Starting phenix.real_space_refine on Thu Mar 5 21:21:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xkq_33264/03_2026/7xkq_33264.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkq_33264/03_2026/7xkq_33264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xkq_33264/03_2026/7xkq_33264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkq_33264/03_2026/7xkq_33264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xkq_33264/03_2026/7xkq_33264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkq_33264/03_2026/7xkq_33264.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 6 5.21 5 S 80 5.16 5 C 15921 2.51 5 N 4405 2.21 5 O 4867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25299 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3660 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 997 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.49, per 1000 atoms: 0.22 Number of scatterers: 25299 At special positions: 0 Unit cell: (126.72, 124.08, 156.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 20 15.00 Mg 6 11.99 O 4867 8.00 N 4405 7.00 C 15921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 992.1 milliseconds 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5956 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 23 sheets defined 47.6% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.661A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.569A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.691A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.991A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.711A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.554A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.685A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 4.140A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.537A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.592A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.782A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.509A pdb=" N LYS A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.531A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.759A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.587A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 381 through 397 removed outlier: 3.994A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 421 removed outlier: 4.176A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.677A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.607A pdb=" N LEU B 487 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.215A pdb=" N GLY C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.672A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.602A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.503A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.902A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.753A pdb=" N ILE C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 381 through 397 Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.666A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.881A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 465 Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.565A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.586A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 243 removed outlier: 3.806A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 4.141A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.575A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.671A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 3.596A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.524A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.576A pdb=" N PHE D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 180 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 3.672A pdb=" N VAL E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.693A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.533A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 360 through 380 Processing helix chain 'E' and resid 380 through 388 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.578A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.786A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.678A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 180 removed outlier: 4.449A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.507A pdb=" N ARG F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.028A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.525A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.635A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 325 removed outlier: 3.764A pdb=" N LEU F 325 " --> pdb=" O PHE F 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 322 through 325' Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 388 removed outlier: 3.684A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 392 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.897A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.594A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 