Starting phenix.real_space_refine on Mon Dec 30 08:28:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wdn_21642/12_2024/6wdn_21642.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wdn_21642/12_2024/6wdn_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_21642/12_2024/6wdn_21642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wdn_21642/12_2024/6wdn_21642.map" model { file = "/net/cci-nas-00/data/ceres_data/6wdn_21642/12_2024/6wdn_21642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wdn_21642/12_2024/6wdn_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-5532/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: 8.21, 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: 3.10 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: 1.32 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: 3.24 Time building geometry restraints manager: 3.59 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: 2.700 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.930 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- 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 12880 Z= 0.328 Angle : 0.741 11.137 17344 Z= 0.461 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 *********************** 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 : 1.552 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: 0.2777 time to fit residues: 105.1894 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 : 1.620 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 12880 Z= 0.180 Angle : 0.639 8.680 17344 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 *********************** 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 : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7187 (m-80) cc_final: 0.6454 (m-80) REVERT: A 191 MET cc_start: 0.7922 (mtp) cc_final: 0.6930 (mtp) REVERT: A 295 ASN cc_start: 0.8970 (t0) cc_final: 0.8610 (t0) REVERT: A 323 HIS cc_start: 0.9003 (t70) cc_final: 0.8743 (t-170) REVERT: B 384 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8301 (t80) REVERT: B 413 CYS cc_start: 0.8639 (m) cc_final: 0.8113 (m) REVERT: B 463 CYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6877 (t) REVERT: C 313 ASP cc_start: 0.8404 (t0) cc_final: 0.8192 (t0) REVERT: G 187 TYR cc_start: 0.8735 (t80) cc_final: 0.8240 (t80) REVERT: G 212 GLU cc_start: 0.8528 (pp20) cc_final: 0.8320 (pp20) REVERT: G 222 ILE cc_start: 0.9016 (tp) cc_final: 0.8684 (tp) REVERT: G 243 MET cc_start: 0.7889 (ttm) cc_final: 0.7610 (ttm) REVERT: G 270 ILE cc_start: 0.8817 (mm) cc_final: 0.8599 (mt) REVERT: G 322 ASP cc_start: 0.8533 (p0) cc_final: 0.8269 (p0) REVERT: G 329 MET cc_start: 0.8555 (ppp) cc_final: 0.8179 (ppp) REVERT: G 330 ASP cc_start: 0.8056 (m-30) cc_final: 0.7803 (m-30) REVERT: H 69 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7428 (ttm110) REVERT: I 246 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8383 (tm-30) REVERT: I 293 GLU cc_start: 0.8082 (mp0) cc_final: 0.7793 (mp0) REVERT: I 328 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8540 (tp30) REVERT: I 332 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8567 (mmtm) REVERT: J 86 LYS cc_start: 0.8130 (tmmt) cc_final: 0.7907 (ttpt) outliers start: 21 outliers final: 9 residues processed: 238 average time/residue: 0.2422 time to fit residues: 85.0463 Evaluate side-chains 208 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 0.0370 overall best weight: 1.2064 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12880 Z= 0.238 Angle : 0.617 10.876 17344 Z= 0.320 Chirality : 0.042 0.203 1907 Planarity : 0.004 0.054 2185 Dihedral : 5.047 35.734 1687 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.74 % Allowed : 17.73 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.83 (0.20), residues: 1516 helix: -1.67 (0.14), residues: 1078 sheet: -3.51 (1.30), residues: 14 loop : -1.85 (0.29), 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 0.019 0.001 PHE E 312 TYR 0.012 0.001 TYR A 410 ARG 0.007 0.000 ARG C 311 *********************** 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 263 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7215 (m-80) cc_final: 0.6542 (m-80) REVERT: A 183 MET cc_start: 0.8634 (ptm) cc_final: 0.8428 (ptm) REVERT: A 295 ASN cc_start: 0.9072 (t0) cc_final: 0.8737 (t0) REVERT: B 311 GLU cc_start: 0.8048 (tt0) cc_final: 0.7814 (tm-30) REVERT: B 384 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8211 (t80) REVERT: B 413 CYS cc_start: 0.8596 (m) cc_final: 0.8064 (m) REVERT: B 463 CYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7033 (t) REVERT: C 194 GLN cc_start: 0.8642 (mm110) cc_final: 0.8374 (tm-30) REVERT: C 213 GLN cc_start: 0.8427 (mp10) cc_final: 0.8120 (mp10) REVERT: C 246 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 261 ASP cc_start: 0.8096 (t70) cc_final: 0.7799 (t70) REVERT: C 284 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: C 296 ASP cc_start: 0.8260 (p0) cc_final: 0.8019 (p0) REVERT: C 313 ASP cc_start: 0.8480 (t0) cc_final: 0.6500 (t0) REVERT: C 316 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8057 (tttm) REVERT: G 176 LEU cc_start: 0.8605 (pp) cc_final: 0.8372 (mp) REVERT: G 222 ILE cc_start: 0.9066 (tp) cc_final: 0.8806 (tp) REVERT: G 224 ILE cc_start: 0.8362 (tp) cc_final: 0.8133 (tt) REVERT: G 243 MET cc_start: 0.8091 (ttm) cc_final: 0.7748 (ttm) REVERT: G 270 ILE cc_start: 0.8822 (mm) cc_final: 0.8589 (mt) REVERT: G 322 ASP cc_start: 0.8559 (p0) cc_final: 0.8347 (p0) REVERT: H 94 GLU cc_start: 0.8244 (tp30) cc_final: 0.7906 (tm-30) REVERT: I 246 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8388 (tm-30) REVERT: I 293 GLU cc_start: 0.8112 (mp0) cc_final: 0.7810 (mp0) REVERT: E 312 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6891 (p90) outliers start: 37 outliers final: 22 residues processed: 246 average time/residue: 0.2437 time to fit residues: 90.0880 Evaluate side-chains 230 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 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 134 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 129 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12880 Z= 0.166 Angle : 0.597 12.678 17344 Z= 0.304 Chirality : 0.041 0.224 1907 Planarity : 0.004 0.054 2185 Dihedral : 4.817 34.649 1687 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.19 % Allowed : 19.81 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.32 (0.21), residues: 1516 helix: -1.27 (0.15), residues: 1093 sheet: -3.23 (1.34), residues: 14 loop : -1.72 (0.31), residues: 409 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 0.023 0.001 PHE G 247 TYR 0.025 0.001 TYR A 410 ARG 0.006 0.000 ARG A 304 *********************** 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 265 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7182 (m-80) cc_final: 0.6561 (m-80) REVERT: A 295 ASN cc_start: 0.9015 (t0) cc_final: 0.8616 (t0) REVERT: B 311 GLU cc_start: 0.7952 (tt0) cc_final: 0.7744 (tm-30) REVERT: B 384 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8293 (t80) REVERT: B 455 ARG cc_start: 0.8416 (mtm110) cc_final: 0.7995 (mtm110) REVERT: B 463 CYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7055 (t) REVERT: C 194 GLN cc_start: 0.8729 (mm110) cc_final: 0.8430 (tm-30) REVERT: C 213 GLN cc_start: 0.8432 (mp10) cc_final: 0.8113 (mp10) REVERT: C 246 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8337 (tm-30) REVERT: C 284 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7645 (mtp) REVERT: C 319 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8973 (pt0) REVERT: G 176 LEU cc_start: 0.8680 (pp) cc_final: 0.8405 (mp) REVERT: G 222 ILE cc_start: 0.9006 (tp) cc_final: 0.8755 (tp) REVERT: G 270 ILE cc_start: 0.8809 (mm) cc_final: 0.8580 (mt) REVERT: G 322 ASP cc_start: 0.8562 (p0) cc_final: 0.8299 (p0) REVERT: H 94 GLU cc_start: 0.8262 (tp30) cc_final: 0.7868 (tm-30) REVERT: I 246 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8471 (tm-30) REVERT: I 293 GLU cc_start: 0.8091 (mp0) cc_final: 0.7789 (mp0) REVERT: I 332 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8490 (mmtm) REVERT: J 73 ILE cc_start: 0.8518 (tp) cc_final: 0.8153 (tt) REVERT: E 312 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6061 (p90) outliers start: 43 outliers final: 23 residues processed: 244 average time/residue: 0.2345 time to fit residues: 84.6358 Evaluate side-chains 225 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 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 