Starting phenix.real_space_refine on Mon Aug 25 01:45:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hha_34757/08_2025/8hha_34757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hha_34757/08_2025/8hha_34757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hha_34757/08_2025/8hha_34757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hha_34757/08_2025/8hha_34757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hha_34757/08_2025/8hha_34757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hha_34757/08_2025/8hha_34757.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24245 Number of models: 1 Model: "" Number of chains: 12 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: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.84, per 1000 atoms: 0.20 Number of scatterers: 24245 At special positions: 0 Unit cell: (130.24, 120.56, 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 15 15.00 Mg 5 11.99 O 4657 8.00 N 4214 7.00 C 15277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 969.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 21 sheets defined 48.1% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.311A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.685A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' 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 removed outlier: 3.667A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.630A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.500A pdb=" N ALA A 285 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.672A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) 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 394 removed outlier: 4.615A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 421 Processing helix chain 'A' and resid 429 through 442 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 155 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.645A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 231 through 252 removed outlier: 3.567A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.820A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.336A 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: 3.588A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.668A 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 345 through 350 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.818A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 485 through 498 Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.300A pdb=" N GLY C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.581A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.656A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.705A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.696A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 393 removed outlier: 3.621A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.652A pdb=" N GLN C 397 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.550A pdb=" N GLN C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 4.101A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.563A 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 139 through 146 Processing helix chain 'D' and resid 163 through 180 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 243 removed outlier: 3.656A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.789A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 323 removed outlier: 4.208A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.725A pdb=" N MET D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 387 removed outlier: 3.584A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'D' and resid 393 through 411 removed outlier: 3.515A pdb=" N LEU D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER D 411 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 removed outlier: 3.820A pdb=" N ARG D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.518A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'E' and resid 163 through 180 Processing helix chain 'E' and resid 191 through 206 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 243 removed outlier: 5.346A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN E 243 " --> pdb=" O PHE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.851A 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 322 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.508A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.787A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.519A pdb=" N GLY E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.584A pdb=" N ARG E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.859A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 206 through 209 removed outlier: 3.809A pdb=" N SER F 209 " --> pdb=" O GLY F 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 209' Processing helix chain 'F' and resid 221 through 242 removed outlier: 5.222A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.078A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 278 through 279 No H-bonds generated for 'chain 'F' and resid 278 through 279' Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.700A 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 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 338 removed outlier: 3.530A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 389 through 392 removed outlier: 3.740A pdb=" N LEU F 392 " --> pdb=" O MET F 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 389 through 392' Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.703A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.554A pdb=" N GLU F 418 " --> pdb=" O HIS F 415 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) 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: 3.878A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 removed outlier: 4.098A pdb=" N THR G 9 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 56 removed outlier: 3.517A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.832A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS G 105 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.575A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 162 removed outlier: 4.622A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 284 removed outlier: 4.386A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU G 216 " --> pdb=" O ILE G 212 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.522A pdb=" N LYS G 245 " --> pdb=" O MET G 241 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN G 246 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 3.792A 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: 4.096A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA E 29 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN E 28 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 8.699A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.592A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.125A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.707A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.650A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.523A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.385A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.864A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.360A pdb=" N VAL C 108 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.555A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N THR D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN D 28 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA D 29 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 removed outlier: 3.532A pdb=" N ASP D 116 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 4.068A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.246A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'E' and resid 95 through 96 removed outlier: 3.517A pdb=" N ALA E 212 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.342A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC2, first strand: chain 'F' and resid 94 through 96 removed outlier: 3.780A pdb=" N ARG F 94 " --> pdb=" O THR F 211 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 113 through 118 removed outlier: 5.625A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N TYR G 175 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG G 186 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR G 172 " --> pdb=" O THR G 184 " (cutoff:3.500A) 1132 hydrogen bonds defined for protein. 3234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 2.66 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: 8229 1.34 - 1.46: 4003 1.46 - 1.58: 12242 1.58 - 1.69: 23 1.69 - 1.81: 154 Bond restraints: 24651 Sorted by residual: bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.75e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" O2B ATP F 602 " pdb=" PB ATP F 602 " ideal model delta sigma weight residual 1.529 1.474 0.055 2.20e-02 2.07e+03 6.29e+00 ... (remaining 24646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 32802 1.86 - 3.71: 549 3.71 - 5.57: 66 5.57 - 7.43: 8 7.43 - 9.28: 2 Bond angle restraints: 33427 Sorted by residual: angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 134.09 5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" C ALA E 274 " pdb=" CA ALA E 274 " pdb=" CB ALA E 274 " ideal model delta sigma weight residual 116.54 110.51 6.03 1.15e+00 7.56e-01 2.75e+01 angle pdb=" O1G ATP F 602 " pdb=" PG ATP F 602 " pdb=" O3B ATP F 602 " ideal model delta sigma weight residual 110.47 103.17 7.30 1.64e+00 3.70e-01 1.97e+01 angle pdb=" C ASN E 97 " pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 121.97 129.93 -7.96 1.80e+00 3.09e-01 1.96e+01 angle pdb=" N VAL D 275 " pdb=" CA VAL D 275 " pdb=" C VAL D 275 " ideal model delta sigma weight residual 111.91 108.45 3.46 8.90e-01 1.26e+00 1.51e+01 ... (remaining 33422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 14134 22.08 - 44.17: 770 44.17 - 66.25: 111 66.25 - 88.33: 41 88.33 - 110.42: 3 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" C5' ADP D 603 " pdb=" O5' ADP D 603 " pdb=" PA ADP D 603 " pdb=" O2A ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 -170.41 110.42 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" CA