (tp30) REVERT: C 261 ASP cc_start: 0.8495 (t70) cc_final: 0.8060 (t70) REVERT: C 319 GLN cc_start: 0.9350 (tm-30) cc_final: 0.8946 (pt0) REVERT: G 212 GLU cc_start: 0.8776 (pp20) cc_final: 0.8366 (pp20) REVERT: G 222 ILE cc_start: 0.9025 (tp) cc_final: 0.8777 (tp) REVERT: G 276 MET cc_start: 0.8560 (tpp) cc_final: 0.8323 (ttm) REVERT: G 322 ASP cc_start: 0.8822 (p0) cc_final: 0.8583 (p0) REVERT: H 94 GLU cc_start: 0.8364 (tp30) cc_final: 0.7839 (tm-30) REVERT: I 196 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: I 212 GLU cc_start: 0.9093 (tp30) cc_final: 0.8763 (tm-30) REVERT: I 246 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8358 (tm-30) REVERT: I 293 GLU cc_start: 0.8518 (mp0) cc_final: 0.8064 (mp0) REVERT: I 311 ARG cc_start: 0.8417 (tpp80) cc_final: 0.8058 (mmm160) REVERT: I 332 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8354 (mmtm) REVERT: J 73 ILE cc_start: 0.8641 (tp) cc_final: 0.8309 (tp) REVERT: E 312 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6591 (p90) outliers start: 51 outliers final: 39 residues processed: 239 average time/residue: 0.0903 time to fit residues: 32.7120 Evaluate side-chains 247 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.098073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069166 restraints weight = 31005.724| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.03 r_work: 0.3125 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12881 Z= 0.176 Angle : 0.681 13.540 17346 Z= 0.337 Chirality : 0.043 0.225 1907 Planarity : 0.004 0.050 2185 Dihedral : 4.803 36.602 1687 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.08 % Allowed : 23.15 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.22), residues: 1516 helix: -0.58 (0.16), residues: 1098 sheet: -2.48 (1.51), residues: 14 loop : -1.42 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 52 TYR 0.021 0.001 TYR G 187 PHE 0.020 0.001 PHE E 312 TRP 0.013 0.001 TRP E 255 HIS 0.006 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00413 (12880) covalent geometry : angle 0.68095 (17344) SS BOND : bond 0.00270 ( 1) SS BOND : angle 1.83157 ( 2) hydrogen bonds : bond 0.03530 ( 609) hydrogen bonds : angle 4.44332 ( 1788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7165 (m-80) cc_final: 0.6444 (m-80) REVERT: A 183 MET cc_start: 0.8705 (ptm) cc_final: 0.8485 (ptm) REVERT: A 191 MET cc_start: 0.8361 (tpp) cc_final: 0.7827 (tpp) REVERT: A 295 ASN cc_start: 0.9083 (t0) cc_final: 0.8749 (t0) REVERT: B 212 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9145 (mp) REVERT: B 271 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7787 (mttp) REVERT: B 311 GLU cc_start: 0.8527 (tt0) cc_final: 0.8195 (tm-30) REVERT: B 384 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8067 (t80) REVERT: B 413 CYS cc_start: 0.8596 (m) cc_final: 0.8119 (m) REVERT: B 442 MET cc_start: 0.8906 (ptp) cc_final: 0.8635 (pmm) REVERT: B 455 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8189 (mtm-85) REVERT: B 463 CYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8056 (t) REVERT: F 52 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8688 (tpp80) REVERT: C 194 GLN cc_start: 0.8699 (mm110) cc_final: 0.8330 (tm-30) REVERT: C 246 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8526 (tm-30) REVERT: C 257 GLU cc_start: 0.8721 (tp30) cc_final: 0.8380 (tp30) REVERT: C 261 ASP cc_start: 0.8650 (t70) cc_final: 0.8203 (t70) REVERT: C 319 GLN cc_start: 0.9353 (tm-30) cc_final: 0.8951 (pt0) REVERT: G 222 ILE cc_start: 0.9121 (tp) cc_final: 0.8879 (tp) REVERT: G 285 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8450 (p) REVERT: G 301 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8416 (mm) REVERT: G 322 ASP cc_start: 0.8826 (p0) cc_final: 0.8582 (p0) REVERT: H 94 GLU cc_start: 0.8294 (tp30) cc_final: 0.7764 (tm-30) REVERT: I 196 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: I 212 GLU cc_start: 0.9134 (tp30) cc_final: 0.8808 (tm-30) REVERT: I 311 ARG cc_start: 0.8433 (tpp80) cc_final: 0.8057 (mmm160) REVERT: I 332 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8345 (mmtm) REVERT: J 73 ILE cc_start: 0.8672 (tp) cc_final: 0.8318 (tp) REVERT: E 312 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6675 (p90) outliers start: 55 outliers final: 44 residues processed: 235 average time/residue: 0.0878 time to fit residues: 31.7309 Evaluate side-chains 246 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 69 