Starting phenix.real_space_refine on Sun Jul 5 04:08:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xkq_33264/07_2026/7xkq_33264.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkq_33264/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xkq_33264/07_2026/7xkq_33264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkq_33264/07_2026/7xkq_33264.map" model { file = "/net/cci-nas-00/data/ceres_data/7xkq_33264/07_2026/7xkq_33264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkq_33264/07_2026/7xkq_33264.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xkq_33264/07_2026/7xkq_33264.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xkq_33264/07_2026/7xkq_33264.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.61, 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.55 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: 4.77 Time building geometry restraints manager: 3.05 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: 14305 17.91 - 35.81: 1017 35.81 - 53.72: 181 53.72 - 71.63: 52 71.63 - 89.54: 26 Dihedral angle restraints: 15581 sinusoidal: 6281 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 15578 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.440 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 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 : 13.480 89.537 9625 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/Z covalent geometry : bond 0.00331 / 0.15 (25720) covalent geometry : angle 0.50485 / 0.28 (34880) hydrogen bonds : bond 0.17333 / 12.13 ( 1212) hydrogen bonds : angle 6.66873 / 4.63 ( 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 : 1.017 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: 0.1674 time to fit residues: 35.9181 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 : 1.006 ------------------------------------------------------------------------------- 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... 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 = 0.3082 r_free = 0.3082 target = 0.056454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.042853 restraints weight = 88081.131| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.83 r_work: 0.2582 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25720 Z= 0.158 Angle : 0.527 6.573 34880 Z= 0.279 Chirality : 0.045 0.171 4018 Planarity : 0.004 0.054 4541 Dihedral : 5.189 78.328 3570 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.44 % Rotamer: Outliers : 0.34 % Allowed : 4.60 % Favored : 95.06 % 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: 1.37 (0.15), residues: 3243 helix: 1.84 (0.15), residues: 1261 sheet: 0.90 (0.22), residues: 548 loop : 0.16 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 71 TYR 0.018 0.001 TYR B 248 PHE 0.023 0.001 PHE B 395 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (25720) covalent geometry : angle 0.52734 / 0.28 (34880) hydrogen bonds : bond 0.04565 / 3.15 ( 1212) hydrogen bonds : angle 5.10075 / 3.59 ( 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 112 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.030 Fit side-chains REVERT: B 60 MET cc_start: 0.9217 (mmm) cc_final: 0.8722 (mmm) REVERT: C 358 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8464 (t0) REVERT: D 253 ASN cc_start: 0.8595 (m-40) cc_final: 0.8051 (m-40) REVERT: E 395 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: H 132 MET cc_start: 0.4016 (ptm) cc_final: 0.3759 (ptt) outliers start: 9 outliers final: 2 residues processed: 108 average time/residue: 0.1692 time to fit residues: 30.6557 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 : 1.048 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 318 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 257 optimal weight: 0.0770 chunk 13 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 181 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 = 0.3102 r_free = 0.3102 target = 0.057201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.043375 restraints weight = 87795.172| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.00 r_work: 0.2596 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25720 Z= 0.107 Angle : 0.465 5.574 34880 Z= 0.245 Chirality : 0.043 0.160 4018 Planarity : 0.004 0.052 4541 Dihedral : 4.966 78.444 3570 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 0.19 % Allowed : 6.62 % Favored : 93.19 % 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: 1.55 (0.15), residues: 3243 helix: 2.00 (0.15), residues: 1275 sheet: 1.03 (0.23), residues: 525 loop : 0.23 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 71 TYR 0.014 0.001 TYR B 248 PHE 0.010 0.001 PHE A 494 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (25720) covalent geometry : angle 0.46474 / 0.24 (34880) hydrogen bonds : bond 0.04057 / 2.81 ( 1212) hydrogen bonds : angle 4.81441 / 3.38 ( 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 