Starting phenix.real_space_refine on Fri Jun 20 22:30:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xkp_33259/06_2025/7xkp_33259.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkp_33259/06_2025/7xkp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xkp_33259/06_2025/7xkp_33259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkp_33259/06_2025/7xkp_33259.map" model { file = "/net/cci-nas-00/data/ceres_data/7xkp_33259/06_2025/7xkp_33259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkp_33259/06_2025/7xkp_33259.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.99, per 1000 atoms: 0.58 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: 6.25 Conformation dependent library (CDL) restraints added in 3.3 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: 3.24 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: 8.74 Time building geometry restraints manager: 7.18 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 54.910 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (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 HIS 0.004 0.001 HIS D 363 PHE 0.017 0.001 PHE B 494 TYR 0.006 0.001 TYR E 341 ARG 0.004 0.000 ARG C 354 Details of bonding type rmsd hydrogen bonds : bond 0.14270 ( 1154) hydrogen bonds : angle 5.89356 ( 3303) covalent geometry : bond 0.00248 (24508) covalent geometry : angle 0.47855 (33203) *********************** 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 : 3.154 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: 2.0061 time to fit residues: 256.6435 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 : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 189 GLN C 474 HIS F 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.042701 restraints weight = 71095.581| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.78 r_work: 0.2549 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 24508 Z= 0.384 Angle : 0.689 8.741 33203 Z= 0.362 Chirality : 0.052 0.223 3834 Planarity : 0.005 0.052 4357 Dihedral : 5.937 148.896 3409 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 0.62 % Allowed : 5.88 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3114 helix: 1.60 (0.15), residues: 1243 sheet: 0.49 (0.22), residues: 538 loop : -0.19 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 363 PHE 0.024 0.002 PHE B 494 TYR 0.016 0.002 TYR E 341 ARG 0.006 0.001 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.06433 ( 1154) hydrogen bonds : angle 5.17583 ( 3303) covalent geometry : bond 0.00936 (24508) covalent geometry : angle 0.68950 (33203) *********************** 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 105 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 2.679 Fit side-chains revert: symmetry clash REVERT: C 74 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9020 (p) REVERT: D 338 MET cc_start: 0.8236 (mmp) cc_final: 0.7989 (mmp) REVERT: E 56 ASP cc_start: 0.9071 (m-30) cc_final: 0.8557 (t0) REVERT: G 131 MET cc_start: 0.6319 (mmp) cc_final: 0.5924 (mmt) outliers start: 16 outliers final: 5 residues processed: 94 average time/residue: 1.5825 time to fit residues: 170.3949 Evaluate side-chains 91 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 74 VAL 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 138 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN B 345 GLN C 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.045182 restraints weight = 69284.194| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.78 r_work: 0.2621 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24508 Z= 0.130 Angle : 0.495 8.682 33203 Z= 0.259 Chirality : 0.044 0.143 3834 Planarity : 0.004 0.045 4357 Dihedral : 5.469 140.660 3409 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Rotamer: Outliers : 0.86 % Allowed : 7.44 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.15), residues: 3114 helix: 1.97 (0.15), residues: 1243 sheet: 0.63 (0.22), residues: 530 loop : -0.01 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.018 0.001 PHE B 494 TYR 0.009 0.001 TYR E 341 ARG 0.002 0.000 ARG E 225 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 1154) hydrogen bonds : angle 4.68585 ( 3303) covalent geometry : bond 0.00304 (24508) covalent geometry : angle 0.49485 (33203) *********************** 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 112 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 338 MET cc_start: 0.8147 (mmp) cc_final: 0.7866 (mmp) REVERT: D 389 MET cc_start: 0.7589 (mpt) cc_final: 0.7369 (mpt) REVERT: E 56 ASP cc_start: 0.9041 (m-30) cc_final: 0.8524 (t0) REVERT: F 202 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8518 (mtt) REVERT: G 131 MET cc_start: 0.6280 (mmp) cc_final: 0.5862 (mmt) outliers start: 22 outliers final: 8 residues processed: 104 average time/residue: 1.4883 time to fit residues: 179.1081 Evaluate side-chains 95 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 53 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 = 0.3126 r_free = 0.3126 target = 0.060016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043724 restraints weight = 70794.081| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.81 r_work: 0.2576 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24508 Z= 0.234 Angle : 0.555 7.967 33203 Z= 0.292 Chirality : 0.046 0.161 3834 Planarity : 0.004 0.051 4357 Dihedral : 5.530 128.878 3409 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 1.52 % Allowed : 8.06 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 3114 helix: 1.81 (0.15), residues: 1253 sheet: 0.56 (0.23), residues: 531 loop : -0.14 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.019 