Starting phenix.real_space_refine on Wed Jul 30 18:40:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wdn_21642/07_2025/6wdn_21642.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wdn_21642/07_2025/6wdn_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_21642/07_2025/6wdn_21642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wdn_21642/07_2025/6wdn_21642.map" model { file = "/net/cci-nas-00/data/ceres_data/6wdn_21642/07_2025/6wdn_21642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wdn_21642/07_2025/6wdn_21642.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'GLU:plan': 4, '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: 8.26, per 1000 atoms: 0.65 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: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.38 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: 3.08 Time building geometry restraints manager: 3.70 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: 2.430 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.380 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.001 TRP C 256 HIS 0.016 0.001 HIS B 260 PHE 0.015 0.001 PHE C 312 TYR 0.031 0.001 TYR H 79 ARG 0.008 0.000 ARG E 252 Details of bonding type rmsd hydrogen bonds : bond 0.28994 ( 609) hydrogen bonds : angle 10.22425 ( 1788) SS BOND : bond 0.00441 ( 1) SS BOND : angle 2.89888 ( 2) covalent geometry : bond 0.00519 (12880) covalent geometry : angle 0.74060 (17344) *********************** 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 : 1.576 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: 0.8352 (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: 0.2546 time to fit residues: 96.4809 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 : 1.406 ------------------------------------------------------------------------------- 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 126 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 71 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.099388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.071082 restraints weight = 30465.006| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.95 r_work: 0.3197 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2307 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= 0.134 Angle : 0.639 8.680 17346 Z= 0.333 Chirality : 0.041 0.192 1907 Planarity : 0.004 0.058 2185 Dihedral : 5.207 32.741 1694 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.56 % Allowed : 14.54 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.19), residues: 1516 helix: -2.28 (0.13), residues: 1078 sheet: -3.73 (1.28), residues: 14 loop : -2.04 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 256 HIS 0.006 0.001 HIS E 304 PHE 0.025 0.001 PHE G 247 TYR 0.013 0.001 TYR E 258 ARG 0.005 0.000 ARG B 261 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 609) hydrogen bonds : angle 5.39381 ( 1788) SS BOND : bond 0.00601 ( 1) SS BOND : angle 2.35287 ( 2) covalent geometry : bond 0.00280 (12880) covalent geometry : angle 0.63902 (17344) *********************** 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: 21 poor density : 228 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7299 (m-80) cc_final: 0.6517 (m-80) REVERT: A 191 MET cc_start: 0.8023 (mtp) cc_final: 0.7124 (mtp) REVERT: A 295 ASN cc_start: 0.9021 (t0) cc_final: 0.8682 (t0) REVERT: A 323 HIS cc_start: 0.9048 (t70) cc_final: 0.8790 (t-170) REVERT: B 384 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8293 (t80) REVERT: B 413 CYS cc_start: 0.8794 (m) cc_final: 0.8306 (m) REVERT: B 463 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7724 (t) REVERT: C 257 GLU cc_start: 0.8784 (tp30) cc_final: 0.8485 (tp30) REVERT: C 313 ASP cc_start: 0.8689 (t0) cc_final: 0.8446 (t0) REVERT: G 187 TYR cc_start: 0.8696 (t80) cc_final: 0.8249 (t80) REVERT: G 212 GLU cc_start: 0.8893 (pp20) cc_final: 0.8641 (pp20) REVERT: G 222 ILE cc_start: 0.9110 (tp) cc_final: 0.8800 (tp) REVERT: G 243 MET cc_start: 0.8423 (ttm) cc_final: 0.8066 (ttm) REVERT: G 253 LEU cc_start: 0.9119 (tp) cc_final: 0.8912 (tt) REVERT: G 270 ILE cc_start: 0.8918 (mm) cc_final: 0.8702 (mt) REVERT: G 322 ASP cc_start: 0.8781 (p0) cc_final: 0.8528 (p0) REVERT: G 329 MET cc_start: 0.8666 (ppp) cc_final: 0.8297 (ppp) REVERT: G 330 ASP cc_start: 0.8091 (m-30) cc_final: 0.7865 (m-30) REVERT: H 69 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7424 (ttm110) REVERT: H 78 LEU cc_start: 0.8258 (tt) cc_final: 0.8047 (tp) REVERT: I 