108 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 1.019 Fit side-chains REVERT: B 60 MET cc_start: 0.9245 (mmm) cc_final: 0.8793 (mmm) REVERT: C 95 MET cc_start: 0.8324 (mmm) cc_final: 0.8117 (tpt) REVERT: D 253 ASN cc_start: 0.8614 (m-40) cc_final: 0.8059 (m-40) REVERT: E 10 MET cc_start: 0.8743 (mtp) cc_final: 0.8418 (mmm) REVERT: H 71 ARG cc_start: 0.6683 (ttp80) cc_final: 0.6425 (ttp80) outliers start: 5 outliers final: 1 residues processed: 108 average time/residue: 0.1655 time to fit residues: 30.3637 Evaluate side-chains 99 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 219 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 HIS C 143 HIS ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.041246 restraints weight = 88534.267| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.82 r_work: 0.2531 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25720 Z= 0.243 Angle : 0.575 5.902 34880 Z= 0.302 Chirality : 0.047 0.154 4018 Planarity : 0.004 0.057 4541 Dihedral : 5.330 79.755 3570 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 0.79 % Allowed : 7.78 % Favored : 91.43 % 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: 1.12 (0.15), residues: 3243 helix: 1.66 (0.15), residues: 1283 sheet: 0.72 (0.22), residues: 538 loop : -0.01 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 102 TYR 0.017 0.001 TYR B 248 PHE 0.019 0.001 PHE F 257 HIS 0.006 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (25720) covalent geometry : angle 0.57464 / 0.30 (34880) hydrogen bonds : bond 0.05231 / 3.60 ( 1212) hydrogen bonds : angle 5.02089 / 3.51 ( 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 119 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.018 Fit side-chains REVERT: B 60 MET cc_start: 0.9400 (mmm) cc_final: 0.8900 (mmm) outliers start: 21 outliers final: 11 residues processed: 113 average time/residue: 0.1505 time to fit residues: 29.3133 Evaluate side-chains 108 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 B residue 395 PHE 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 34 ILE 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: 4.9990 chunk 275 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 254 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN 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 = 0.056029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.042409 restraints weight = 87806.736| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.82 r_work: 0.2565 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25720 Z= 0.144 Angle : 0.496 7.126 34880 Z= 0.260 Chirality : 0.044 0.146 4018 Planarity : 0.004 0.055 4541 Dihedral : 5.147 80.984 3570 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 0.67 % Allowed : 9.17 % Favored : 90.16 % 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: 1.29 (0.15), residues: 3243 helix: 1.85 (0.15), residues: 1278 sheet: 0.80 (0.23), residues: 524 loop : 0.04 (0.17), residues: 1441 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 0.014 0.001 PHE C 398 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (25720) covalent geometry : angle 0.49606 / 0.26 (34880) hydrogen bonds : bond 0.04325 / 2.99 ( 1212) hydrogen bonds : angle 4.80868 / 3.36 ( 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 119 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.996 Fit side-chains REVERT: B 60 MET cc_start: 0.9351 (mmm) cc_final: 0.8918 (mmm) REVERT: E 10 MET cc_start: 0.8921 (mtp) cc_final: 0.8540 (mmm) REVERT: G 165 PHE cc_start: 0.7920 (p90) cc_final: 0.7428 (p90) REVERT: H 71 ARG cc_start: 0.6162 (ttp80) cc_final: 0.5932 (ttp80) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 0.1502 time to fit residues: 29.1775 Evaluate side-chains 109 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 314 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 301 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 90 VAL 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: 0.0970 chunk 309 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3067 r_free = 0.3067 target = 0.055948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.042297 restraints weight = 88346.218| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.83 r_work: 0.2556 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25720 Z= 0.157 Angle : 0.503 11.206 34880 Z= 0.262 Chirality : 0.044 0.142 4018 Planarity : 0.004 0.054 4541 Dihedral : 5.091 81.831 3570 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Rotamer: Outliers : 0.67 % Allowed : 9.76 % Favored : 89.56 % 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: 1.33 (0.15), residues: 3243 helix: 1.90 (0.15), residues: 1278 sheet: 0.82 (0.23), residues: 528 loop : 0.05 (0.17), residues: 1437 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 0.013 0.001 PHE F 257 HIS 0.004 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (25720) covalent