0.002 PHE B 494 TYR 0.013 0.001 TYR E 341 ARG 0.004 0.000 ARG D 402 Details of bonding type rmsd hydrogen bonds : bond 0.05184 ( 1154) hydrogen bonds : angle 4.76034 ( 3303) covalent geometry : bond 0.00565 (24508) covalent geometry : angle 0.55494 (33203) *********************** 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 124 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 2.937 Fit side-chains revert: symmetry clash REVERT: B 250 MET cc_start: 0.9464 (OUTLIER) cc_final: 0.9256 (ttt) REVERT: B 487 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8965 (tt) REVERT: C 74 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.9024 (p) REVERT: D 338 MET cc_start: 0.8173 (mmp) cc_final: 0.7896 (mmp) REVERT: E 218 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.8922 (mtt) REVERT: F 202 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8333 (mtt) REVERT: G 131 MET cc_start: 0.6270 (mmp) cc_final: 0.5924 (mmt) outliers start: 39 outliers final: 17 residues processed: 114 average time/residue: 1.3920 time to fit residues: 185.1183 Evaluate side-chains 105 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 2.833 ------------------------------------------------------------------------------- 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 B residue 250 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 487 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 292 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 297 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.061405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.045164 restraints weight = 70217.262| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.79 r_work: 0.2618 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1157 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= 0.128 Angle : 0.486 8.788 33203 Z= 0.254 Chirality : 0.044 0.143 3834 Planarity : 0.004 0.046 4357 Dihedral : 5.258 142.936 3409 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 1.13 % Allowed : 9.31 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 3114 helix: 1.98 (0.15), residues: 1252 sheet: 0.61 (0.23), residues: 531 loop : -0.02 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 363 PHE 0.017 0.001 PHE B 494 TYR 0.009 0.001 TYR E 341 ARG 0.002 0.000 ARG D 402 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 1154) hydrogen bonds : angle 4.56801 ( 3303) covalent geometry : bond 0.00298 (24508) covalent geometry : angle 0.48600 (33203) *********************** 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 116 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8626 (mp0) REVERT: D 338 MET cc_start: 0.8153 (mmp) cc_final: 0.7878 (mmp) REVERT: E 218 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8875 (mtt) REVERT: F 202 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8365 (mtt) REVERT: G 131 MET cc_start: 0.6329 (mmp) cc_final: 0.5962 (mmt) outliers start: 29 outliers final: 18 residues processed: 110 average time/residue: 1.3726 time to fit residues: 175.4708 Evaluate side-chains 104 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 2.818 ------------------------------------------------------------------------------- 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 459 GLU Chi-restraints excluded: chain B residue 314 THR 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 105 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 10 MET 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 F residue 344 VAL Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 165 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 230 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 131 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.060786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.044499 restraints weight = 70175.777| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.81 r_work: 0.2594 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24508 Z= 0.173 Angle : 0.518 9.729 33203 Z= 0.269 Chirality : 0.045 0.149 3834 Planarity : 0.004 0.049 4357 Dihedral : 5.300 158.908 3409 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 1.29 % Allowed : 9.86 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.15), residues: 3114 helix: 1.96 (0.15), residues: 1252 sheet: 0.60 (0.23), residues: 531 loop : -0.05 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.017 0.001 PHE B 494 TYR 0.010 0.001 TYR E 341 ARG 0.003 0.000 ARG D 402 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 1154) hydrogen bonds : angle 4.58499 ( 3303) covalent geometry : bond 0.00415 (24508) covalent geometry : angle 0.51789 (33203) *********************** 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 : 4.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: B 250 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.9239 (ttt) REVERT: B 478 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7529 (p) REVERT: D 338 MET cc_start: 0.8162 (mmp) cc_final: 0.7884 (mmp) REVERT: E 218 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8907 (mtt) REVERT: F 202 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8437 (mtt) REVERT: G 131 MET cc_start: 0.6274 (mmp) cc_final: 0.5917 (mmt) outliers start: 33 outliers final: 20 residues processed: 112 average time/residue: 2.3549 time to fit residues: 309.3884 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 : 4.487 ------------------------------------------------------------------------------- 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 250 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 478 THR 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 