Starting phenix.real_space_refine (version: dev) on Fri May 13 13:51:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/05_2022/6wdn_21642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/05_2022/6wdn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/05_2022/6wdn_21642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/05_2022/6wdn_21642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/05_2022/6wdn_21642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/05_2022/6wdn_21642.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 7.81, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 5.22 Conformation dependent library (CDL) restraints added in 2.0 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: 0.48 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: 3.12 Time building geometry restraints manager: 5.65 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: 99.54 - 106.43: 286 106.43 - 113.33: 6921 113.33 - 120.23: 5115 120.23 - 127.12: 4909 127.12 - 134.02: 113 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 2.440 nonbonded pdb=" OE2 GLU B 115 " pdb=" OH TYR B 130 " model vdw 2.172 2.440 nonbonded pdb=" OG SER C 225 " pdb=" OH TYR C 299 " model vdw 2.193 2.440 nonbonded pdb=" O GLN A 336 " pdb=" OG SER A 339 " model vdw 2.214 2.440 nonbonded pdb=" O ASP B 392 " pdb=" OG1 THR B 395 " model vdw 2.218 2.440 ... (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 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.090 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.090 Process input model: 35.330 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer Outliers : 0.52 % 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 261 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 267 average time/residue: 0.2532 time to fit residues: 96.5287 Evaluate side-chains 185 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1091 time to fit residues: 2.8647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 45 optimal weight: 0.0370 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 295 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 408 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN B 439 GLN C 198 ASN C 287 GLN G 196 GLN I 304 HIS ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 287 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 12880 Z= 0.186 Angle : 0.628 8.821 17344 Z= 0.326 Chirality : 0.041 0.188 1907 Planarity : 0.004 0.059 2185 Dihedral : 5.074 22.405 1685 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 1.41 % 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: -3.53 (0.19), residues: 1516 helix: -2.23 (0.13), residues: 1075 sheet: -3.43 (1.72), residues: 10 loop : -2.04 (0.28), residues: 431 *********************** 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 242 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 223 time to evaluate : 1.642 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 231 average time/residue: 0.2135 time to fit residues: 74.0846 Evaluate side-chains 202 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1103 time to fit residues: 3.8383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 113 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 12880 Z= 0.280 Angle : 0.632 10.395 17344 Z= 0.326 Chirality : 0.043 0.203 1907 Planarity : 0.004 0.055 2185 Dihedral : 5.025 23.245 1685 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.20), residues: 1516 helix: -1.68 (0.15), residues: 1083 sheet: -3.24 (1.75), residues: 10 loop : -1.90 (0.29), residues: 423 *********************** 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 238 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 1.497 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 223 average time/residue: 0.2036 time to fit residues: 69.0547 Evaluate side-chains 201 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1146 time to fit residues: 5.7072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3043 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= 0.165 Angle : 0.587 12.616 17344 Z= 0.297 Chirality : 0.040 0.208 1907 Planarity : 0.004 0.074 2185 Dihedral : 4.720 21.731 1685 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.19 (0.21), residues: 1516 helix: -1.16 (0.15), residues: 1078 sheet: -3.22 (1.72), residues: 10 loop : -1.75 (0.29), residues: 428 *********************** 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 235 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 213 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 224 average time/residue: 0.2141 time to fit residues: 72.7139 Evaluate side-chains 200 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 1.626 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1154 time to fit residues: 4.3153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN C 304 HIS ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 GLN E 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 12880 Z= 0.458 Angle : 0.742 11.477 17344 Z= 0.377 Chirality : 0.047 0.234 1907 Planarity : 0.005 0.063 2185 Dihedral : 5.150 24.124 1685 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 2.37 % 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: -2.29 (0.20), residues: 1516 helix: -1.22 (0.15), residues: 1089 sheet: -3.32 (1.28), residues: 14 loop : -1.81 (0.29), residues: 413 *********************** 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 220 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 1.669 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 211 average time/residue: 0.2087 time to fit residues: 67.3159 Evaluate side-chains 199 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1144 time to fit residues: 5.8813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN G 184 GLN I 177 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12880 Z= 0.217 Angle : 0.646 13.964 17344 Z= 0.325 Chirality : 0.042 0.249 1907 Planarity : 0.004 0.058 2185 Dihedral : 4.878 22.721 1685 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 1.41 % 