geometry : angle 0.50309 / 0.26 (34880) hydrogen bonds : bond 0.04338 / 2.99 ( 1212) hydrogen bonds : angle 4.75203 / 3.32 ( 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 116 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.951 Fit side-chains REVERT: B 60 MET cc_start: 0.9365 (mmm) cc_final: 0.8935 (mmm) REVERT: E 10 MET cc_start: 0.8948 (mtp) cc_final: 0.8624 (mmm) REVERT: G 165 PHE cc_start: 0.7928 (p90) cc_final: 0.7481 (p90) REVERT: H 71 ARG cc_start: 0.6190 (ttp80) cc_final: 0.5913 (ttp80) outliers start: 18 outliers final: 11 residues processed: 111 average time/residue: 0.1529 time to fit residues: 29.1893 Evaluate side-chains 107 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 314 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain F residue 301 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 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: 7.9990 chunk 230 optimal weight: 0.0980 chunk 97 optimal weight: 6.9990 chunk 291 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3070 r_free = 0.3070 target = 0.056076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.042466 restraints weight = 87768.796| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.82 r_work: 0.2563 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25720 Z= 0.146 Angle : 0.492 10.098 34880 Z= 0.256 Chirality : 0.044 0.144 4018 Planarity : 0.004 0.054 4541 Dihedral : 5.047 81.853 3570 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 0.94 % Allowed : 9.88 % Favored : 89.19 % 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: 1.94 (0.15), residues: 1279 sheet: 0.84 (0.23), residues: 528 loop : 0.05 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.015 0.001 TYR B 248 PHE 0.017 0.001 PHE C 398 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (25720) covalent geometry : angle 0.49163 / 0.26 (34880) hydrogen bonds : bond 0.04202 / 2.90 ( 1212) hydrogen bonds : angle 4.71633 / 3.29 ( 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 125 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.060 Fit side-chains REVERT: A 404 LYS cc_start: 0.8813 (ptmm) cc_final: 0.8494 (ptpp) REVERT: B 60 MET cc_start: 0.9355 (mmm) cc_final: 0.8929 (mmm) REVERT: B 137 MET cc_start: 0.9299 (mmm) cc_final: 0.8820 (mmt) REVERT: B 404 LYS cc_start: 0.9236 (mmtp) cc_final: 0.9001 (mmtt) REVERT: E 10 MET cc_start: 0.8962 (mtp) cc_final: 0.8615 (mmm) REVERT: G 165 PHE cc_start: 0.7895 (p90) cc_final: 0.7429 (p90) outliers start: 25 outliers final: 15 residues processed: 120 average time/residue: 0.1518 time to fit residues: 31.1045 Evaluate side-chains 112 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 314 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 301 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 268 optimal weight: 10.0000 chunk 300 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 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 = 0.3040 r_free = 0.3040 target = 0.054909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.041272 restraints weight = 88417.022| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.82 r_work: 0.2530 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25720 Z= 0.231 Angle : 0.553 10.184 34880 Z= 0.288 Chirality : 0.046 0.147 4018 Planarity : 0.004 0.055 4541 Dihedral : 5.235 81.597 3570 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 0.86 % Allowed : 10.33 % Favored : 88.81 % 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: 1.18 (0.15), residues: 3243 helix: 1.80 (0.15), residues: 1270 sheet: 0.77 (0.23), residues: 524 loop : -0.06 (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 0.017 0.001 PHE F 257 HIS 0.005 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (25720) covalent geometry : angle 0.55325 / 0.29 (34880) hydrogen bonds : bond 0.04820 / 3.32 ( 1212) hydrogen bonds : angle 4.85881 / 3.39 ( 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 119 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.710 Fit side-chains REVERT: A 404 LYS cc_start: 0.8845 (ptmm) cc_final: 0.8527 (ptpp) REVERT: B 60 MET cc_start: 0.9408 (mmm) cc_final: 0.8916 (mmm) REVERT: B 137 MET cc_start: 0.9354 (mmm) cc_final: 0.8903 (mmt) REVERT: G 165 PHE cc_start: 0.7959 (p90) cc_final: 0.7487 (p90) REVERT: H 71 ARG cc_start: 0.6014 (ttp80) cc_final: 0.5797 (ttp80) outliers start: 23 outliers final: 21 residues processed: 114 average time/residue: 0.1405 time to fit residues: 27.3376 Evaluate side-chains 117 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 314 THR 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 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 285 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 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 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: 0.5980 chunk 282 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 