262 ILE 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 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 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 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 120 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12880 Z= 0.352 Angle : 0.677 12.039 17344 Z= 0.344 Chirality : 0.045 0.231 1907 Planarity : 0.004 0.050 2185 Dihedral : 5.019 38.490 1687 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.64 % Allowed : 21.44 % Favored : 74.93 % 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: -1.14 (0.15), residues: 1092 sheet: -3.27 (1.34), residues: 14 loop : -1.68 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 255 HIS 0.006 0.001 HIS A 248 PHE 0.024 0.002 PHE G 247 TYR 0.020 0.002 TYR A 410 ARG 0.006 0.000 ARG A 304 *********************** 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 243 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 1.655 Fit side-chains revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7185 (m-80) cc_final: 0.6544 (m-80) REVERT: A 183 MET cc_start: 0.8639 (ptm) cc_final: 0.8414 (ptm) REVERT: A 191 MET cc_start: 0.8296 (tpp) cc_final: 0.7299 (mmm) REVERT: A 295 ASN cc_start: 0.9052 (t0) cc_final: 0.8660 (t0) REVERT: B 271 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7843 (mtmm) REVERT: B 384 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8219 (t80) REVERT: B 413 CYS cc_start: 0.8545 (m) cc_final: 0.8033 (m) REVERT: B 463 CYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7230 (t) REVERT: C 246 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8380 (tm-30) REVERT: G 176 LEU cc_start: 0.8594 (pp) cc_final: 0.8344 (mp) REVERT: G 222 ILE cc_start: 0.9072 (tp) cc_final: 0.8807 (tp) REVERT: H 94 GLU cc_start: 0.8248 (tp30) cc_final: 0.7853 (tm-30) REVERT: I 212 GLU cc_start: 0.8883 (tp30) cc_final: 0.8521 (tm-30) REVERT: I 293 GLU cc_start: 0.8147 (mp0) cc_final: 0.7815 (mp0) REVERT: I 332 LYS cc_start: 0.8670 (mmtm) cc_final: 0.8415 (mmtm) REVERT: E 312 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6297 (p90) outliers start: 49 outliers final: 39 residues processed: 222 average time/residue: 0.2212 time to fit residues: 75.8138 Evaluate side-chains 225 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 197 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL 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 274 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12880 Z= 0.225 Angle : 0.628 11.418 17344 Z= 0.319 Chirality : 0.042 0.244 1907 Planarity : 0.004 0.055 2185 Dihedral : 4.867 36.302 1687 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.64 % Allowed : 22.85 % Favored : 73.52 % 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: -1.87 (0.21), residues: 1516 helix: -0.94 (0.15), residues: 1096 sheet: -2.91 (1.39), residues: 14 loop : -1.56 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 255 HIS 0.005 0.001 HIS E 304 PHE 0.021 0.001 PHE E 312 TYR 0.021 0.001 TYR A 410 ARG 0.004 0.000 ARG A 304 *********************** 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 254 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7162 (m-80) cc_final: 0.6529 (m-80) REVERT: A 191 MET cc_start: 0.8262 (tpp) cc_final: 0.7447 (mmm) REVERT: A 295 ASN cc_start: 0.9003 (t0) cc_final: 0.8622 (t0) REVERT: A 338 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8931 (m-80) REVERT: B 271 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7832 (mtmm) REVERT: B 311 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7705 (tm-30) REVERT: B 384 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.8168 (t80) REVERT: B 413 CYS cc_start: 0.8542 (m) cc_final: 0.8012 (m) REVERT: B 463 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7163 (t) REVERT: C 194 GLN cc_start: 0.8733 (mm110) cc_final: 0.8297 (tm-30) REVERT: C 246 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 319 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8909 (pt0) REVERT: G 222 ILE cc_start: 0.8969 (tp) cc_final: 0.8712 (tp) REVERT: H 94 GLU cc_start: 0.8338 (tp30) cc_final: 0.7924 (tm-30) REVERT: I 196 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: I 212 GLU cc_start: 0.8892 (tp30) cc_final: 0.8589 (tm-30) REVERT: I 246 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8177 (tm-30) REVERT: I 293 GLU cc_start: 0.8117 (mp0) cc_final: 0.7788 (mp0) REVERT: I 332 LYS cc_start: 0.8722 (mmtm) cc_final: 0.8434 (mmtm) REVERT: J 73 ILE cc_start: 0.8692 (tp) cc_final: 0.8353 (tp) REVERT: E 312 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6381 (p90) outliers start: 49 outliers final: 32 residues processed: 235 average time/residue: 0.2170 time to fit residues: 77.1899 Evaluate side-chains 228 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 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 197 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 74 VAL 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 312 PHE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 144 optimal weight: 0.0970 chunk 90 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN I 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12880 Z= 0.174 Angle : 0.624 11.129 17344 Z= 0.315 Chirality : 0.041 0.235 1907 Planarity : 0.004 0.051 2185 Dihedral : 4.727 35.204 1687 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.56 % Allowed : 23.22 % 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: -1.57 (0.21), residues: 1516 helix: -0.69 (0.16), residues: 1106 sheet: -2.63 (1.42), residues: 14 loop : -1.56 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 255 HIS 0.005 0.001 HIS E 304 PHE 0.020 0.001 PHE E 312 TYR 0.022 0.001 TYR A 410 ARG 0.008 0.000 ARG D 52 *********************** 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 253 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7183 (m-80) cc_final: 0.6588 (m-80) REVERT: A 191 MET cc_start: 0.8124 (tpp) cc_final: 0.7424 (mmm) REVERT: A 236 MET cc_start: 0.8634 (mtt) cc_final: 0.8037 (mmt) REVERT: A 295 ASN cc_start: 0.8995 (t0) cc_final: 0.8629 (t0) REVERT: A 338 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8909 (m-80) REVERT: B 311 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 384 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8130 (t80) REVERT: B 463 CYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7223 (t) REVERT: C 194 GLN cc_start: 0.8723 (mm110) cc_final: 0.8309 (tm-30) REVERT: C 246 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8447 (tm-30) REVERT: C 319 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8944 (pt0) REVERT: G 222 ILE cc_start: 0.8935 (tp) cc_final: 0.8669 (tp) REVERT: G 301 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8381 (mm) REVERT: H 94 GLU cc_start: 0.8342 (tp30) cc_final: 0.7855 (tm-30) REVERT: I 196 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: I 212 GLU cc_start: 0.8772 (tp30) cc_final: 0.8436 (tm-30) REVERT: I 332 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8458 (mmtm) REVERT: J 73 ILE cc_start: 0.8479 (tp) cc_final: 0.8140 (tp) REVERT: J 77 PHE cc_start: 0.8697 (m-80) cc_final: 0.8455 (m-80) REVERT: E 312 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6184 (p90) outliers start: 48 outliers final: 32 residues processed: 233 average time/residue: 0.2191 time to fit residues: 77.4591 Evaluate side-chains 233 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 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 213 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 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 86 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 0.2980 chunk 138 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 A 403 GLN ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12880 Z= 0.162 Angle : 0.628 11.669 17344 Z= 0.315 Chirality : 0.040 0.253 1907 Planarity : 0.003 0.053 2185 Dihedral : 4.572 35.124 1687 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.12 % Allowed : 24.41 % 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: -1.24 (0.22), residues: 1516 helix: -0.43 (0.16), residues: 1097 sheet: -2.48 (1.42), residues: 14 loop : -1.47 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 260 HIS 0.011 0.001 HIS A 323 PHE 0.020 0.001 PHE E 312 TYR 0.022 0.001 TYR A 410 ARG 0.006 0.000 ARG I 311 *********************** 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 253 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7054 (m-80) cc_final: 0.6476 (m-80) REVERT: A 191 MET cc_start: 0.8047 (tpp) cc_final: 0.7465 (mmm) REVERT: A 236 MET cc_start: 0.8657 (mtt) cc_final: 0.8056 (mmt) REVERT: A 295 ASN cc_start: 0.8983 (t0) cc_final: 0.8641 (t0) REVERT: A 338 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8770 (m-80) REVERT: B 271 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7821 (mttp) REVERT: B 311 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7964 (tm-30) REVERT: B 384 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7891 (t80) REVERT: B 463 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7139 (t) REVERT: C 194 GLN cc_start: 0.8698 (mm110) cc_final: 0.8272 (tm-30) REVERT: C 261 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7410 (t70) REVERT: G 212 GLU cc_start: 0.8456 (pp20) cc_final: 0.8053 (pp20) REVERT: G 222 ILE cc_start: 0.8946 (tp) cc_final: 0.8670 (tp) REVERT: G 246 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8163 (tt0) REVERT: G 335 ARG cc_start: 0.8282 (tpp-160) cc_final: 0.7687 (tpp-160) REVERT: H 94 GLU cc_start: 0.8285 (tp30) cc_final: 0.7828 (tm-30) REVERT: I 196 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: I 212 GLU cc_start: 0.8704 (tp30) cc_final: 0.8411 (tm-30) REVERT: I 276 MET cc_start: 0.7959 (mmm) cc_final: 0.7543 (mtt) REVERT: I 319 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8136 (tm-30) REVERT: I 328 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8515 (tp30) REVERT: I 332 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8077 (mmtt) REVERT: J 73 ILE cc_start: 0.8355 (tp) cc_final: 0.8035 (tp) REVERT: J 77 PHE cc_start: 0.8559 (m-80) cc_final: 0.8356 (m-80) REVERT: E 312 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.6445 (p90) outliers start: 42 outliers final: 27 residues processed: 237 average time/residue: 0.2589 time to fit residues: 92.9373 Evaluate side-chains 225 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 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 213 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE 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 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 134 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12880 Z= 0.196 Angle : 0.653 12.163 17344 Z= 0.326 Chirality : 0.042 0.250 1907 Planarity : 0.004 0.050 2185 Dihedral : 4.625 36.251 1687 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.74 % Allowed : 25.15 % Favored : 72.11 % 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: -1.12 (0.22), residues: 1516 helix: -0.38 (0.16), residues: 1097 sheet: -2.52 (1.97), residues: 10 loop : -1.33 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 260 HIS 0.005 0.001 HIS E 304 PHE 0.020 0.001 PHE E 312 TYR 0.022 0.001 TYR A 410 ARG 0.009 0.000 ARG D 52 *********************** 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 231 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7073 (m-80) cc_final: 0.6483 (m-80) REVERT: A 114 MET cc_start: 0.8364 (mtp) cc_final: 0.8087 (mtp) REVERT: A 191 MET cc_start: 0.8017 (tpp) cc_final: 0.7482 (mmm) REVERT: A 236 MET cc_start: 0.8669 (mtt) cc_final: 0.8068 (mmt) REVERT: A 295 ASN cc_start: 0.8992 (t0) cc_final: 0.8644 (t0) REVERT: A 335 MET cc_start: 0.9132 (mmm) cc_final: 0.8796 (mmm) REVERT: B 311 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 384 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.8095 (t80) REVERT: B 463 CYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7114 (t) REVERT: C 253 LEU cc_start: 0.8478 (mp) cc_final: 0.8241 (mp) REVERT: G 222 ILE cc_start: 0.8972 (tp) cc_final: 0.8690 (tp) REVERT: G 301 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8372 (mm) REVERT: G 335 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.7719 (tpp-160) REVERT: H 94 GLU cc_start: 0.8312 (tp30) cc_final: 0.7836 (tm-30) REVERT: I 196 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: I 212 GLU cc_start: 0.8701 (tp30) cc_final: 0.8464 (tm-30) REVERT: I 219 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8543 (mmmm) REVERT: I 276 MET cc_start: 0.8044 (mmm) cc_final: 0.7670 (mtt) REVERT: I 328 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8533 (tp30) REVERT: I 332 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8126 (mmtt) REVERT: J 