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: -0.90 (0.16), residues: 1086 sheet: -2.98 (1.33), residues: 14 loop : -1.67 (0.30), residues: 416 *********************** 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 212 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 1.598 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 205 average time/residue: 0.2189 time to fit residues: 68.0407 Evaluate side-chains 194 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 1.579 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1109 time to fit residues: 4.3227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 12880 Z= 0.285 Angle : 0.670 11.800 17344 Z= 0.337 Chirality : 0.044 0.268 1907 Planarity : 0.004 0.100 2185 Dihedral : 4.905 23.101 1685 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 1.34 % 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: -1.72 (0.21), residues: 1516 helix: -0.79 (0.16), residues: 1091 sheet: -2.96 (1.33), residues: 14 loop : -1.63 (0.31), residues: 411 *********************** 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 204 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.695 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 198 average time/residue: 0.2272 time to fit residues: 68.4001 Evaluate side-chains 189 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1353 time to fit residues: 4.2559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.7980 chunk 43 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 13 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 0.0020 chunk 138 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 overall best weight: 0.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3758 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= 0.165 Angle : 0.639 10.763 17344 Z= 0.321 Chirality : 0.041 0.252 1907 Planarity : 0.004 0.086 2185 Dihedral : 4.605 21.077 1685 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.52 % 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: -1.31 (0.22), residues: 1516 helix: -0.44 (0.16), residues: 1087 sheet: -2.85 (1.34), residues: 14 loop : -1.64 (0.30), residues: 415 *********************** 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 211 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 1.599 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 209 average time/residue: 0.2157 time to fit residues: 67.8918 Evaluate side-chains 196 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1156 time to fit residues: 2.6758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 12880 Z= 0.286 Angle : 0.692 12.634 17344 Z= 0.348 Chirality : 0.044 0.260 1907 Planarity : 0.004 0.107 2185 Dihedral : 4.771 22.746 1685 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.59 % 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: -1.36 (0.21), residues: 1516 helix: -0.48 (0.16), residues: 1090 sheet: -2.87 (1.32), residues: 14 loop : -1.63 (0.30), residues: 412 *********************** 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 196 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 1.623 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 192 average time/residue: 0.2112 time to fit residues: 61.9818 Evaluate side-chains 183 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 2.155 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1261 time to fit residues: 3.0406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 12880 Z= 0.230 Angle : 0.688 12.789 17344 Z= 0.342 Chirality : 0.043 0.251 1907 Planarity : 0.004 0.101 2185 Dihedral : 4.699 22.542 1685 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.52 % 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: -1.24 (0.22), residues: 1516 helix: -0.40 (0.16), residues: 1100 sheet: -2.90 (1.32), residues: 14 loop : -1.57 (0.31), residues: 402 ********************** 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 198 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 191 time to evaluate : 1.545 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 194 average time/residue: 0.2131 time to fit residues: 62.5728 Evaluate side-chains 193 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1140 time to fit residues: 2.9804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 6 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.100165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071379 restraints weight = 30584.026| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.98 r_work: 0.3303 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work: 0.3284 rms_B_bonded: 2.76 restraints_weight: 0.1250 r_work: 0.3275 rms_B_bonded: 2.80 restraints_weight: 0.0625 r_work: 0.3265 rms_B_bonded: 2.86 restraints_weight: 0.0312 r_work: 0.3255 rms_B_bonded: 2.94 restraints_weight: 0.0156 r_work: 0.3245 rms_B_bonded: 3.03 restraints_weight: 0.0078 r_work: 0.3235 rms_B_bonded: 3.15 restraints_weight: 0.0039 r_work: 0.3224 rms_B_bonded: 3.28 restraints_weight: 0.0020 r_work: 0.3213 rms_B_bonded: 3.42 restraints_weight: 0.0010 r_work: 0.3202 rms_B_bonded: 3.58 restraints_weight: 0.0005 r_work: 0.3190 rms_B_bonded: 3.77 restraints_weight: 0.0002 r_work: 0.3178 rms_B_bonded: 3.96 restraints_weight: 0.0001 r_work: 0.3166 rms_B_bonded: 4.18 restraints_weight: 0.0001 r_work: 0.3153 rms_B_bonded: 4.42 restraints_weight: 0.0000 r_work: 0.3139 rms_B_bonded: 4.69 restraints_weight: 0.0000 r_work: 0.3125 rms_B_bonded: 4.97 restraints_weight: 0.0000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 12880 Z= 0.198 Angle : 0.679 12.676 17344 Z= 0.337 Chirality : 0.042 0.249 1907 Planarity : 0.004 0.097 2185 Dihedral : 4.620 21.802 1685 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.22 % 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: -1.07 (0.22), residues: 1516 helix: -0.26 (0.16), residues: 1094 sheet: -2.97 (1.29), residues: 14 loop : -1.57 (0.30), residues: 408 =============================================================================== Job complete usr+sys time: 2504.07 seconds wall clock time: 46 minutes 37.57 seconds (2797.57 seconds total)