Starting phenix.real_space_refine on Thu Mar 5 17:29:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xkp_33259/03_2026/7xkp_33259.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkp_33259/03_2026/7xkp_33259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xkp_33259/03_2026/7xkp_33259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkp_33259/03_2026/7xkp_33259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xkp_33259/03_2026/7xkp_33259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkp_33259/03_2026/7xkp_33259.map" } resolution = 3.0 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= 0.001 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 2 5.49 5 Mg 1 5.21 5 S 77 5.16 5 C 15232 2.51 5 N 4193 2.21 5 O 4600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24105 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, '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: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, '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': 2, 'PTRANS': 8, 'TRANS': 272} Chain: "F" 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} Time building chain proxies: 5.57, per 1000 atoms: 0.23 Number of scatterers: 24105 At special positions: 0 Unit cell: (128.48, 126.72, 157.52, 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 77 16.00 P 2 15.00 Mg 1 11.99 O 4600 8.00 N 4193 7.00 C 15232 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: 1.93 Conformation dependent library (CDL) restraints added in 1.2 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5710 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 23 sheets defined 48.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.296A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.568A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.882A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 201 through 216 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 Proline residue: A 239 - end of helix removed outlier: 3.599A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.996A 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 289 through 299 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 393 removed outlier: 3.772A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.769A pdb=" N ALA A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 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 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 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 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 251 removed outlier: 3.559A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.608A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.982A 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 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.532A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.514A pdb=" N PHE B 350 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 351 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 4.134A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 421 removed outlier: 4.716A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 440 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 Processing helix chain 'B' and resid 468 through 478 Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.550A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 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: 3.563A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.645A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.877A 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 289 through 299 removed outlier: 3.740A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 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 400 removed outlier: 4.416A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.690A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 467 removed outlier: 4.362A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.595A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.540A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 179 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 242 removed outlier: 3.670A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.803A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.753A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 385 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.583A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.678A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 4.080A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) 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: 5.204A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.711A 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: 3.641A 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 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.420A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.568A pdb=" N ARG E 404 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 3.799A 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 442 Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.661A pdb=" N ARG E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.970A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.584A pdb=" N LEU F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.637A 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 176 Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 226 removed outlier: 3.556A pdb=" N ARG F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 242 removed outlier: 3.800A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.921A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.556A 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 322 removed outlier: 3.599A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 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 387 Processing helix chain 'F' and resid 388 through 392 removed outlier: 3.661A pdb=" N GLU F 391 " --> pdb=" O GLY