246 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8605 (tm-30) REVERT: I 293 GLU cc_start: 0.8523 (mp0) cc_final: 0.8187 (mp0) REVERT: I 311 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7960 (mmm160) REVERT: I 328 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8655 (tp30) REVERT: I 332 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8549 (mmtm) REVERT: J 57 LEU cc_start: 0.8879 (mp) cc_final: 0.8666 (mp) REVERT: J 86 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7997 (ttpt) outliers start: 21 outliers final: 9 residues processed: 238 average time/residue: 0.2249 time to fit residues: 79.2606 Evaluate side-chains 211 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 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 128 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.097662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068947 restraints weight = 31338.126| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.02 r_work: 0.3124 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12881 Z= 0.171 Angle : 0.617 7.296 17346 Z= 0.322 Chirality : 0.043 0.204 1907 Planarity : 0.004 0.054 2185 Dihedral : 5.054 35.687 1687 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.74 % Allowed : 17.58 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.20), residues: 1516 helix: -1.71 (0.14), residues: 1083 sheet: -3.55 (1.29), residues: 14 loop : -1.87 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 255 HIS 0.006 0.001 HIS E 304 PHE 0.020 0.001 PHE E 312 TYR 0.012 0.001 TYR G 187 ARG 0.007 0.000 ARG C 311 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 609) hydrogen bonds : angle 4.94032 ( 1788) SS BOND : bond 0.00398 ( 1) SS BOND : angle 2.20704 ( 2) covalent geometry : bond 0.00391 (12880) covalent geometry : angle 0.61610 (17344) *********************** 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 252 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7371 (m-80) cc_final: 0.6643 (m-80) REVERT: A 183 MET cc_start: 0.8769 (ptm) cc_final: 0.8520 (ptm) REVERT: A 295 ASN cc_start: 0.9105 (t0) cc_final: 0.8763 (t0) REVERT: B 311 GLU cc_start: 0.8457 (tt0) cc_final: 0.8032 (tm-30) REVERT: B 384 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8220 (t80) REVERT: B 413 CYS cc_start: 0.8694 (m) cc_final: 0.8216 (m) REVERT: B 463 CYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7928 (t) REVERT: C 246 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8514 (tm-30) REVERT: C 257 GLU cc_start: 0.8784 (tp30) cc_final: 0.8315 (tp30) REVERT: C 284 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8320 (mtp) REVERT: C 296 ASP cc_start: 0.8545 (p0) cc_final: 0.8278 (p0) REVERT: C 313 ASP cc_start: 0.8766 (t0) cc_final: 0.7121 (t0) REVERT: C 316 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8192 (tttm) REVERT: G 176 LEU cc_start: 0.8673 (pp) cc_final: 0.8468 (mp) REVERT: G 222 ILE cc_start: 0.9137 (tp) cc_final: 0.8892 (tp) REVERT: G 224 ILE cc_start: 0.8363 (tp) cc_final: 0.8140 (tt) REVERT: G 243 MET cc_start: 0.8593 (ttm) cc_final: 0.8219 (ttm) REVERT: G 270 ILE cc_start: 0.8882 (mm) cc_final: 0.8644 (mt) REVERT: H 94 GLU cc_start: 0.8318 (tp30) cc_final: 0.7893 (tm-30) REVERT: I 212 GLU cc_start: 0.9118 (tp30) cc_final: 0.8606 (tm-30) REVERT: I 246 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8624 (tm-30) REVERT: I 293 GLU cc_start: 0.8588 (mp0) cc_final: 0.8207 (mp0) REVERT: I 311 ARG cc_start: 0.8374 (tpp80) cc_final: 0.7974 (mmm160) REVERT: E 312 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.7061 (p90) outliers start: 37 outliers final: 24 residues processed: 235 average time/residue: 0.2204 time to fit residues: 77.9222 Evaluate side-chains 225 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 E residue 214 LEU Chi-restraints excluded: chain E residue 312 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.098701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070032 restraints weight = 30688.034| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.01 r_work: 0.3147 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2990 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= 0.142 Angle : 0.601 6.732 17346 Z= 0.310 Chirality : 0.042 0.223 1907 Planarity : 0.004 0.055 2185 Dihedral : 4.902 35.638 1687 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.26 % Allowed : 19.96 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.21), residues: 1516 helix: -1.34 (0.15), residues: 1081 sheet: -3.31 (1.32), residues: 14 loop : -1.67 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 255 HIS 0.006 0.001 HIS E 304 PHE 0.019 0.001 PHE E 312 TYR 0.025 0.001 TYR A 410 ARG 0.006 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 609) hydrogen bonds : angle 4.66486 ( 1788) SS BOND : bond 0.00397 ( 1) SS BOND : angle 2.11119 ( 2) covalent geometry : bond 0.00319 (12880) covalent geometry : angle 0.60108 (17344) *********************** 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 260 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7308 (m-80) cc_final: 0.6624 (m-80) REVERT: A 114 MET cc_start: 0.8532 (mtp) cc_final: 0.8305 (mtp) REVERT: A 295 ASN cc_start: 0.9117 (t0) cc_final: 0.8754 (t0) REVERT: B 271 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7760 (mtmm) REVERT: B 311 GLU cc_start: 0.8384 (tt0) cc_final: 0.7968 (tm-30) REVERT: B 384 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8297 (t80) REVERT: B 413 CYS cc_start: 0.8683 (m) cc_final: 0.8201 (m) REVERT: B 442 MET cc_start: 0.8880 (ptp) cc_final: 0.8628 (pmm) REVERT: B 463 CYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7984 (t) REVERT: C 194 GLN cc_start: 0.8734 (mm110) cc_final: 0.8358 (tm-30) REVERT: C 213 GLN cc_start: 0.8671 (mp10) cc_final: 0.8355 (mp10) REVERT: C 246 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 257 GLU cc_start: 0.8763 (tp30) cc_final: 0.8354 (tp30) REVERT: C 284 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8269 (mtp) REVERT: G 176 LEU cc_start: 0.8699 (pp) cc_final: 0.8475 (mp) REVERT: G 222 ILE cc_start: 0.9098 (tp) cc_final: 0.8863 (tp) REVERT: G 253 LEU cc_start: 0.9120 (tp) cc_final: 0.8873 (tt) REVERT: G 270 ILE cc_start: 0.8907 (mm) cc_final: 0.8676 (mt) REVERT: H 94 GLU cc_start: 0.8159 (tp30) cc_final: 0.7706 (tm-30) REVERT: I 212 GLU cc_start: 0.9183 (tp30) cc_final: 0.8736 (tm-30) REVERT: I 246 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8613 (tm-30) REVERT: I 293 GLU cc_start: 0.8595 (mp0) cc_final: 0.8217 (mp0) REVERT: I 311 ARG cc_start: 0.8326 (tpp80) cc_final: 0.7949 (mmm160) REVERT: I 332 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8340 (mmtm) REVERT: J 73 ILE cc_start: 0.8544 (tp) cc_final: 0.8202 (tp) REVERT: E 312 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6509 (p90) outliers start: 44 outliers final: 27 residues processed: 240 average time/residue: 0.2317 time to fit residues: 83.7607 Evaluate side-chains 230 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 267 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain D residue 78 LEU 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 209 ASP Chi-restraints excluded: chain I residue 266 VAL 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 312 PHE 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 112 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 0.0770 chunk 3 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 326 GLN C 339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.097729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068970 restraints weight = 31237.312| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.03 r_work: 0.3120 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12881 Z= 0.177 Angle : 0.625 9.808 17346 Z= 0.321 Chirality : 0.043 0.229 1907 Planarity : 0.004 0.051 2185 Dihedral : 4.916 36.992 1687 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.64 % Allowed : 21.22 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.21), residues: 1516 helix: -1.17 (0.15), residues: 1090 sheet: -3.26 (1.32), residues: 14 loop : -1.60 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 255 HIS 0.005 0.001 HIS E 304 PHE 0.027 0.001 PHE G 247 TYR 0.021 0.001 TYR A 410 ARG 0.005 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 609) hydrogen bonds : angle 4.60839 ( 1788) SS BOND : bond 0.00377 ( 1) SS BOND : angle 2.14720 ( 2) covalent geometry : bond 0.00411 (12880) covalent geometry : angle 0.62411 (17344) *********************** 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 255 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7302 (m-80) cc_final: 0.6665 (m-80) REVERT: A 183 MET cc_start: 0.8695 (ptm) cc_final: 0.8460 (ptm) REVERT: A 189 ASN cc_start: 0.8799 (t0) cc_final: 0.8580 (t0) REVERT: A 295 ASN cc_start: 0.9081 (t0) cc_final: 0.8703 (t0) REVERT: B 271 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7735 (mtmm) REVERT: B 311 GLU cc_start: 0.8380 (tt0) cc_final: 0.8025 (tm-30) REVERT: B 384 