470 Processing helix chain 'G' and resid 3 through 58 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 59 through 63 removed outlier: 3.853A pdb=" N ALA G 63 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 4.243A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.618A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER G 124 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 162 removed outlier: 3.955A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 284 Proline residue: G 218 - end of helix removed outlier: 4.131A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 106 removed outlier: 3.995A pdb=" N ARG H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN H 105 " --> pdb=" O GLU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 129 removed outlier: 4.726A pdb=" N LEU H 118 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.995A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.120A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.622A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.741A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.574A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.405A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.534A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.352A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.194A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.601A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.348A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.320A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.360A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.488A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.518A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.508A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASP F 252 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA F 186 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.326A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 136 through 137 removed outlier: 9.424A pdb=" N ILE G 137 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL G 117 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.336A pdb=" N GLU G 204 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU H 41 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL H 6 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU H 17 " --> pdb=" O VAL H 6 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 30 through 33 removed outlier: 3.885A pdb=" N ALA H 27 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 32 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL H 25 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS H 26 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA H 49 " --> pdb=" O LYS H 26 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3444 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: 4.69 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7659 1.33 - 1.45: 3166 1.45 - 1.57: 14702 1.57 - 1.69: 33 1.69 - 1.81: 160 Bond restraints: 25720 Sorted by residual: bond pdb=" N GLU A 54 " pdb=" CA GLU A 54 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.47e+00 bond pdb=" N PHE A 55 " pdb=" CA PHE A 55 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.22e-02 6.72e+03 6.39e+00 bond pdb=" N ASN A 57 " pdb=" CA ASN A 57 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.35e-02 5.49e+03 4.51e+00 bond pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.04e+00 bond pdb=" CA ALA A 56 " pdb=" CB ALA A 56 " ideal model delta sigma weight residual 1.528 1.496 0.032 1.59e-02 3.96e+03 4.04e+00 ... (remaining 25715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 33919 1.25 - 2.51: 738 2.51 - 3.76: 182 3.76 - 5.02: 32 5.02 - 6.27: 9 Bond angle restraints: 34880 Sorted by residual: angle pdb=" C GLU A 54 " pdb=" CA GLU A 54 " pdb=" CB GLU A 54 " ideal model delta sigma weight residual 109.71 103.44 6.27 1.83e+00 2.99e-01 1.18e+01 angle pdb=" CA PHE A 55 " pdb=" CB PHE A 55 " pdb=" CG PHE A 55 " ideal model delta sigma weight residual 113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" C PHE A 55 " pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 120.29 124.89 -4.60 1.42e+00 4.96e-01 1.05e+01 angle pdb=" N GLY A 58 " pdb=" CA GLY A 58 " pdb=" C GLY A 58 " ideal model delta sigma weight residual 115.00 110.52 4.48 1.44e+00 4.82e-01 9.67e+00 angle pdb=" N VAL E 207 " pdb=" CA VAL E 207 " pdb=" C VAL E 207 " ideal model delta sigma weight residual 112.96 109.88 3.08 1.00e+00 1.00e+00 9.51e+00 ... (remaining 34875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14367 17.91 - 35.81: 1076 35.81 - 53.72: 226 53.72 - 71.63: 69 71.63 - 89.54: 29 Dihedral angle restraints: 15767 sinusoidal: 6467 harmonic: 9300 Sorted by residual: dihedral pdb=" CA GLN D 217 " pdb=" C GLN D 217 " pdb=" N MET D 218 " pdb=" CA MET D 218 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA VAL H 15 " pdb=" C VAL H 15 " pdb=" N TYR H 16 " pdb=" CA TYR H 16 