F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.631A pdb=" N LEU F 398 " --> pdb=" O ASP F 394 " (cutoff:3.500A) removed outlier: 3.668A 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 442 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.791A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 removed outlier: 3.541A pdb=" N ARG G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 58 removed outlier: 3.631A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.971A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 145 through 162 removed outlier: 3.836A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 284 removed outlier: 3.757A pdb=" N ILE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.746A pdb=" N SER G 261 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.963A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.395A 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: 6.746A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLN A 341 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLY A 360 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE A 343 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.353A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.915A 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: 6.814A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.584A pdb=" N ILE B 159 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.531A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 356 " --> pdb=" O GLN B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.531A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.480A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.292A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 108 removed outlier: 8.839A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 10 removed outlier: 6.720A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.514A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.445A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.933A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.440A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.538A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.303A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 135 through 137 removed outlier: 3.997A pdb=" N LEU G 135 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 117 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N TYR G 175 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) 1154 hydrogen bonds defined for protein. 3303 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: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8203 1.34 - 1.46: 3528 1.46 - 1.57: 12620 1.57 - 1.69: 3 1.69 - 1.81: 154 Bond restraints: 24508 Sorted by residual: bond pdb=" CA ASP C 289 " pdb=" CB ASP C 289 " ideal model delta sigma weight residual 1.532 1.546 -0.015 1.33e-02 5.65e+03 1.22e+00 bond pdb=" CD GLU D 464 " pdb=" OE1 GLU D 464 " ideal model delta sigma weight residual 1.249 1.229 0.020 1.90e-02 2.77e+03 1.14e+00 bond pdb=" CB ASP C 289 " pdb=" CG ASP C 289 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.05e+00 bond pdb=" C4 ADP F 602 " pdb=" C5 ADP F 602 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C ARG G 256 " pdb=" O ARG G 256 " ideal model delta sigma weight residual 1.237 1.249 -0.012 1.19e-02 7.06e+03 1.02e+00 ... (remaining 24503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 32758 1.69 - 3.39: 386 3.39 - 5.08: 51 5.08 - 6.78: 7 6.78 - 8.47: 1 Bond angle restraints: 33203 Sorted by residual: angle pdb=" CA GLY B 340 " pdb=" C GLY B 340 " pdb=" N GLN B 341 " ideal model delta sigma weight residual 114.23 117.49 -3.26 8.80e-01 1.29e+00 1.37e+01 angle pdb=" C GLY C 288 " pdb=" N ASP C 289 " pdb=" CA ASP C 289 " ideal model delta sigma weight residual 124.82 130.29 -5.47 1.78e+00 3.16e-01 9.44e+00 angle pdb=" N GLU E 379 " pdb=" CA GLU E 379 " pdb=" CB GLU E 379 " ideal model delta sigma weight residual 110.16 114.58 -4.42 1.48e+00 4.57e-01 8.91e+00 angle pdb=" C VAL F 214 " pdb=" N PHE F 215 " pdb=" CA PHE F 215 " ideal model delta sigma weight residual 122.42 117.89 4.53 1.55e+00 4.16e-01 8.54e+00 angle pdb=" N GLU E 337 " pdb=" CA GLU E 337 " pdb=" CB GLU E 337 " ideal model delta sigma weight residual 110.16 114.39 -4.23 1.48e+00 4.57e-01 8.17e+00 ... (remaining 33198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 14520 29.88 - 59.76: 350 59.76 - 89.63: 46 89.63 - 119.51: 2 119.51 - 149.39: 1 Dihedral angle restraints: 14919 sinusoidal: 5997 harmonic: 8922 Sorted by residual: dihedral pdb=" CA ALA G 108 " pdb=" C ALA G 108 " pdb=" N SER G 109 " pdb=" CA SER G 109 " ideal model delta harmonic sigma weight residual 180.00 145.71 34.29 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" C5' ADP F 602 " pdb=" O5' ADP F 602 " pdb=" PA ADP F 602 " pdb=" O2A ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 89.39 -149.39 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O2A ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PA ADP F 602 " pdb=" PB ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 50.84 -110.84 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 14916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2604 0.037 - 0.074: 853 0.074 - 0.111: 289 0.111 - 0.148: 86 0.148 - 0.185: 2 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CB VAL D 463 " pdb=" CA VAL D 463 " pdb=" CG1 VAL D 463 " pdb=" CG2 VAL D 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA GLU D 464 " pdb=" N GLU D 464 " pdb=" C GLU D 464 " pdb=" CB GLU D 464 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA GLU A 459 " pdb=" N GLU A 459 " pdb=" C GLU A 459 " pdb=" CB GLU A 459 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 3831 not shown) Planarity restraints: 4357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS G 65 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO G 66 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO G 66 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 