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 301 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 38 ASN 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 19 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 304 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.061895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.045554 restraints weight = 70022.951| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.83 r_work: 0.2631 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24508 Z= 0.113 Angle : 0.476 10.873 33203 Z= 0.247 Chirality : 0.043 0.142 3834 Planarity : 0.004 0.045 4357 Dihedral : 5.103 160.591 3409 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.15), residues: 3114 helix: 2.13 (0.15), residues: 1246 sheet: 0.69 (0.23), residues: 540 loop : 0.06 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 363 PHE 0.015 0.001 PHE B 494 TYR 0.008 0.001 TYR E 341 ARG 0.001 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 1154) hydrogen bonds : angle 4.43651 ( 3303) covalent geometry : bond 0.00259 (24508) covalent geometry : angle 0.47632 (33203) *********************** 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 115 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8556 (mp0) REVERT: B 250 MET cc_start: 0.9407 (ttp) cc_final: 0.9193 (ttt) REVERT: B 478 THR cc_start: 0.7824 (OUTLIER) cc_final: 0.7550 (p) REVERT: C 74 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.9002 (p) REVERT: D 338 MET cc_start: 0.8153 (mmp) cc_final: 0.7871 (mmp) REVERT: D 389 MET cc_start: 0.7332 (mpt) cc_final: 0.7108 (mpp) REVERT: E 218 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8886 (mtt) REVERT: F 202 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8442 (mtt) REVERT: G 131 MET cc_start: 0.6322 (mmp) cc_final: 0.5950 (mmt) outliers start: 30 outliers final: 19 residues processed: 109 average time/residue: 1.4356 time to fit residues: 181.7803 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 : 2.713 ------------------------------------------------------------------------------- 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 459 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 402 LEU 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 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 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 Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 31 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 249 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 = 0.3137 r_free = 0.3137 target = 0.060531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.044326 restraints weight = 70433.679| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.81 r_work: 0.2591 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24508 Z= 0.195 Angle : 0.528 11.240 33203 Z= 0.274 Chirality : 0.045 0.159 3834 Planarity : 0.004 0.047 4357 Dihedral : 5.166 162.502 3409 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 1.29 % Allowed : 10.67 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 3114 helix: 2.00 (0.15), residues: 1251 sheet: 0.61 (0.23), residues: 540 loop : -0.04 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.017 0.001 PHE B 494 TYR 0.010 0.001 TYR E 341 ARG 0.003 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 1154) hydrogen bonds : angle 4.54488 ( 3303) covalent geometry : bond 0.00472 (24508) covalent geometry : angle 0.52814 (33203) *********************** 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 118 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8616 (mp0) REVERT: B 250 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.9239 (ttt) REVERT: B 402 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7495 (pp) REVERT: B 407 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7941 (mp10) REVERT: B 478 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7567 (p) REVERT: C 74 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.9032 (p) REVERT: D 338 MET cc_start: 0.8162 (mmp) cc_final: 0.7889 (mmp) REVERT: D 389 MET cc_start: 0.7385 (mpt) cc_final: 0.7118 (mpp) REVERT: E 218 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8914 (mtt) REVERT: F 202 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8375 (mtt) REVERT: G 131 MET cc_start: 0.6346 (mmp) cc_final: 0.6005 (mmt) outliers start: 33 outliers final: 23 residues processed: 112 average time/residue: 1.3537 time to fit residues: 176.6017 Evaluate side-chains 113 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 2.630 ------------------------------------------------------------------------------- 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 459 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 402 LEU 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 C residue 499 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE 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 Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 277 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 264 optimal weight: 0.0770 chunk 230 optimal weight: 0.4980 chunk 134 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 overall best weight: 1.7142 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.061506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.045245 restraints weight = 70098.626| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.80 r_work: 0.2619 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24508 Z= 0.123 Angle : 0.490 11.839 33203 Z= 0.252 Chirality : 0.043 0.141 3834 Planarity : 0.004 0.045 4357 Dihedral : 4.957 158.675 3409 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 