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ARG E 454 " pdb=" C ARG E 454 " pdb=" N LEU E 455 " pdb=" CA LEU E 455 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 15764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3014 0.046 - 0.092: 738 0.092 - 0.138: 260 0.138 - 0.184: 4 0.184 - 0.231: 2 Chirality restraints: 4018 Sorted by residual: chirality pdb=" CA PHE A 55 " pdb=" N PHE A 55 " pdb=" C PHE A 55 " pdb=" CB PHE A 55 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLU A 54 " pdb=" N GLU A 54 " pdb=" C GLU A 54 " pdb=" CB GLU A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN A 57 " pdb=" N ASN A 57 " pdb=" C ASN A 57 " pdb=" CB ASN A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 4015 not shown) Planarity restraints: 4541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 53 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C VAL A 53 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL A 53 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU A 54 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 428 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO F 429 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 429 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 429 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 315 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO E 316 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.026 5.00e-02 4.00e+02 ... (remaining 4538 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 173 2.55 - 3.14: 20029 3.14 - 3.73: 38325 3.73 - 4.31: 53238 4.31 - 4.90: 92004 Nonbonded interactions: 203769 Sorted by model distance: nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 1.967 2.170 nonbonded pdb=" O3G ATP F 501 " pdb="MG MG F 502 " model vdw 1.968 2.170 nonbonded pdb=" O3B ATP C 600 " pdb="MG MG C 601 " model vdw 1.979 2.170 nonbonded pdb=" O3G ATP C 600 " pdb="MG MG C 601 " model vdw 1.983 2.170 nonbonded pdb=" O3B ATP E 501 " pdb="MG MG E 502 " model vdw 2.002 2.170 ... (remaining 203764 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 'A' and resid 24 through 501) selection = (chain 'B' and (resid 24 through 54 or (resid 55 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 56 through 501)) selection = (chain 'C' and (resid 24 through 54 or (resid 55 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 56 through 501)) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.640 Find NCS groups from input model: 0.570 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 : 0.003 0.037 25720 Z= 0.149 Angle : 0.505 6.275 34880 Z= 0.276 Chirality : 0.044 0.231 4018 Planarity : 0.004 0.056 4541 Dihedral : 14.152 89.537 9811 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 3243 helix: 1.66 (0.15), residues: 1249 sheet: 0.87 (0.22), residues: 540 loop : 0.13 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 71 TYR 0.016 0.001 TYR B 248 PHE 0.013 0.001 PHE B 494 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00331 (25720) covalent geometry : angle 0.50485 (34880) hydrogen bonds : bond 0.17333 ( 1212) hydrogen bonds : angle 6.66873 ( 3444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.635 Fit side-chains REVERT: C 60 MET cc_start: 0.8503 (mmt) cc_final: 0.8278 (mmt) REVERT: D 253 ASN cc_start: 0.7710 (m-40) cc_final: 0.7227 (m-40) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1594 time to fit residues: 33.3995 Evaluate side-chains 101 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN C 358 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.056514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.042866 restraints weight = 88022.720| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.84 r_work: 0.2587 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25720 Z= 0.158 Angle : 0.532 6.603 34880 Z= 0.281 Chirality : 0.045 0.161 4018 Planarity : 0.004 0.054 4541 Dihedral : 7.895 87.384 3756 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.38 % Rotamer: Outliers : 0.37 % Allowed : 4.79 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.15), residues: 3243 helix: 1.83 (0.15), residues: 1262 sheet: 0.89 (0.22), residues: 548 loop : 0.15 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 115 TYR 0.018 0.001 TYR B 248 PHE 0.022 0.001 PHE B 395 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00366 (25720) covalent geometry : angle 0.53193 (34880) hydrogen bonds : bond 0.04451 ( 1212) hydrogen bonds : angle 5.04838 ( 3444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.723 Fit side-chains REVERT: B 60 MET cc_start: 0.9212 (mmm) cc_final: 0.8739 (mmm) REVERT: C 358 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8446 (t0) REVERT: D 253 ASN cc_start: 0.8609 (m-40) cc_final: 0.8062 (m-40) REVERT: E 395 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8091 (tp30) REVERT: H 132 MET cc_start: 0.4035 (ptm) cc_final: 0.3754 (ptt) outliers start: 10 outliers final: 2 residues processed: 109 average time/residue: 0.1557 time to fit residues: 28.4524 Evaluate side-chains 100 