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 64 optimal weight: 0.2980 chunk 145 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN ** I 184 GLN ** 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 = 0.3822 r_free = 0.3822 target = 0.099958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071065 restraints weight = 30593.571| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.02 r_work: 0.3168 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12881 Z= 0.129 Angle : 0.664 13.642 17346 Z= 0.330 Chirality : 0.042 0.247 1907 Planarity : 0.004 0.053 2185 Dihedral : 4.678 34.511 1687 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.34 % Allowed : 24.26 % Favored : 72.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.22), residues: 1516 helix: -0.41 (0.16), residues: 1095 sheet: -2.28 (1.52), residues: 14 loop : -1.38 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 52 TYR 0.029 0.001 TYR E 187 PHE 0.021 0.001 PHE E 312 TRP 0.011 0.001 TRP E 255 HIS 0.006 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00293 (12880) covalent geometry : angle 0.66351 (17344) SS BOND : bond 0.00276 ( 1) SS BOND : angle 1.73163 ( 2) hydrogen bonds : bond 0.03279 ( 609) hydrogen bonds : angle 4.29267 ( 1788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.553 Fit side-chains REVERT: A 191 MET cc_start: 0.8329 (tpp) cc_final: 0.7895 (tpp) REVERT: A 295 ASN cc_start: 0.9058 (t0) cc_final: 0.8739 (t0) REVERT: B 212 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9139 (mp) REVERT: B 271 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7813 (mttp) REVERT: B 311 GLU cc_start: 0.8547 (tt0) cc_final: 0.8252 (tm-30) REVERT: B 384 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.8025 (t80) REVERT: B 455 ARG cc_start: 0.8699 (mtm110) cc_final: 0.8071 (mtm110) REVERT: B 463 CYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8062 (t) REVERT: F 52 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8665 (tpp80) REVERT: C 194 GLN cc_start: 0.8674 (mm110) cc_final: 0.8308 (tm-30) REVERT: C 246 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8550 (tm-30) REVERT: C 257 GLU cc_start: 0.8611 (tp30) cc_final: 0.8328 (tp30) REVERT: C 319 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8970 (pt0) REVERT: G 212 GLU cc_start: 0.8749 (pp20) cc_final: 0.8322 (pp20) REVERT: G 222 ILE cc_start: 0.9073 (tp) cc_final: 0.8816 (tp) REVERT: G 285 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8391 (p) REVERT: G 301 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8429 (mm) REVERT: G 322 ASP cc_start: 0.8815 (p0) cc_final: 0.8600 (p0) REVERT: H 94 GLU cc_start: 0.8341 (tp30) cc_final: 0.7773 (tm-30) REVERT: I 196 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: I 212 GLU cc_start: 0.9071 (tp30) cc_final: 0.8744 (tm-30) REVERT: I 311 ARG cc_start: 0.8428 (tpp80) cc_final: 0.8081 (mmm160) REVERT: I 332 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8204 (mmtm) REVERT: J 73 ILE cc_start: 0.8503 (tp) cc_final: 0.8155 (tp) REVERT: E 312 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6800 (p90) outliers start: 45 outliers final: 35 residues processed: 229 average time/residue: 0.0838 time to fit residues: 29.6057 Evaluate side-chains 237 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 36 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.100359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071484 restraints weight = 30751.756| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.03 r_work: 0.3154 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12881 Z= 0.128 Angle : 0.673 13.208 17346 Z= 0.335 Chirality : 0.042 0.249 1907 Planarity : 0.004 0.051 2185 Dihedral : 4.662 34.416 1687 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 3.34 % Allowed : 24.41 % Favored : 72.26 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.22), residues: 1516 helix: -0.29 (0.16), residues: 1094 sheet: -2.28 (1.50), residues: 14 loop : -1.32 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 52 TYR 0.030 0.001 TYR E 187 PHE 0.022 0.001 PHE G 247 TRP 0.011 0.001 TRP E 255 HIS 0.011 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00290 (12880) covalent geometry : angle 0.67284 (17344) SS BOND : bond 0.00313 ( 1) SS BOND : angle 1.76255 ( 2) hydrogen bonds : bond 0.03264 ( 609) hydrogen bonds : angle 4.28042 ( 1788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.09 seconds wall clock time: 49 minutes 10.48 seconds (2950.48 seconds total)