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8178 (t80) REVERT: B 413 CYS cc_start: 0.8691 (m) cc_final: 0.8219 (m) REVERT: B 463 CYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8052 (t) REVERT: C 194 GLN cc_start: 0.8756 (mm110) cc_final: 0.8358 (tm-30) REVERT: C 213 GLN cc_start: 0.8729 (mp10) cc_final: 0.8415 (mp10) REVERT: C 246 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 257 GLU cc_start: 0.8711 (tp30) cc_final: 0.8293 (tp30) REVERT: C 284 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: C 319 GLN cc_start: 0.9386 (tm-30) cc_final: 0.8990 (pt0) REVERT: G 176 LEU cc_start: 0.8716 (pp) cc_final: 0.8487 (mp) REVERT: G 222 ILE cc_start: 0.9119 (tp) cc_final: 0.8869 (tp) REVERT: H 94 GLU cc_start: 0.8357 (tp30) cc_final: 0.7867 (tm-30) REVERT: I 212 GLU cc_start: 0.9198 (tp30) cc_final: 0.8797 (tm-30) REVERT: I 246 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8623 (tm-30) REVERT: I 293 GLU cc_start: 0.8592 (mp0) cc_final: 0.8222 (mp0) REVERT: I 311 ARG cc_start: 0.8417 (tpp80) cc_final: 0.8019 (mmm160) REVERT: I 332 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8429 (mmtm) REVERT: J 73 ILE cc_start: 0.8637 (tp) cc_final: 0.8285 (tp) REVERT: E 312 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6211 (p90) outliers start: 49 outliers final: 41 residues processed: 234 average time/residue: 0.2536 time to fit residues: 91.1954 Evaluate side-chains 243 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 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 C residue 312 PHE Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain D residue 78 LEU 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 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 198 ASN Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 276 MET 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 312 PHE 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 76 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 E 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.097270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068445 restraints weight = 31352.848| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.03 r_work: 0.3110 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3222 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 : 0.644 9.384 17346 Z= 0.330 Chirality : 0.044 0.237 1907 Planarity : 0.004 0.055 2185 Dihedral : 4.953 37.624 1687 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.93 % Allowed : 22.85 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.21), residues: 1516 helix: -1.01 (0.15), residues: 1097 sheet: -2.91 (1.40), residues: 14 loop : -1.60 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 255 HIS 0.005 0.001 HIS E 304 PHE 0.022 0.001 PHE G 247 TYR 0.012 0.001 TYR B 114 ARG 0.005 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 609) hydrogen bonds : angle 4.59967 ( 1788) SS BOND : bond 0.00308 ( 1) SS BOND : angle 2.04591 ( 2) covalent geometry : bond 0.00453 (12880) covalent geometry : angle 0.64382 (17344) *********************** 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 260 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7306 (m-80) cc_final: 0.6617 (m-80) REVERT: A 114 MET cc_start: 0.8594 (mtt) cc_final: 0.8391 (mtp) REVERT: A 191 MET cc_start: 0.8063 (tpp) cc_final: 0.7007 (tpp) REVERT: A 295 ASN cc_start: 0.9074 (t0) cc_final: 0.8720 (t0) REVERT: A 338 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8905 (m-80) REVERT: B 271 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7749 (mtmm) REVERT: B 311 GLU cc_start: 0.8404 (tt0) cc_final: 0.8075 (tm-30) REVERT: B 384 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8190 (t80) REVERT: B 413 CYS cc_start: 0.8669 (m) cc_final: 0.8188 (m) REVERT: B 442 MET cc_start: 0.8873 (ptp) cc_final: 0.8608 (pmm) REVERT: B 455 ARG cc_start: 0.8718 (mtm110) cc_final: 0.8049 (mtm110) REVERT: B 463 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8112 (t) REVERT: C 194 GLN cc_start: 0.8744 (mm110) cc_final: 0.8328 (tm-30) REVERT: C 213 GLN cc_start: 0.8734 (mp10) cc_final: 0.8394 (mt0) REVERT: C 246 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 257 GLU cc_start: 0.8736 (tp30) cc_final: 0.8433 (tp30) REVERT: C 319 GLN cc_start: 0.9395 (tm-30) cc_final: 0.9067 (pt0) REVERT: G 222 ILE cc_start: 0.9080 (tp) cc_final: 0.8834 (tp) REVERT: H 94 GLU cc_start: 0.8360 (tp30) cc_final: 0.7860 (tm-30) REVERT: I 196 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: I 212 GLU cc_start: 0.9197 (tp30) cc_final: 0.8813 (tm-30) REVERT: I 293 GLU cc_start: 0.8608 (mp0) cc_final: 0.8217 (mp0) REVERT: I 311 ARG cc_start: 0.8476 (tpp80) cc_final: 0.8099 (mmm160) REVERT: I 332 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8372 (mmtm) REVERT: E 312 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6537 (p90) outliers start: 53 outliers final: 39 residues processed: 239 average time/residue: 0.2127 time to fit residues: 77.3139 Evaluate side-chains 238 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 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 254 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 78 LEU 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 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 266 VAL Chi-restraints excluded: chain I residue 276 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 132 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 339 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 = 0.3812 r_free = 0.3812 target = 0.099209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.070401 restraints weight = 30797.472| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.02 r_work: 0.3149 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12881 Z= 0.131 Angle : 0.629 11.410 17346 Z= 0.319 Chirality : 0.042 0.262 1907 Planarity : 0.004 0.052 2185 Dihedral : 4.783 35.943 1687 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.86 % Allowed : 23.59 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.21), residues: 1516 helix: -0.78 (0.16), residues: 1096 sheet: -2.75 (1.39), residues: 14 loop : -1.52 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 255 HIS 0.006 0.001 HIS A 248 PHE 0.020 0.001 PHE E 312 TYR 0.011 0.001 TYR E 258 ARG 0.008 0.000 ARG D 52 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 609) hydrogen bonds : angle 4.41369 ( 1788) SS BOND : bond 0.00292 ( 1) SS BOND : angle 1.86917 ( 2) covalent geometry : bond 0.00295 (12880) covalent geometry : angle 0.62913 (17344) *********************** 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: 52 poor density : 212 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7254 (m-80) cc_final: 0.6598 (m-80) REVERT: A 183 MET cc_start: 0.8693 (ptm) cc_final: 0.8460 (ptm) REVERT: A 191 MET cc_start: 0.8223 (tpp) cc_final: 0.7583 (tpp) REVERT: A 295 ASN cc_start: 0.9052 (t0) cc_final: 0.8690 (t0) REVERT: A 338 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8934 (m-80) REVERT: B 212 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9176 (mp) REVERT: B 311 GLU cc_start: 0.8516 (tt0) cc_final: 0.8149 (tm-30) REVERT: B 384 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8046 (t80) REVERT: B 413 CYS cc_start: 0.8669 (m) cc_final: 0.8194 (m) REVERT: B 442 MET cc_start: 0.8865 (ptp) cc_final: 0.8616 (pmm) REVERT: B 463 CYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8167 (t) REVERT: C 194 GLN cc_start: 0.8709 (mm110) cc_final: 0.8335 (tm-30) REVERT: C 246 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8045 (tm-30) REVERT: C 257 GLU cc_start: 0.8697 (tp30) cc_final: 0.8411 (tp30) REVERT: C 278 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8391 (mtp) REVERT: C 319 GLN cc_start: 0.9333 (tm-30) cc_final: 0.8935 (pt0) REVERT: G 222 ILE cc_start: 0.9030 (tp) cc_final: 0.8779 (tp) REVERT: G 253 LEU cc_start: 0.9109 (tp) cc_final: 0.8886 (tt) REVERT: G 270 ILE cc_start: 0.8851 (mm) cc_final: 0.8607 (mt) REVERT: G 301 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8482 (mm) REVERT: H 94 GLU cc_start: 0.8382 (tp30) cc_final: 0.7841 (tm-30) REVERT: I 196 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: I 212 GLU cc_start: 0.9094 (tp30) cc_final: 0.8758 (tm-30) REVERT: I 246 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8562 (tm-30) REVERT: I 293 GLU cc_start: 0.8571 (mp0) cc_final: 0.8182 (mp0) REVERT: I 311 ARG cc_start: 0.8466 (tpp80) cc_final: 0.8106 (mmm160) REVERT: I 332 LYS cc_start: 0.8594 (mmtm) cc_final: 0.8317 (mmtm) REVERT: J 73 ILE cc_start: 0.8634 (tp) cc_final: 0.8293 (tp) REVERT: E 312 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6454 (p90) outliers start: 52 outliers final: 37 residues processed: 243 average time/residue: 0.2686 time to fit residues: 99.8540 Evaluate side-chains 243 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 173 ILE 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 278 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 204 