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain G residue 43 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 104 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 135 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 318 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.042134 restraints weight = 88639.462| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.83 r_work: 0.2562 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25720 Z= 0.181 Angle : 0.521 5.775 34880 Z= 0.275 Chirality : 0.045 0.152 4018 Planarity : 0.004 0.054 4541 Dihedral : 7.794 87.125 3756 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Rotamer: Outliers : 0.45 % Allowed : 6.85 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.15), residues: 3243 helix: 1.84 (0.15), residues: 1276 sheet: 0.90 (0.22), residues: 536 loop : 0.04 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 126 TYR 0.016 0.001 TYR B 248 PHE 0.014 0.001 PHE F 257 HIS 0.005 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00424 (25720) covalent geometry : angle 0.52106 (34880) hydrogen bonds : bond 0.04819 ( 1212) hydrogen bonds : angle 4.96197 ( 3444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.948 Fit side-chains REVERT: B 60 MET cc_start: 0.9316 (mmm) cc_final: 0.8849 (mmm) REVERT: D 253 ASN cc_start: 0.8764 (m-40) cc_final: 0.8164 (m-40) REVERT: H 71 ARG cc_start: 0.6694 (ttp80) cc_final: 0.6444 (ttp80) outliers start: 12 outliers final: 5 residues processed: 111 average time/residue: 0.1509 time to fit residues: 28.5065 Evaluate side-chains 103 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain G residue 43 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 219 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 49 optimal weight: 0.0570 chunk 23 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.056020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.042378 restraints weight = 87897.920| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.83 r_work: 0.2562 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25720 Z= 0.162 Angle : 0.502 5.928 34880 Z= 0.265 Chirality : 0.044 0.151 4018 Planarity : 0.004 0.055 4541 Dihedral : 7.569 87.146 3756 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 0.60 % Allowed : 8.60 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.15), residues: 3243 helix: 1.93 (0.15), residues: 1272 sheet: 0.87 (0.23), residues: 524 loop : 0.10 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.016 0.001 TYR B 248 PHE 0.013 0.001 PHE F 257 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00380 (25720) covalent geometry : angle 0.50214 (34880) hydrogen bonds : bond 0.04342 ( 1212) hydrogen bonds : angle 4.81041 ( 3444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.892 Fit side-chains REVERT: B 60 MET cc_start: 0.9352 (mmm) cc_final: 0.8891 (mmm) REVERT: D 213 MET cc_start: 0.9340 (mtt) cc_final: 0.9109 (mtt) REVERT: D 253 ASN cc_start: 0.8789 (m-40) cc_final: 0.8178 (m-40) REVERT: G 165 PHE cc_start: 0.7899 (p90) cc_final: 0.7439 (p90) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 0.1414 time to fit residues: 27.8136 Evaluate side-chains 107 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 133 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 254 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 209 optimal weight: 8.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS G 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.041452 restraints weight = 88339.083| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.82 r_work: 0.2535 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25720 Z= 0.219 Angle : 0.549 6.888 34880 Z= 0.289 Chirality : 0.045 0.164 4018 Planarity : 0.004 0.055 4541 Dihedral : 7.655 87.163 3756 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 0.97 % Allowed : 9.73 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3243 helix: 1.76 (0.15), residues: 1278 sheet: 0.77 (0.23), residues: 524 loop : -0.00 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 71 TYR 0.015 0.001 TYR B 248 PHE 0.016 0.001 PHE C 398 HIS 0.006 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00521 (25720) covalent geometry : angle 0.54931 (34880) hydrogen bonds : bond 0.04870 ( 1212) hydrogen bonds : angle 4.91651 ( 3444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.840 Fit side-chains REVERT: B 60 MET cc_start: 0.9391 (mmm) cc_final: 0.8891 (mmm) REVERT: G 165 PHE cc_start: 0.7938 (p90) cc_final: 0.7448 (p90) REVERT: H 71 ARG cc_start: 0.6263 (ttp80) cc_final: 0.6013 (ttp80) outliers start: 26 outliers final: 17 residues processed: 118 average time/residue: 0.1448 time to fit residues: 29.5115 Evaluate side-chains 114 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 230 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 307 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS E 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.053800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.040161 restraints weight = 