73 ILE cc_start: 0.8432 (tp) cc_final: 0.8094 (tp) REVERT: J 77 PHE cc_start: 0.8594 (m-80) cc_final: 0.8380 (m-80) outliers start: 37 outliers final: 28 residues processed: 219 average time/residue: 0.2267 time to fit residues: 74.9737 Evaluate side-chains 224 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 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 213 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 267 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 67 LEU Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 274 SER 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 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 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 67 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12880 Z= 0.192 Angle : 0.655 11.825 17344 Z= 0.327 Chirality : 0.042 0.248 1907 Planarity : 0.004 0.053 2185 Dihedral : 4.605 35.924 1687 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.45 % Allowed : 25.67 % Favored : 71.88 % 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: -1.03 (0.22), residues: 1516 helix: -0.29 (0.16), residues: 1100 sheet: -2.27 (1.50), residues: 14 loop : -1.38 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 260 HIS 0.004 0.001 HIS E 304 PHE 0.018 0.001 PHE G 247 TYR 0.023 0.001 TYR E 187 ARG 0.008 0.000 ARG J 52 ********************** 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 223 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 1.718 Fit side-chains REVERT: A 114 MET cc_start: 0.8365 (mtp) cc_final: 0.8097 (mtp) REVERT: A 191 MET cc_start: 0.7963 (tpp) cc_final: 0.7508 (mmm) REVERT: A 295 ASN cc_start: 0.8981 (t0) cc_final: 0.8633 (t0) REVERT: B 271 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7821 (mttp) REVERT: B 384 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.8053 (t80) REVERT: B 463 CYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7041 (t) REVERT: G 212 GLU cc_start: 0.8484 (pp20) cc_final: 0.7988 (pp20) REVERT: G 222 ILE cc_start: 0.8948 (tp) cc_final: 0.8664 (tp) REVERT: G 276 MET cc_start: 0.8093 (tpp) cc_final: 0.7714 (ttm) REVERT: G 285 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8257 (p) REVERT: G 301 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8364 (mm) REVERT: H 94 GLU cc_start: 0.8379 (tp30) cc_final: 0.7868 (tm-30) REVERT: I 196 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: I 212 GLU cc_start: 0.8716 (tp30) cc_final: 0.8494 (tm-30) REVERT: I 276 MET cc_start: 0.8097 (mmm) cc_final: 0.7758 (mtt) REVERT: I 332 LYS cc_start: 0.8631 (mmtm) cc_final: 0.8384 (mmtm) REVERT: J 73 ILE cc_start: 0.8488 (tp) cc_final: 0.8146 (tp) REVERT: J 77 PHE cc_start: 0.8531 (m-80) cc_final: 0.8330 (m-80) outliers start: 33 outliers final: 25 residues processed: 213 average time/residue: 0.2162 time to fit residues: 70.4534 Evaluate side-chains 213 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 267 THR 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 67 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 274 SER 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 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 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 109 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 0.0770 chunk 6 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.100189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071067 restraints weight = 30678.217| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.03 r_work: 0.3169 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12880 Z= 0.202 Angle : 0.669 12.697 17344 Z= 0.333 Chirality : 0.042 0.249 1907 Planarity : 0.004 0.050 2185 Dihedral : 4.608 36.163 1687 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.67 % Allowed : 25.59 % Favored : 71.74 % 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: -0.98 (0.22), residues: 1516 helix: -0.26 (0.16), residues: 1103 sheet: -2.19 (1.54), residues: 14 loop : -1.36 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 255 HIS 0.004 0.001 HIS E 304 PHE 0.018 0.001 PHE G 247 TYR 0.030 0.001 TYR E 187 ARG 0.008 0.000 ARG J 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.93 seconds wall clock time: 52 minutes 43.02 seconds (3163.02 seconds total)