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 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 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 276 MET 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 125 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.098732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.069589 restraints weight = 31470.853| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.06 r_work: 0.3133 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3602 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= 0.145 Angle : 0.646 12.766 17346 Z= 0.324 Chirality : 0.042 0.226 1907 Planarity : 0.003 0.053 2185 Dihedral : 4.733 36.825 1687 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.86 % Allowed : 23.66 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1516 helix: -0.61 (0.16), residues: 1096 sheet: -2.48 (1.47), residues: 14 loop : -1.46 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 255 HIS 0.006 0.001 HIS A 248 PHE 0.021 0.001 PHE E 312 TYR 0.021 0.001 TYR G 187 ARG 0.004 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 609) hydrogen bonds : angle 4.40276 ( 1788) SS BOND : bond 0.00312 ( 1) SS BOND : angle 1.85762 ( 2) covalent geometry : bond 0.00334 (12880) covalent geometry : angle 0.64575 (17344) *********************** 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 259 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7179 (m-80) cc_final: 0.6516 (m-80) REVERT: A 191 MET cc_start: 0.8253 (tpp) cc_final: 0.7650 (tpp) REVERT: A 236 MET cc_start: 0.8669 (mtt) cc_final: 0.8099 (mmt) REVERT: A 295 ASN cc_start: 0.9080 (t0) cc_final: 0.8749 (t0) REVERT: A 338 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8919 (m-80) REVERT: B 212 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9156 (mp) REVERT: B 311 GLU cc_start: 0.8544 (tt0) cc_final: 0.8242 (tm-30) REVERT: B 384 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.8114 (t80) REVERT: B 413 CYS cc_start: 0.8584 (m) cc_final: 0.8106 (m) REVERT: B 442 MET cc_start: 0.8900 (ptp) cc_final: 0.8626 (pmm) REVERT: B 463 CYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8120 (t) REVERT: F 52 ARG cc_start: 0.8918 (tpp80) cc_final: 0.8674 (tpp80) REVERT: C 194 GLN cc_start: 0.8696 (mm110) cc_final: 0.8327 (tm-30) REVERT: C 246 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8010 (tm-30) REVERT: C 257 GLU cc_start: 0.8722 (tp30) cc_final: 0.8404 (tp30) REVERT: C 278 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8413 (mtp) REVERT: C 319 GLN cc_start: 0.9342 (tm-30) cc_final: 0.8953 (pt0) REVERT: G 222 ILE cc_start: 0.9105 (tp) cc_final: 0.8861 (tp) REVERT: G 301 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8449 (mm) REVERT: H 94 GLU cc_start: 0.8283 (tp30) cc_final: 0.7752 (tm-30) REVERT: I 192 ILE cc_start: 0.8890 (pt) cc_final: 0.8397 (pt) REVERT: I 196 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: I 212 GLU cc_start: 0.9100 (tp30) cc_final: 0.8765 (tm-30) REVERT: I 246 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8370 (tm-30) REVERT: I 293 GLU cc_start: 0.8574 (mp0) cc_final: 0.8130 (mp0) REVERT: I 311 ARG cc_start: 0.8446 (tpp80) cc_final: 0.8083 (mmm160) REVERT: I 332 LYS cc_start: 0.8570 (mmtm) cc_final: 0.8275 (mmtm) REVERT: J 73 ILE cc_start: 0.8637 (tp) cc_final: 0.8294 (tp) REVERT: E 312 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6655 (p90) outliers start: 52 outliers final: 40 residues processed: 237 average time/residue: 0.2262 time to fit residues: 82.0683 Evaluate side-chains 246 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 1.812 ------------------------------------------------------------------------------- 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 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 173 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 291 LEU 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 C residue 278 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 183 VAL 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 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 276 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 159 ASN ** 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 = 0.3813 r_free = 0.3813 target = 0.099219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070139 restraints weight = 31130.506| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.06 r_work: 0.3147 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3718 