89959.884| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 2.82 r_work: 0.2495 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 25720 Z= 0.332 Angle : 0.645 10.934 34880 Z= 0.337 Chirality : 0.049 0.161 4018 Planarity : 0.005 0.058 4541 Dihedral : 7.973 88.229 3756 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 1.20 % Allowed : 10.55 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3243 helix: 1.44 (0.15), residues: 1281 sheet: 0.54 (0.23), residues: 534 loop : -0.19 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.015 0.002 TYR B 248 PHE 0.019 0.002 PHE F 257 HIS 0.008 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00790 (25720) covalent geometry : angle 0.64532 (34880) hydrogen bonds : bond 0.05648 ( 1212) hydrogen bonds : angle 5.16283 ( 3444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.848 Fit side-chains REVERT: A 404 LYS cc_start: 0.8941 (ptmm) cc_final: 0.8605 (ptpp) REVERT: B 60 MET cc_start: 0.9458 (mmm) cc_final: 0.8959 (mmm) REVERT: B 404 LYS cc_start: 0.9269 (mmtp) cc_final: 0.8978 (mmtt) REVERT: C 95 MET cc_start: 0.8981 (mmm) cc_final: 0.8742 (mmm) REVERT: G 10 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8144 (ttt90) REVERT: H 71 ARG cc_start: 0.6047 (ttp80) cc_final: 0.5757 (ttp80) outliers start: 32 outliers final: 26 residues processed: 127 average time/residue: 0.1446 time to fit residues: 31.0738 Evaluate side-chains 122 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 14 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 230 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 291 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** 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 = 0.3089 r_free = 0.3089 target = 0.056818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043071 restraints weight = 87340.841| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.93 r_work: 0.2583 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 25720 Z= 0.102 Angle : 0.477 10.304 34880 Z= 0.251 Chirality : 0.043 0.148 4018 Planarity : 0.004 0.056 4541 Dihedral : 7.312 88.288 3756 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Rotamer: Outliers : 0.82 % Allowed : 11.00 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.15), residues: 3243 helix: 1.92 (0.15), residues: 1276 sheet: 0.80 (0.23), residues: 518 loop : 0.02 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.015 0.001 TYR B 248 PHE 0.016 0.001 PHE C 398 HIS 0.004 0.001 HIS F 173 Details of bonding type rmsd covalent geometry : bond 0.00215 (25720) covalent geometry : angle 0.47702 (34880) hydrogen bonds : bond 0.03813 ( 1212) hydrogen bonds : angle 4.71879 ( 3444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.045 Fit side-chains REVERT: A 404 LYS cc_start: 0.8795 (ptmm) cc_final: 0.8512 (ptpp) REVERT: B 60 MET cc_start: 0.9359 (mmm) cc_final: 0.8954 (mmm) REVERT: D 64 MET cc_start: 0.9417 (mmt) cc_final: 0.8812 (mmt) REVERT: D 456 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8560 (t) REVERT: G 165 PHE cc_start: 0.7936 (p90) cc_final: 0.7649 (p90) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 0.1416 time to fit residues: 29.6657 Evaluate side-chains 114 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 268 optimal weight: 0.1980 chunk 300 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 225 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 254 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** 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 = 0.3043 r_free = 0.3043 target = 0.055049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.041391 restraints weight = 88347.603| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.82 r_work: 0.2535 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25720 Z= 0.214 Angle : 0.543 10.485 34880 Z= 0.283 Chirality : 0.045 0.262 4018 Planarity : 0.004 0.058 4541 Dihedral : 7.433 86.121 3756 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 1.01 % Allowed : 11.30 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3243 helix: 1.86 (0.15), residues: 1270 sheet: 0.73 (0.23), residues: 524 loop : -0.07 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 71 TYR 0.014 0.001 TYR B 248 PHE 0.016 0.001 PHE F 257 HIS 0.005 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00506 (25720) covalent geometry : angle 0.54252 (34880) hydrogen bonds : bond 0.04694 ( 1212) hydrogen bonds : angle 4.84312 ( 3444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.825 Fit side-chains REVERT: A 404 LYS cc_start: 0.8869 (ptmm) cc_final: 0.8570 (ptpp) REVERT: B 60 MET cc_start: 0.9402 (mmm) cc_final: 0.8931 (mmm) REVERT: D 456 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8615 (t) REVERT: E 48 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9321 (mt) outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 0.1445 time to fit residues: 30.5399 Evaluate side-chains 119 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 299 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 262 optimal weight: 0.9980 chunk 282 