66 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 341 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO D 342 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 342 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 342 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO D 221 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.023 5.00e-02 4.00e+02 ... (remaining 4354 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 209 2.65 - 3.21: 22411 3.21 - 3.78: 35930 3.78 - 4.34: 50864 4.34 - 4.90: 85715 Nonbonded interactions: 195129 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O1B ADP F 602 " model vdw 2.089 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.214 2.170 nonbonded pdb=" O LEU B 402 " pdb=" OG1 THR B 406 " model vdw 2.240 3.040 nonbonded pdb=" OE1 GLN G 50 " pdb=" OH TYR G 220 " model vdw 2.251 3.040 nonbonded pdb=" NH2 ARG A 106 " pdb=" O GLY A 119 " model vdw 2.265 3.120 ... (remaining 195124 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.690 Find NCS groups from input model: 0.390 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 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 : 0.002 0.038 24508 Z= 0.115 Angle : 0.479 8.472 33203 Z= 0.259 Chirality : 0.043 0.185 3834 Planarity : 0.004 0.047 4357 Dihedral : 13.187 149.390 9209 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.63 (0.15), residues: 3114 helix: 2.17 (0.15), residues: 1254 sheet: 0.89 (0.23), residues: 524 loop : 0.18 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 354 TYR 0.006 0.001 TYR E 341 PHE 0.017 0.001 PHE B 494 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00248 (24508) covalent geometry : angle 0.47855 (33203) hydrogen bonds : bond 0.14270 ( 1154) hydrogen bonds : angle 5.89356 ( 3303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: G 131 MET cc_start: 0.6235 (mmp) cc_final: 0.5952 (mtp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.8224 time to fit residues: 104.2806 Evaluate side-chains 87 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN C 474 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.059861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.043603 restraints weight = 71105.561| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.81 r_work: 0.2571 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 24508 Z= 0.300 Angle : 0.617 7.869 33203 Z= 0.324 Chirality : 0.049 0.215 3834 Planarity : 0.005 0.050 4357 Dihedral : 5.710 147.431 3409 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 0.55 % Allowed : 5.49 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.21 (0.15), residues: 3114 helix: 1.83 (0.15), residues: 1245 sheet: 0.65 (0.22), residues: 535 loop : -0.04 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 354 TYR 0.020 0.001 TYR B 438 PHE 0.021 0.002 PHE B 494 HIS 0.008 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00729 (24508) covalent geometry : angle 0.61690 (33203) hydrogen bonds : bond 0.05711 ( 1154) hydrogen bonds : angle 5.03971 ( 3303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: D 338 MET cc_start: 0.8191 (mmp) cc_final: 0.7935 (mmp) REVERT: E 56 ASP cc_start: 0.9080 (m-30) cc_final: 0.8553 (t0) REVERT: G 131 MET cc_start: 0.6309 (mmp) cc_final: 0.5846 (mmt) outliers start: 14 outliers final: 4 residues processed: 92 average time/residue: 0.8552 time to fit residues: 89.1087 Evaluate side-chains 89 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 111 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 198 optimal weight: 0.4980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.061383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.045094 restraints weight = 70154.097| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.81 r_work: 0.2615 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24508 Z= 0.140 Angle : 0.499 8.824 33203 Z= 0.261 Chirality : 0.044 0.147 3834 Planarity : 0.004 0.047 4357 Dihedral : 5.430 139.458 3409 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.46 % Rotamer: Outliers : 0.70 % Allowed : 6.82 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.36 (0.15), residues: 3114 helix: 1.99 (0.15), residues: 1255 sheet: 0.66 (0.22), residues: 530 loop : 0.02 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 402 TYR 0.009 0.001 TYR E 341 PHE 0.018 0.001 PHE B 494 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00327 (24508) covalent geometry : angle 0.49901 (33203) hydrogen bonds : bond 0.04538 ( 1154) hydrogen bonds : angle 4.70007 ( 3303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: C 74 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.9011 (p) REVERT: D 338 MET cc_start: 0.8167 (mmp) cc_final: 0.7895 (mmp) REVERT: D 389 MET cc_start: 0.7668 (mpt) cc_final: 0.7371 (mpt) REVERT: E 56 ASP cc_start: 0.9048 (m-30) cc_final: 0.8530 (t0) REVERT: F 202 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8469 (mtt) REVERT: G 131 MET cc_start: 0.6286 (mmp) cc_final: 0.5861 (mmt) outliers start: 18 outliers final: 7 residues processed: 99 average time/residue: 0.7595 time to fit residues: 86.1935 Evaluate side-chains 94 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 3 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 294 optimal weight: 0.2980 chunk 203 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.044342 restraints weight = 70611.775| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.79 r_work: 0.2598 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24508 Z= 0.195 Angle : 0.526 8.149 33203 Z= 0.276 Chirality : 0.045 0.152 3834 Planarity : 0.004 0.049 4357 Dihedral : 5.404 127.251 3409 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 1.25 % Allowed : 7.71 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.27 (0.15), residues: 3114 helix: 1.95 (0.15), residues: 1247 sheet: 0.61 (0.23), residues: 531 loop : -0.04 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 402 TYR 0.011 0.001 TYR E 341 PHE 0.018 0.001 PHE B 494 