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= 0.140 Angle : 0.655 12.844 17346 Z= 0.330 Chirality : 0.042 0.231 1907 Planarity : 0.004 0.051 2185 Dihedral : 4.690 36.517 1687 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.64 % Allowed : 23.89 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1516 helix: -0.50 (0.16), residues: 1091 sheet: -2.40 (1.48), residues: 14 loop : -1.45 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 255 HIS 0.006 0.001 HIS A 248 PHE 0.019 0.001 PHE E 312 TYR 0.022 0.001 TYR G 187 ARG 0.009 0.000 ARG D 52 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 609) hydrogen bonds : angle 4.36348 ( 1788) SS BOND : bond 0.00292 ( 1) SS BOND : angle 1.82398 ( 2) covalent geometry : bond 0.00322 (12880) covalent geometry : angle 0.65427 (17344) *********************** 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 258 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7214 (m-80) cc_final: 0.6553 (m-80) REVERT: A 183 MET cc_start: 0.8514 (ptm) cc_final: 0.8249 (ptm) REVERT: A 191 MET cc_start: 0.8180 (tpp) cc_final: 0.7745 (tpp) REVERT: A 236 MET cc_start: 0.8669 (mtt) cc_final: 0.8096 (mmt) REVERT: A 295 ASN cc_start: 0.9058 (t0) cc_final: 0.8719 (t0) REVERT: B 168 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7813 (tt) REVERT: B 212 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9138 (mp) REVERT: B 271 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7749 (mttp) REVERT: B 311 GLU cc_start: 0.8530 (tt0) cc_final: 0.8193 (tm-30) REVERT: B 384 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.8000 (t80) REVERT: B 413 CYS cc_start: 0.8542 (m) cc_final: 0.8075 (m) REVERT: B 442 MET cc_start: 0.8919 (ptp) cc_final: 0.8640 (pmm) REVERT: B 463 CYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8066 (t) REVERT: C 194 GLN cc_start: 0.8694 (mm110) cc_final: 0.8302 (tm-30) REVERT: C 246 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8563 (tm-30) REVERT: C 257 GLU cc_start: 0.8723 (tp30) cc_final: 0.8456 (tp30) REVERT: C 278 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8364 (mtp) REVERT: C 319 GLN cc_start: 0.9341 (tm-30) cc_final: 0.8985 (pt0) REVERT: G 212 GLU cc_start: 0.8745 (pp20) cc_final: 0.8323 (pp20) REVERT: G 222 ILE cc_start: 0.9082 (tp) cc_final: 0.8835 (tp) REVERT: G 270 ILE cc_start: 0.8831 (mm) cc_final: 0.8589 (mt) REVERT: G 285 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8410 (p) REVERT: G 301 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8460 (mm) REVERT: H 94 GLU cc_start: 0.8356 (tp30) cc_final: 0.7789 (tm-30) REVERT: I 192 ILE cc_start: 0.8876 (pt) cc_final: 0.8388 (pt) REVERT: I 196 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: I 212 GLU cc_start: 0.9114 (tp30) cc_final: 0.8775 (tm-30) REVERT: I 246 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8327 (tm-30) REVERT: I 311 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8092 (mmm160) REVERT: I 328 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8612 (tp30) REVERT: I 332 LYS cc_start: 0.8577 (mmtm) cc_final: 0.8052 (mmtt) REVERT: J 73 ILE cc_start: 0.8454 (tp) cc_final: 0.8105 (tp) outliers start: 49 outliers final: 36 residues processed: 240 average time/residue: 0.2065 time to fit residues: 76.0137 Evaluate side-chains 242 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 291 LEU 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 267 THR Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 186 LEU 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 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 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 293 GLU 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 120 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 40 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.099470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070466 restraints weight = 30583.231| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.01 r_work: 0.3151 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3814 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= 0.142 Angle : 0.665 13.264 17346 Z= 0.334 Chirality : 0.042 0.247 1907 Planarity : 0.003 0.053 2185 Dihedral : 4.696 36.354 1687 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.49 % Allowed : 24.11 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1516 helix: -0.43 (0.16), residues: 1094 sheet: -2.35 (1.49), residues: 14 loop : -1.39 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 255 HIS 0.012 0.001 HIS A 