300 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3057 r_free = 0.3057 target = 0.055561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.041981 restraints weight = 87985.046| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.81 r_work: 0.2546 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25720 Z= 0.168 Angle : 0.512 10.449 34880 Z= 0.266 Chirality : 0.044 0.148 4018 Planarity : 0.004 0.055 4541 Dihedral : 5.162 81.921 3570 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 0.97 % Allowed : 10.40 % Favored : 88.63 % 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: 1.24 (0.15), residues: 3243 helix: 1.88 (0.15), residues: 1270 sheet: 0.79 (0.23), residues: 524 loop : -0.05 (0.17), residues: 1449 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 0.014 0.001 PHE F 257 HIS 0.004 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (25720) covalent geometry : angle 0.51165 / 0.27 (34880) hydrogen bonds : bond 0.04436 / 3.06 ( 1212) hydrogen bonds : angle 4.77011 / 3.33 ( 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 124 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.243 Fit side-chains REVERT: A 404 LYS cc_start: 0.8773 (ptmm) cc_final: 0.8484 (ptpp) REVERT: B 60 MET cc_start: 0.9385 (mmm) cc_final: 0.8952 (mmm) REVERT: D 253 ASN cc_start: 0.8864 (m-40) cc_final: 0.8191 (m-40) REVERT: G 165 PHE cc_start: 0.7966 (p90) cc_final: 0.7493 (p90) REVERT: H 71 ARG cc_start: 0.6050 (ttp80) cc_final: 0.5833 (ttp80) outliers start: 26 outliers final: 22 residues processed: 120 average time/residue: 0.1629 time to fit residues: 33.1565 Evaluate side-chains 118 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 314 THR 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 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 168 ILE 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 F residue 329 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 77 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3079 r_free = 0.3079 target = 0.056425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.042818 restraints weight = 87680.733| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.82 r_work: 0.2574 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25720 Z= 0.120 Angle : 0.481 10.564 34880 Z= 0.249 Chirality : 0.043 0.147 4018 Planarity : 0.004 0.054 4541 Dihedral : 5.001 82.379 3570 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 0.67 % Allowed : 10.89 % Favored : 88.44 % 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: 1.39 (0.15), residues: 3243 helix: 1.99 (0.15), residues: 1276 sheet: 0.85 (0.23), residues: 532 loop : 0.04 (0.17), residues: 1435 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 0.018 0.001 PHE C 398 HIS 0.003 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (25720) covalent geometry : angle 0.48061 / 0.25 (34880) hydrogen bonds : bond 0.03953 / 2.73 ( 1212) hydrogen bonds : angle 4.65012 / 3.24 ( 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 117 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.060 Fit side-chains REVERT: B 60 MET cc_start: 0.9356 (mmm) cc_final: 0.8948 (mmm) REVERT: D 253 ASN cc_start: 0.8843 (m-40) cc_final: 0.8166 (m-40) REVERT: G 165 PHE cc_start: 0.7912 (p90) cc_final: 0.7439 (p90) REVERT: H 71 ARG cc_start: 0.6037 (ttp80) cc_final: 0.5813 (ttp80) outliers start: 18 outliers final: 16 residues processed: 114 average time/residue: 0.1537 time to fit residues: 30.0251 Evaluate side-chains 113 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 90 VAL 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: 8.9990 chunk 1 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 308 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 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 = 0.3020 r_free = 0.3020 target = 0.054164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.040551 restraints weight = 89553.084| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 2.81 r_work: 0.2509 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 25720 Z= 0.318 Angle : 0.622 10.251 34880 Z= 0.323 Chirality : 0.048 0.160 4018 Planarity : 0.004 0.057 4541 Dihedral : 5.381 81.523 3570 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 0.94 % Allowed : 10.85 % Favored : 88.22 % 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: 1.00 (0.15), residues: 3243 helix: 1.64 (0.15), residues: 1287 sheet: 0.62 (0.22), residues: 537 loop : -0.15 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 240 TYR 0.014 0.002 TYR B 248 PHE 0.019 0.002 PHE F 257 HIS 0.007 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.32 (25720) covalent geometry : angle 0.62199 / 0.32 (34880) hydrogen bonds : bond 0.05330 / 3.66 ( 1212) hydrogen bonds : angle 4.99876 / 3.48 ( 3444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4431.05 seconds wall clock time: 77 minutes 12.97 seconds (4632.97 seconds total)