ARG A 93 " pdb=" C ARG A 93 " pdb=" N ILE A 94 " pdb=" CA ILE A 94 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU G 213 " pdb=" C LEU G 213 " pdb=" N ASP G 214 " pdb=" CA ASP G 214 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2444 0.035 - 0.070: 946 0.070 - 0.105: 313 0.105 - 0.139: 143 0.139 - 0.174: 6 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CB VAL F 275 " pdb=" CA VAL F 275 " pdb=" CG1 VAL F 275 " pdb=" CG2 VAL F 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA LEU G 217 " pdb=" N LEU G 217 " pdb=" C LEU G 217 " pdb=" CB LEU G 217 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CB VAL D 275 " pdb=" CA VAL D 275 " pdb=" CG1 VAL D 275 " pdb=" CG2 VAL D 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 71 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO G 72 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 382 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C LEU B 382 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU B 382 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG B 383 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 322 " 0.012 2.00e-02 2.50e+03 1.50e-02 3.91e+00 pdb=" CG PHE D 322 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE D 322 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 322 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE D 322 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 322 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 322 " 0.000 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 157 2.56 - 3.14: 19467 3.14 - 3.73: 36897 3.73 - 4.31: 51370 4.31 - 4.90: 88206 Nonbonded interactions: 196097 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O4 PO4 D 602 " model vdw 1.970 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 602 " model vdw 2.021 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 2.034 2.170 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 2.062 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.067 2.170 ... (remaining 196092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.940 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24651 Z= 0.150 Angle : 0.603 9.282 33427 Z= 0.349 Chirality : 0.044 0.174 3852 Planarity : 0.004 0.108 4362 Dihedral : 14.058 110.416 9347 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1252 sheet: 0.98 (0.23), residues: 511 loop : -0.23 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 333 TYR 0.017 0.001 TYR G 175 PHE 0.034 0.001 PHE D 322 HIS 0.007 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00307 (24651) covalent geometry : angle 0.60284 (33427) hydrogen bonds : bond 0.14903 ( 1132) hydrogen bonds : angle 6.20264 ( 3234) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 389 TYR cc_start: 0.8151 (t80) cc_final: 0.7842 (t80) REVERT: G 113 TYR cc_start: 0.6064 (p90) cc_final: 0.5592 (p90) REVERT: G 189 LEU cc_start: 0.6972 (mm) cc_final: 0.6671 (mm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1408 time to fit residues: 38.8248 Evaluate side-chains 129 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.065856 restraints weight = 62398.604| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.44 r_work: 0.2867 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24651 Z= 0.170 Angle : 0.569 8.565 33427 Z= 0.298 Chirality : 0.046 0.252 3852 Planarity : 0.005 0.074 4362 Dihedral : 7.932 106.055 3546 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 0.35 % Allowed : 4.21 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3115 helix: 1.35 (0.15), residues: 1244 sheet: 0.91 (0.22), residues: 519 loop : -0.25 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 333 TYR 0.015 0.001 TYR G 262 PHE 0.031 0.001 PHE G 160 HIS 0.006 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00406 (24651) covalent geometry : angle 0.56851 (33427) hydrogen bonds : bond 0.04569 ( 1132) hydrogen bonds : angle 5.05700 ( 3234) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 113 TYR cc_start: 0.6104 (p90) cc_final: 0.5480 (p90) REVERT: G 131 MET cc_start: 0.6519 (mmm) cc_final: 0.6119 (mmm) outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.1455 time to fit residues: 33.4908 Evaluate side-chains 130 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 65 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 287 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 111 optimal weight: 0.0000 chunk 88 optimal weight: 7.9990 chunk 283 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 overall best weight: 2.5590 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.081673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.066089 restraints weight = 62257.526| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.39 r_work: 0.2873 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24651 Z= 0.148 Angle : 0.533 7.223 33427 Z= 0.279 Chirality : 0.045 0.252 3852 Planarity : 0.004 0.050 4362 Dihedral : 7.465 96.700 3546 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 0.51 % Allowed : 6.35 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.15), residues: 3115 helix: 1.44 (0.15), residues: 1241 sheet: 0.83 (0.22), residues: 525 loop : -0.28 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 186 TYR 0.015 0.001 TYR A 461 PHE 0.027 0.001 PHE G 160 HIS 0.005 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00352 (24651) covalent geometry : angle 0.53309 (33427) hydrogen bonds : bond 0.04186 ( 1132) hydrogen bonds : angle 4.77593 ( 3234) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: B 395 PHE cc_start: 0.6586 (t80) cc_final: 0.6183 (t80) REVERT: G 113 TYR cc_start: 0.6157 (p90) cc_final: 0.5573 (p90) REVERT: G 131 MET cc_start: 0.6518 (mmm) cc_final: 0.6040 (mmm) outliers start: 13 outliers final: 11 residues processed: 145 average time/residue: 0.1343 time to fit residues: 31.6354 Evaluate side-chains 141 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 174 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 115 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 124 optimal weight: 0.0010 chunk 282 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 266 GLN B 474 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.067093 restraints weight = 62151.795| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.43 r_work: 0.2897 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24651 Z= 0.098 Angle : 0.488 8.626 33427 Z= 0.253 Chirality : 0.043 0.161 3852 Planarity : 0.004 0.047 4362 Dihedral : 7.120 85.728 3546 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.59 % Rotamer: Outliers : 0.74 % Allowed : 7.55 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.15), residues: 3115 helix: 1.66 (0.15), residues: 1240 sheet: 0.92 (0.22), residues: 524 loop : -0.20 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 333 TYR 0.016 0.001 TYR G 169 PHE 0.018 0.001 PHE G 160 HIS 0.004 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00216 (24651) covalent geometry : angle 0.48772 (33427) hydrogen bonds : bond 0.03518 ( 1132) hydrogen bonds : angle 4.55595 ( 3234) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: B 389 TYR cc_start: 0.7916 (t80) cc_final: 0.7705 (t80) REVERT: B 395 PHE cc_start: 0.6629 (t80) cc_final: 0.6164 (t80) REVERT: B 466 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7173 (mm-40) REVERT: C 476 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.8207 (mtm-85) REVERT: F 5 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8186 (mtp-110) REVERT: G 113 TYR cc_start: 0.6112 (p90) cc_final: 0.5510 (p90) REVERT: G 131 MET cc_start: 0.6550 (mmm) cc_final: 0.6089 (mmm) outliers start: 19 outliers final: 13 residues processed: 161 average time/residue: 0.1439 time to fit residues: 38.1088 Evaluate side-chains 149 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 174 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 94 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 299 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 GLN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.065099 restraints weight = 62957.664| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.61 r_work: 0.2846 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24651 Z= 0.121 Angle : 0.495 6.873 33427 Z= 0.257 Chirality : 0.044 0.164 3852 Planarity : 0.004 0.049 4362 Dihedral : 7.003 88.981 3546 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 1.05 % Allowed : 8.10 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.15), residues: 3115 helix: 1.67 (0.15), residues: 1242 sheet: 0.90 (0.22), residues: 525 loop : -0.18 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 333 TYR 0.012 0.001 TYR G 262 PHE 0.023 0.001 PHE G 160 HIS 0.005 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00283 (24651) covalent geometry : angle 0.49531 (33427) hydrogen bonds : bond 0.03679 ( 1132) hydrogen bonds : angle 4.49027 ( 3234) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8416 (tpt) cc_final: 0.8102 (tpp) REVERT: B 245 MET cc_start: 0.8592 (ttm) cc_final: 0.8211 (mtt) REVERT: B 389 TYR cc_start: 0.7922 (t80) cc_final: 0.7686 (t80) REVERT: B 395 PHE cc_start: 0.6585 (t80) cc_final: 0.6129 (t80) REVERT: B 466 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7155 (mm-40) REVERT: E 131 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: F 5 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8206 (mtp-110) REVERT: G 113 TYR cc_start: 0.6109 (p90) cc_final: 0.5534 (p90) REVERT: G 131 MET cc_start: 0.6584 (mmm) cc_final: 0.6112 (mmm) outliers start: 27 outliers final: 20 residues processed: 162 average time/residue: 0.1345 time to fit residues: 35.5949 Evaluate side-chains 154 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 174 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 280 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 GLN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.065582 restraints weight = 62699.638| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.42 r_work: 0.2862 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24651 Z= 0.118 Angle : 0.491 7.771 33427 Z= 0.254 Chirality : 0.044 0.157 3852 Planarity : 0.004 0.065 4362 Dihedral : 6.916 89.622 3546 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 1.44 % Allowed : 8.57 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.15), residues: 3115 helix: 1.70 (0.15), residues: 1244 sheet: 0.98 (0.23), residues: 524 loop : -0.17 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 405 TYR 0.012 0.001 TYR G 262 PHE 0.016 0.001 PHE G 160 HIS 0.005 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00276 (24651) covalent geometry : angle 0.49075 (33427) hydrogen bonds : bond 0.03593 ( 1132) hydrogen bonds : angle 4.45085 ( 3234) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: B 245 MET cc_start: 0.8590 (ttm) cc_final: 0.8215 (mtt) REVERT: B 389 TYR cc_start: 0.7933 (t80) cc_final: 0.7699 (t80) REVERT: B 395 PHE cc_start: 0.6511 (t80) cc_final: 0.6025 (t80) REVERT: B 466 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7079 (mm-40) REVERT: E 131 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: F 5 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8209 (mtp-110) REVERT: G 113 TYR cc_start: 0.6199 (p90) cc_final: 0.5642 (p90) outliers start: 37 outliers final: 24 residues processed: 166 average time/residue: 0.1299 time to fit residues: 36.7177 Evaluate side-chains 160 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 188 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 305 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 GLN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.063841 restraints weight = 63288.366| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.41 r_work: 0.2819 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24651 Z= 0.210 Angle : 0.568 8.965 33427 Z= 0.296 Chirality : 0.046 0.157 3852 Planarity : 0.004 0.056 4362 Dihedral : 7.130 96.200 3546 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 1.32 % Allowed : 9.07 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3115 helix: 1.46 (0.15), residues: 1244 sheet: 0.88 (0.23), residues: 509 loop : -0.34 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 271 TYR 0.014 0.001 TYR G 262 PHE 0.019 0.002 PHE B 494 HIS 0.005 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00504 (24651) covalent geometry : angle 0.56798 (33427) hydrogen bonds : bond 0.04434 ( 1132) hydrogen bonds : angle 4.65233 ( 3234) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: B 245 MET cc_start: 0.8797 (ttm) cc_final: 0.8417 (mtt) REVERT: B 395 PHE cc_start: 0.6557 (t80) cc_final: 0.6087 (t80) REVERT: B 466 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7343 (mm-40) REVERT: D 116 ASP cc_start: 0.8428 (m-30) cc_final: 0.8191 (m-30) REVERT: E 131 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: F 5 ARG cc_start: 0.8967 (ttm-80) cc_final: 0.8400 (mtp-110) REVERT: G 113 TYR cc_start: 0.6409 (p90) cc_final: 0.5830 (p90) outliers start: 34 outliers final: 28 residues processed: 158 average time/residue: 0.1422 time to fit residues: 37.3140 Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 174 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 143 optimal weight: 0.0030 chunk 278 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 chunk 221 optimal weight: 9.9990 chunk 7 optimal weight: 0.0970 chunk 213 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 154 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 GLN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.066636 restraints weight = 62287.834| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.41 r_work: 0.2883 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 24651 Z= 0.091 Angle : 0.473 9.640 33427 Z= 0.246 Chirality : 0.043 0.154 3852 Planarity : 0.004 0.071 4362 Dihedral : 6.793 85.359 3546 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 0.78 % Allowed : 9.77 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.15), residues: 3115 helix: 1.77 (0.15), residues: 1250 sheet: 0.98 (0.23), residues: 521 loop : -0.15 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.015 0.001 TYR A 461 PHE 0.014 0.001 PHE C 494 HIS 0.004 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00195 (24651) covalent geometry : angle 0.47307 (33427) hydrogen bonds : bond 0.03236 ( 1132) hydrogen bonds : angle 4.41222 ( 3234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: B 245 MET cc_start: 0.8543 (ttm) cc_final: 0.8172 (mtt) REVERT: B 395 PHE cc_start: 0.6522 (t80) cc_final: 0.6062 (t80) REVERT: B 466 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7155 (mm-40) REVERT: D 87 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8630 (m) REVERT: E 131 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: F 5 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8186 (mtp-110) REVERT: F 469 MET cc_start: 0.6872 (mtp) cc_final: 0.6630 (mtm) REVERT: G 113 TYR cc_start: 0.6095 (p90) cc_final: 0.5593 (p90) outliers start: 20 outliers final: 17 residues processed: 160 average time/residue: 0.1426 time to fit residues: 38.3040 Evaluate side-chains 151 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 188 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 146 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 277 optimal weight: 9.9990 chunk 279 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 114 optimal weight: 0.0670 chunk 290 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 overall best weight: 2.