HIS 0.005 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00470 (24508) covalent geometry : angle 0.52589 (33203) hydrogen bonds : bond 0.04821 ( 1154) hydrogen bonds : angle 4.68078 ( 3303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.9255 (ttt) REVERT: D 338 MET cc_start: 0.8167 (mmp) cc_final: 0.7888 (mmp) REVERT: E 56 ASP cc_start: 0.9049 (m-30) cc_final: 0.8531 (t0) REVERT: F 202 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8413 (mtt) REVERT: G 131 MET cc_start: 0.6325 (mmp) cc_final: 0.5939 (mmt) outliers start: 32 outliers final: 18 residues processed: 109 average time/residue: 0.6842 time to fit residues: 86.1803 Evaluate side-chains 104 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 150 optimal weight: 2.9990 chunk 52 optimal weight: 0.0000 chunk 306 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 279 optimal weight: 0.6980 chunk 291 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.046189 restraints weight = 69204.402| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.82 r_work: 0.2646 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24508 Z= 0.099 Angle : 0.463 9.052 33203 Z= 0.241 Chirality : 0.043 0.141 3834 Planarity : 0.004 0.045 4357 Dihedral : 5.056 139.919 3409 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 1.17 % Allowed : 8.53 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.55 (0.15), residues: 3114 helix: 2.18 (0.15), residues: 1242 sheet: 0.72 (0.22), residues: 536 loop : 0.14 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 89 TYR 0.007 0.001 TYR E 341 PHE 0.016 0.001 PHE B 494 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00217 (24508) covalent geometry : angle 0.46282 (33203) hydrogen bonds : bond 0.03868 ( 1154) hydrogen bonds : angle 4.47299 ( 3303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: B 250 MET cc_start: 0.9404 (ttp) cc_final: 0.9198 (ttt) REVERT: C 74 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8994 (p) REVERT: D 338 MET cc_start: 0.8159 (mmp) cc_final: 0.7887 (mmp) REVERT: E 56 ASP cc_start: 0.9042 (m-30) cc_final: 0.8514 (t0) REVERT: F 202 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8434 (mtt) REVERT: G 131 MET cc_start: 0.6306 (mmp) cc_final: 0.5899 (mmt) outliers start: 30 outliers final: 16 residues processed: 112 average time/residue: 0.6871 time to fit residues: 89.3303 Evaluate side-chains 103 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 177 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 275 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.042850 restraints weight = 71015.014| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.78 r_work: 0.2547 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 24508 Z= 0.350 Angle : 0.638 8.977 33203 Z= 0.335 Chirality : 0.050 0.186 3834 Planarity : 0.005 0.051 4357 Dihedral : 5.610 160.266 3409 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 1.29 % Allowed : 9.82 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.15), residues: 3114 helix: 1.70 (0.15), residues: 1251 sheet: 0.46 (0.22), residues: 541 loop : -0.21 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 402 TYR 0.016 0.001 TYR E 341 PHE 0.022 0.002 PHE B 494 HIS 0.008 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00849 (24508) covalent geometry : angle 0.63759 (33203) hydrogen bonds : bond 0.05849 ( 1154) hydrogen bonds : angle 4.86466 ( 3303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8583 (mp0) REVERT: B 176 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8813 (m) REVERT: D 338 MET cc_start: 0.8187 (mmp) cc_final: 0.7917 (mmp) REVERT: F 202 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8300 (mtt) REVERT: G 131 MET cc_start: 0.6352 (mmp) cc_final: 0.5997 (mmt) outliers start: 33 outliers final: 22 residues processed: 112 average time/residue: 0.7102 time to fit residues: 92.0875 Evaluate side-chains 108 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 208 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 301 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.061348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.045152 restraints weight = 69748.628| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.78 r_work: 0.2618 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24508 Z= 0.125 Angle : 0.492 10.564 33203 Z= 0.256 Chirality : 0.044 0.140 3834 Planarity : 0.004 0.046 4357 Dihedral : 5.213 160.907 3409 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 1.25 % Allowed : 10.09 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.31 (0.15), residues: 3114 helix: 2.01 (0.15), residues: 1245 sheet: 0.60 (0.23), residues: 530 loop : -0.06 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 402 TYR 0.009 0.001 TYR E 341 PHE 0.016 0.001 PHE B 494 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00290 (24508) covalent geometry : angle 0.49207 (33203) hydrogen bonds : bond 0.04268 ( 1154) hydrogen bonds : angle 4.54572 ( 3303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8557 (mp0) REVERT: D 338 MET cc_start: 0.8140 (mmp) cc_final: 0.7866 (mmp) REVERT: D 389 MET cc_start: 0.7297 (mpt) cc_final: 0.6955 (mpp) REVERT: F 202 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8486 (mtt) REVERT: F 271 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8917 (mtp) REVERT: G 131 MET cc_start: 0.6337 (mmp) cc_final: 0.5933 (mmt) outliers start: 32 outliers final: 21 residues processed: 110 average time/residue: 0.7401 time to fit residues: 94.3636 Evaluate side-chains 106 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 271 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 214 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 295 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.043616 restraints weight = 70517.574| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.80 r_work: 0.2569 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 24508 Z= 0.246 Angle : 0.567 11.036 33203 Z= 0.295 Chirality : 0.047 0.165 3834 