1.29 % Allowed : 10.83 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.15), residues: 3114 helix: 2.10 (0.15), residues: 1251 sheet: 0.66 (0.23), residues: 540 loop : 0.02 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 363 PHE 0.015 0.001 PHE B 494 TYR 0.008 0.001 TYR E 341 ARG 0.002 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 1154) hydrogen bonds : angle 4.44155 ( 3303) covalent geometry : bond 0.00287 (24508) covalent geometry : angle 0.48986 (33203) *********************** 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 118 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8691 (mp0) REVERT: B 407 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7924 (mp10) REVERT: B 478 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7535 (p) REVERT: C 74 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.9015 (p) REVERT: D 338 MET cc_start: 0.8136 (mmp) cc_final: 0.7863 (mmp) REVERT: D 389 MET cc_start: 0.7272 (mpt) cc_final: 0.7006 (mpp) REVERT: E 218 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8883 (mtt) REVERT: F 202 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8460 (mtt) REVERT: G 131 MET cc_start: 0.6343 (mmp) cc_final: 0.5987 (mmt) outliers start: 33 outliers final: 24 residues processed: 110 average time/residue: 1.4304 time to fit residues: 182.9078 Evaluate side-chains 112 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 2.797 ------------------------------------------------------------------------------- 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 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 C residue 499 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 10 MET 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 F residue 469 MET Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 246 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 chunk 234 optimal weight: 2.9990 chunk 95 optimal weight: 0.0170 chunk 200 optimal weight: 0.9980 chunk 251 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.063029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.046767 restraints weight = 69459.949| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.84 r_work: 0.2661 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24508 Z= 0.092 Angle : 0.468 12.747 33203 Z= 0.238 Chirality : 0.043 0.187 3834 Planarity : 0.004 0.043 4357 Dihedral : 4.703 153.521 3409 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 1.09 % Allowed : 10.99 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.16), residues: 3114 helix: 2.24 (0.15), residues: 1250 sheet: 0.76 (0.23), residues: 545 loop : 0.14 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 447 PHE 0.014 0.001 PHE B 494 TYR 0.006 0.001 TYR F 238 ARG 0.003 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 1154) hydrogen bonds : angle 4.30449 ( 3303) covalent geometry : bond 0.00199 (24508) covalent geometry : angle 0.46813 (33203) ********************** 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 116 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 2.637 Fit side-chains revert: symmetry clash REVERT: A 459 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8677 (mp0) REVERT: B 478 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7548 (p) REVERT: C 74 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.9002 (p) REVERT: D 338 MET cc_start: 0.8109 (mmp) cc_final: 0.7877 (mmp) REVERT: D 389 MET cc_start: 0.7238 (mpt) cc_final: 0.7020 (mpp) REVERT: D 464 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: E 218 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.8861 (mtt) REVERT: F 202 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8405 (mtt) REVERT: G 65 HIS cc_start: 0.7453 (t-90) cc_final: 0.6570 (m-70) REVERT: G 131 MET cc_start: 0.6345 (mmp) cc_final: 0.5919 (mmt) outliers start: 28 outliers final: 16 residues processed: 108 average time/residue: 1.4223 time to fit residues: 178.0606 Evaluate side-chains 107 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 2.631 ------------------------------------------------------------------------------- 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 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 D residue 59 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 213 MET 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 F residue 344 VAL Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 288 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 286 optimal weight: 0.8980 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.060797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.044445 restraints weight = 70147.027| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.82 r_work: 0.2597 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1369 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= 0.187 Angle : 0.535 12.761 33203 Z= 0.275 Chirality : 0.045 0.179 3834 Planarity : 0.004 0.046 4357 Dihedral : 4.983 156.155 3409 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.09 % Allowed : 11.06 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.15), residues: 3114 helix: 2.07 (0.15), residues: 1252 sheet: 0.68 (0.23), residues: 540 loop : 0.02 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.017 0.001 PHE B 494 TYR 0.010 0.001 TYR E 341 ARG 0.004 0.000 ARG B 354 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 1154) hydrogen bonds : angle 4.50229 ( 3303) covalent geometry : bond 0.00450 (24508) covalent geometry : angle 0.53521 (33203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11587.30 seconds wall clock time: 203 minutes 30.40 seconds (12210.40 seconds total)