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 GLN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.065404 restraints weight = 62914.980| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.42 r_work: 0.2858 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24651 Z= 0.129 Angle : 0.498 9.905 33427 Z= 0.257 Chirality : 0.044 0.154 3852 Planarity : 0.004 0.072 4362 Dihedral : 6.759 86.052 3546 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 0.90 % Allowed : 10.09 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.15), residues: 3115 helix: 1.73 (0.15), residues: 1247 sheet: 1.00 (0.23), residues: 519 loop : -0.20 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 412 TYR 0.036 0.001 TYR B 389 PHE 0.014 0.001 PHE B 494 HIS 0.003 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00306 (24651) covalent geometry : angle 0.49785 (33427) hydrogen bonds : bond 0.03565 ( 1132) hydrogen bonds : angle 4.42659 ( 3234) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8019 (mm-30) REVERT: B 245 MET cc_start: 0.8589 (ttm) cc_final: 0.8211 (mtt) REVERT: B 395 PHE cc_start: 0.6538 (t80) cc_final: 0.6092 (t80) REVERT: B 466 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7221 (mm-40) REVERT: C 447 ASP cc_start: 0.8466 (p0) cc_final: 0.8208 (t0) REVERT: D 87 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8625 (m) REVERT: E 131 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: F 5 ARG cc_start: 0.8744 (ttm-80) cc_final: 0.8222 (mtp-110) REVERT: F 469 MET cc_start: 0.6839 (mtp) cc_final: 0.6572 (mtm) REVERT: G 113 TYR cc_start: 0.6072 (p90) cc_final: 0.5560 (p90) outliers start: 23 outliers final: 20 residues processed: 154 average time/residue: 0.1336 time to fit residues: 34.6745 Evaluate side-chains 156 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 226 optimal weight: 0.0170 chunk 207 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 chunk 60 optimal weight: 0.0670 overall best weight: 3.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.080083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.064536 restraints weight = 63068.684| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.42 r_work: 0.2835 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24651 Z= 0.166 Angle : 0.537 10.539 33427 Z= 0.277 Chirality : 0.045 0.155 3852 Planarity : 0.004 0.074 4362 Dihedral : 6.884 92.017 3546 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 0.97 % Allowed : 10.09 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.15), residues: 3115 helix: 1.59 (0.15), residues: 1248 sheet: 0.86 (0.23), residues: 521 loop : -0.24 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 333 TYR 0.027 0.001 TYR B 389 PHE 0.016 0.001 PHE B 494 HIS 0.004 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00400 (24651) covalent geometry : angle 0.53659 (33427) hydrogen bonds : bond 0.04040 ( 1132) hydrogen bonds : angle 4.53332 ( 3234) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: B 245 MET cc_start: 0.8650 (ttm) cc_final: 0.8265 (mtt) REVERT: B 395 PHE cc_start: 0.6391 (t80) cc_final: 0.5930 (t80) REVERT: B 466 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7150 (mm-40) REVERT: C 447 ASP cc_start: 0.8458 (p0) cc_final: 0.8186 (t0) REVERT: D 87 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8675 (m) REVERT: E 131 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: F 5 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8229 (mtp-110) REVERT: G 113 TYR cc_start: 0.6209 (p90) cc_final: 0.5667 (p90) outliers start: 25 outliers final: 21 residues processed: 153 average time/residue: 0.1276 time to fit residues: 32.9329 Evaluate side-chains 153 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 174 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 136 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 258 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 104 optimal weight: 0.0570 chunk 253 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS D 169 GLN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.064679 restraints weight = 63080.315| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.43 r_work: 0.2840 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24651 Z= 0.148 Angle : 0.520 10.278 33427 Z= 0.269 Chirality : 0.044 0.154 3852 Planarity : 0.004 0.074 4362 Dihedral : 6.865 92.770 3546 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 1.01 % Allowed : 10.05 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.15), residues: 3115 helix: 1.59 (0.15), residues: 1248 sheet: 0.83 (0.23), residues: 521 loop : -0.25 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 333 TYR 0.026 0.001 TYR B 389 PHE 0.015 0.001 PHE B 494 HIS 0.004 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00354 (24651) covalent geometry : angle 0.51971 (33427) hydrogen bonds : bond 0.03871 ( 1132) hydrogen bonds : angle 4.50530 ( 3234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3873.01 seconds wall clock time: 67 minutes 25.22 seconds (4045.22 seconds total)