Planarity : 0.004 0.049 4357 Dihedral : 5.308 163.826 3409 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 1.17 % Allowed : 10.32 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.09 (0.15), residues: 3114 helix: 1.83 (0.15), residues: 1252 sheet: 0.49 (0.23), residues: 530 loop : -0.19 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 402 TYR 0.013 0.001 TYR E 341 PHE 0.019 0.002 PHE B 494 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00597 (24508) covalent geometry : angle 0.56661 (33203) hydrogen bonds : bond 0.05146 ( 1154) hydrogen bonds : angle 4.69538 ( 3303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8651 (mp0) REVERT: B 478 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7469 (p) REVERT: D 338 MET cc_start: 0.8164 (mmp) cc_final: 0.7891 (mmp) REVERT: D 389 MET cc_start: 0.7361 (mpt) cc_final: 0.6968 (tpp) REVERT: F 202 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8346 (mtt) REVERT: G 131 MET cc_start: 0.6356 (mmp) cc_final: 0.6045 (mmt) outliers start: 30 outliers final: 21 residues processed: 110 average time/residue: 0.7443 time to fit residues: 94.4657 Evaluate side-chains 107 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 240 optimal weight: 6.9990 chunk 301 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 309 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 119 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.043897 restraints weight = 70835.652| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.81 r_work: 0.2577 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24508 Z= 0.207 Angle : 0.551 11.747 33203 Z= 0.285 Chirality : 0.046 0.159 3834 Planarity : 0.004 0.048 4357 Dihedral : 5.261 163.738 3409 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.25 % Allowed : 10.52 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.07 (0.15), residues: 3114 helix: 1.83 (0.15), residues: 1252 sheet: 0.50 (0.23), residues: 528 loop : -0.21 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 402 TYR 0.013 0.001 TYR E 341 PHE 0.017 0.001 PHE B 494 HIS 0.005 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00502 (24508) covalent geometry : angle 0.55060 (33203) hydrogen bonds : bond 0.04917 ( 1154) hydrogen bonds : angle 4.65362 ( 3303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8661 (mp0) REVERT: B 478 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7492 (p) REVERT: D 338 MET cc_start: 0.8161 (mmp) cc_final: 0.7889 (mmp) REVERT: D 389 MET cc_start: 0.7435 (mpt) cc_final: 0.7050 (tpp) REVERT: F 202 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8421 (mtt) REVERT: F 271 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.8908 (mtp) REVERT: G 131 MET cc_start: 0.6362 (mmp) cc_final: 0.6058 (mmt) outliers start: 32 outliers final: 21 residues processed: 110 average time/residue: 0.7364 time to fit residues: 93.5702 Evaluate side-chains 108 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 271 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 101 optimal weight: 4.9990 chunk 284 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 297 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 88 optimal weight: 0.0970 chunk 151 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.044141 restraints weight = 70708.977| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.80 r_work: 0.2586 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24508 Z= 0.191 Angle : 0.543 12.435 33203 Z= 0.280 Chirality : 0.045 0.155 3834 Planarity : 0.004 0.048 4357 Dihedral : 5.230 165.138 3409 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 1.13 % Allowed : 10.63 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.11 (0.15), residues: 3114 helix: 1.86 (0.15), residues: 1251 sheet: 0.50 (0.23), residues: 528 loop : -0.19 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 402 TYR 0.011 0.001 TYR E 341 PHE 0.017 0.001 PHE B 494 HIS 0.005 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00460 (24508) covalent geometry : angle 0.54270 (33203) hydrogen bonds : bond 0.04777 ( 1154) hydrogen bonds : angle 4.62206 ( 3303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8657 (mp0) REVERT: B 478 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7487 (p) REVERT: D 338 MET cc_start: 0.8155 (mmp) cc_final: 0.7883 (mmp) REVERT: D 389 MET cc_start: 0.7437 (mpt) cc_final: 0.7023 (tpp) REVERT: F 202 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8421 (mtt) REVERT: F 271 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.8901 (mtp) REVERT: G 131 MET cc_start: 0.6359 (mmp) cc_final: 0.6057 (mmt) outliers start: 29 outliers final: 22 residues processed: 109 average time/residue: 0.7563 time to fit residues: 95.2122 Evaluate side-chains 109 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 271 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 294 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 286 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.045485 restraints weight = 69878.703| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.81 r_work: 0.2628 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24508 Z= 0.112 Angle : 0.495 12.702 33203 Z= 0.253 Chirality : 0.043 0.180 3834 Planarity : 0.004 0.045 4357 Dihedral : 5.030 165.183 3409 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 0.97 % Allowed : 10.75 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % 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: 1.33 (0.15), residues: 3114 helix: 2.05 (0.15), residues: 1251 sheet: 0.60 (0.23), residues: 528 loop : -0.05 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 139 TYR 0.008 0.001 TYR E 341 PHE 0.016 0.001 PHE B 494 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00255 (24508) covalent geometry : angle 0.49464 (33203) hydrogen bonds : bond 0.04019 ( 1154) hydrogen bonds : angle 4.46370 ( 3303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5307.21 seconds wall clock time: 91 minutes 48.32 seconds (5508.32 seconds total)