323 PHE 0.023 0.001 PHE G 247 TYR 0.027 0.001 TYR E 187 ARG 0.004 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 609) hydrogen bonds : angle 4.34206 ( 1788) SS BOND : bond 0.00292 ( 1) SS BOND : angle 1.80956 ( 2) covalent geometry : bond 0.00325 (12880) covalent geometry : angle 0.66477 (17344) ********************** 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: 47 poor density : 200 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8506 (mtt) cc_final: 0.8224 (mtp) REVERT: A 183 MET cc_start: 0.8544 (ptm) cc_final: 0.8311 (ptm) REVERT: A 191 MET cc_start: 0.8168 (tpp) cc_final: 0.7767 (tpp) REVERT: A 295 ASN cc_start: 0.9066 (t0) cc_final: 0.8734 (t0) REVERT: B 168 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7806 (tt) REVERT: B 212 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9138 (mp) REVERT: B 271 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7777 (mttp) REVERT: B 311 GLU cc_start: 0.8534 (tt0) cc_final: 0.8225 (tm-30) REVERT: B 384 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.8052 (t80) REVERT: B 413 CYS cc_start: 0.8509 (m) cc_final: 0.8051 (m) REVERT: B 442 MET cc_start: 0.8898 (ptp) cc_final: 0.8618 (pmm) REVERT: B 463 CYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8086 (t) REVERT: C 194 GLN cc_start: 0.8664 (mm110) cc_final: 0.8293 (tm-30) REVERT: C 246 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8574 (tm-30) REVERT: C 257 GLU cc_start: 0.8634 (tp30) cc_final: 0.8292 (tp30) REVERT: C 278 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8347 (mtp) REVERT: C 319 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8991 (pt0) REVERT: G 212 GLU cc_start: 0.8782 (pp20) cc_final: 0.8344 (pp20) REVERT: G 222 ILE cc_start: 0.9080 (tp) cc_final: 0.8830 (tp) REVERT: G 270 ILE cc_start: 0.8834 (mm) cc_final: 0.8595 (mt) REVERT: G 285 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8396 (p) REVERT: G 301 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8409 (mm) REVERT: G 328 GLU cc_start: 0.8889 (tp30) cc_final: 0.8570 (mm-30) REVERT: H 94 GLU cc_start: 0.8365 (tp30) cc_final: 0.7784 (tm-30) REVERT: I 192 ILE cc_start: 0.8869 (pt) cc_final: 0.8065 (pt) REVERT: I 196 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7160 (mp10) REVERT: I 212 GLU cc_start: 0.9110 (tp30) cc_final: 0.8788 (tm-30) REVERT: I 293 GLU cc_start: 0.8492 (mp0) cc_final: 0.8029 (mp0) REVERT: I 311 ARG cc_start: 0.8446 (tpp80) cc_final: 0.8059 (mmm160) REVERT: I 328 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8600 (tp30) REVERT: I 332 LYS cc_start: 0.8553 (mmtm) cc_final: 0.8068 (mmtt) REVERT: J 73 ILE cc_start: 0.8473 (tp) cc_final: 0.8130 (tp) outliers start: 47 outliers final: 37 residues processed: 229 average time/residue: 0.2016 time to fit residues: 70.8289 Evaluate side-chains 238 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 291 LEU 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 267 THR Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 183 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 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 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 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 290 VAL Chi-restraints excluded: chain E residue 293 GLU 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 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.098453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069462 restraints weight = 30833.321| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.01 r_work: 0.3131 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12881 Z= 0.171 Angle : 0.683 12.965 17346 Z= 0.344 Chirality : 0.044 0.250 1907 Planarity : 0.004 0.051 2185 Dihedral : 4.768 37.408 1687 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.41 % Allowed : 24.55 % Favored : 72.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1516 helix: -0.44 (0.16), residues: 1087 sheet: -2.33 (1.54), residues: 14 loop : -1.28 (0.33), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 255 HIS 0.006 0.001 HIS A 248 PHE 0.022 0.001 PHE G 247 TYR 0.031 0.001 TYR E 187 ARG 0.004 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 609) hydrogen bonds : angle 4.42423 ( 1788) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.82599 ( 2) covalent geometry : bond 0.00397 (12880) covalent geometry : angle 0.68242 (17344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6628.97 seconds wall clock time: 116 minutes 41.79 seconds (7001.79 seconds total)