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 287 optimal weight: 8.9990 chunk 283 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 300 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** 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 = 0.3046 r_free = 0.3046 target = 0.055170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041520 restraints weight = 88256.120| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.82 r_work: 0.2542 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25720 Z= 0.191 Angle : 0.533 11.162 34880 Z= 0.277 Chirality : 0.045 0.369 4018 Planarity : 0.004 0.057 4541 Dihedral : 7.440 86.771 3756 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.38 % Rotamer: Outliers : 1.08 % Allowed : 11.30 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 3243 helix: 1.83 (0.15), residues: 1270 sheet: 0.69 (0.23), residues: 539 loop : -0.11 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.014 0.001 TYR B 248 PHE 0.022 0.001 PHE C 398 HIS 0.005 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00452 (25720) covalent geometry : angle 0.53256 (34880) hydrogen bonds : bond 0.04584 ( 1212) hydrogen bonds : angle 4.83357 ( 3444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.900 Fit side-chains REVERT: A 404 LYS cc_start: 0.8821 (ptmm) cc_final: 0.8548 (ptpp) REVERT: B 60 MET cc_start: 0.9394 (mmm) cc_final: 0.8955 (mmm) REVERT: B 137 MET cc_start: 0.9402 (mmt) cc_final: 0.9166 (mmt) REVERT: D 271 MET cc_start: 0.9336 (mmm) cc_final: 0.9092 (mtp) REVERT: D 456 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8662 (t) REVERT: E 48 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9342 (mt) outliers start: 29 outliers final: 23 residues processed: 122 average time/residue: 0.1527 time to fit residues: 32.2404 Evaluate side-chains 124 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 77 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 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 189 GLN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043030 restraints weight = 87193.864| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.98 r_work: 0.2577 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25720 Z= 0.102 Angle : 0.483 10.622 34880 Z= 0.250 Chirality : 0.043 0.313 4018 Planarity : 0.004 0.055 4541 Dihedral : 7.076 87.623 3756 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Rotamer: Outliers : 1.08 % Allowed : 11.30 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.15), residues: 3243 helix: 2.03 (0.15), residues: 1278 sheet: 0.81 (0.23), residues: 530 loop : 0.03 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 71 TYR 0.015 0.001 TYR B 248 PHE 0.010 0.001 PHE D 125 HIS 0.004 0.001 HIS F 173 Details of bonding type rmsd covalent geometry : bond 0.00220 (25720) covalent geometry : angle 0.48319 (34880) hydrogen bonds : bond 0.03750 ( 1212) hydrogen bonds : angle 4.63321 ( 3444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.916 Fit side-chains REVERT: A 404 LYS cc_start: 0.8824 (ptmm) cc_final: 0.8561 (ptpp) REVERT: B 60 MET cc_start: 0.9353 (mmm) cc_final: 0.8935 (mmm) REVERT: B 137 MET cc_start: 0.9386 (mmt) cc_final: 0.9148 (mmt) REVERT: B 478 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8838 (t) REVERT: D 253 ASN cc_start: 0.8851 (m-40) cc_final: 0.8182 (m-40) REVERT: D 456 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8511 (t) REVERT: E 48 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9346 (mt) REVERT: G 165 PHE cc_start: 0.7954 (p90) cc_final: 0.7475 (p90) outliers start: 29 outliers final: 22 residues processed: 127 average time/residue: 0.1409 time to fit residues: 31.1855 Evaluate side-chains 124 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 47 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 322 optimal weight: 30.0000 chunk 101 optimal weight: 0.1980 chunk 308 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** 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 = 0.3047 r_free = 0.3047 target = 0.055194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.041332 restraints weight = 88537.519| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.97 r_work: 0.2528 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25720 Z= 0.214 Angle : 0.554 11.282 34880 Z= 0.286 Chirality : 0.046 0.355 4018 Planarity : 0.004 0.056 4541 Dihedral : 7.317 87.745 3756 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 0.97 % Allowed : 11.52 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3243 helix: 1.88 (0.15), residues: 1279 sheet: 0.72 (0.23), residues: 536 loop : -0.10 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 71 TYR 0.014 0.001 TYR B 248 PHE 0.018 0.001 PHE C 398 HIS 0.004 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00506 (25720) covalent geometry : angle 0.55434 (34880) hydrogen bonds : bond 0.04667 ( 1212) hydrogen bonds : angle 4.79912 ( 3444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.66 seconds wall clock time: 75 minutes 50.57 seconds (4550.57 seconds total)