Starting phenix.real_space_refine on Sat Jun 21 03:36:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hha_34757/06_2025/8hha_34757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hha_34757/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hha_34757/06_2025/8hha_34757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hha_34757/06_2025/8hha_34757.map" model { file = "/net/cci-nas-00/data/ceres_data/8hha_34757/06_2025/8hha_34757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hha_34757/06_2025/8hha_34757.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.37, per 1000 atoms: 0.59 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: 6.26 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.16 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: 7.83 Time building geometry restraints manager: 7.34 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 53.740 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.160 ------------------------------------------------------------------------------- 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 : 6.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (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 HIS 0.007 0.001 HIS B 470 PHE 0.034 0.001 PHE D 322 TYR 0.017 0.001 TYR G 175 ARG 0.007 0.000 ARG D 333 Details of bonding type rmsd hydrogen bonds : bond 0.14903 ( 1132) hydrogen bonds : angle 6.20264 ( 3234) covalent geometry : bond 0.00307 (24651) covalent geometry : angle 0.60284 (33427) *********************** 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 : 2.565 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: 0.3296 time to fit residues: 91.3208 Evaluate side-chains 128 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 125 optimal weight: 0.4980 chunk 242 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 281 optimal weight: 7.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.079227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.063671 restraints weight = 62776.406| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.42 r_work: 0.2819 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 24651 Z= 0.301 Angle : 0.683 9.577 33427 Z= 0.358 Chirality : 0.050 0.261 3852 Planarity : 0.006 0.073 4362 Dihedral : 8.183 115.150 3546 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 0.47 % Allowed : 5.53 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3115 helix: 0.93 (0.15), residues: 1250 sheet: 0.69 (0.23), residues: 513 loop : -0.48 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 425 PHE 0.036 0.002 PHE G 160 TYR 0.019 0.002 TYR G 262 ARG 0.006 0.001 ARG C 365 Details of bonding type rmsd hydrogen bonds : bond 0.05560 ( 1132) hydrogen bonds : angle 5.23900 ( 3234) covalent geometry : bond 0.00727 (24651) covalent geometry : angle 0.68286 (33427) *********************** 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 144 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 2.771 Fit side-chains revert: symmetry clash REVERT: B 395 PHE cc_start: 0.6613 (t80) cc_final: 0.6311 (t80) REVERT: G 113 TYR cc_start: 0.6127 (p90) cc_final: 0.5519 (p90) outliers start: 12 outliers final: 9 residues processed: 139 average time/residue: 0.3348 time to fit residues: 77.2810 Evaluate side-chains 132 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 2.927 ------------------------------------------------------------------------------- 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 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 F residue 301 THR 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 267 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 274 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.080970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.065351 restraints weight = 61916.586| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.42 r_work: 0.2857 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1044 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 : 0.546 8.292 33427 Z= 0.286 Chirality : 0.045 0.186 3852 Planarity : 0.004 0.051 4362 Dihedral : 7.625 101.789 3546 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 0.62 % Allowed : 7.48 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1242 sheet: 0.69 (0.22), residues: 527 loop : -0.39 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 470 PHE 0.027 0.001 PHE G 160 TYR 0.014 0.001 TYR F 427 ARG 0.005 0.000 ARG G 186 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 1132) hydrogen bonds : angle 4.84625 ( 3234) covalent geometry : bond 0.00352 (24651) covalent geometry : angle 0.54639 (33427) *********************** 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 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 2.760 Fit side-chains revert: symmetry clash REVERT: B 395 PHE cc_start: 0.6623 (t80) cc_final: 0.6209 (t80) REVERT: G 113 TYR cc_start: 0.6111 (p90) cc_final: 0.5515 (p90) outliers start: 16 outliers final: 12 residues processed: 147 average time/residue: 0.3264 time to fit residues: 80.4364 Evaluate side-chains 139 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 2.770 ------------------------------------------------------------------------------- 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 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 61 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 254 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 241 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS ** 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 = 0.3240 r_free = 0.3240 target = 0.079068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063158 restraints weight = 63561.514| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.63 r_work: 0.2803 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24651 Z= 0.169 Angle : 0.549 7.713 33427 Z= 0.286 Chirality : 0.045 0.165 3852 Planarity : 0.004 0.052 4362 Dihedral : 7.444 98.554 3546 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 1.44 % Allowed : 8.22 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3115 helix: 1.31 (0.15), residues: 1243 sheet: 0.68 (0.22), residues: 527 loop : -0.41 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 470 PHE 0.023 0.001 PHE G 160 TYR 0.017 0.001 TYR A 461 ARG 0.004 0.000 ARG D 333 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 1132) hydrogen bonds : angle 4.74719 ( 3234) covalent geometry : bond 0.00403 (24651) covalent geometry : angle 0.54918 (33427) *********************** 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: 37 poor density : 129 time to evaluate : 2.988 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8467 (tpt) cc_final: 0.8119 (tpp) REVERT: B 395 PHE cc_start: 0.6697 (t80) cc_final: 0.6305 (t80) REVERT: B 466 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7239 (mm-40) REVERT: E 131 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: G 113 TYR cc_start: 0.6015 (p90) cc_final: 0.5360 (p90) outliers start: 37 outliers final: 26 residues processed: 158 average time/residue: 0.3295 time to fit residues: 89.7645 Evaluate side-chains 154 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 2.819 ------------------------------------------------------------------------------- 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 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 462 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 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 65 HIS Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 241 MET Chi-restraints excluded: chain G residue 257 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 139 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 297 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN 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 = 0.3239 r_free = 0.3239 target = 0.079004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.063203 restraints weight = 63560.403| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.62 r_work: 0.2807 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24651 Z= 0.166 Angle : 0.539 7.504 33427 Z= 0.281 Chirality : 0.045 0.160 3852 Planarity : 0.004 0.062 4362 Dihedral : 7.368 97.677 3546 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.85 % Rotamer: Outliers : 1.36 % Allowed : 9.35 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3115 helix: 1.35 (0.15), residues: 1243 sheet: 0.67 (0.22), residues: 526 loop : -0.40 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 470 PHE 0.023 0.001 PHE G 160 TYR 0.014 0.001 TYR F 427 ARG 0.004 0.000 ARG D 333 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 1132) hydrogen bonds : angle 4.70895 ( 3234) covalent geometry : bond 0.00396 (24651) covalent geometry : angle 0.53903 (33427) *********************** 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 163 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 2.802 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8302 (tpt) cc_final: 0.8098 (tpp) REVERT: B 245 MET cc_start: 0.8721 (ttm) cc_final: 0.8303 (mtt) REVERT: B 395 PHE cc_start: 0.6614 (t80) cc_final: 0.6178 (t80) REVERT: B 466 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7215 (mm-40) REVERT: C 60 MET cc_start: 0.9341 (mmp) cc_final: 0.9012 (mmt) REVERT: E 131 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: F 5 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8180 (mtp-110) REVERT: G 113 TYR cc_start: 0.5970 (p90) cc_final: 0.5336 (p90) outliers start: 35 outliers final: 28 residues processed: 155 average time/residue: 0.3241 time to fit residues: 86.0469 Evaluate side-chains 156 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 3.007 ------------------------------------------------------------------------------- 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 A residue 450 VAL 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 193 SER Chi-restraints excluded: chain C residue 314 THR 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 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 383 ILE Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 174 HIS Chi-restraints excluded: chain G residue 241 MET Chi-restraints excluded: chain G residue 257 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 136 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 280 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 219 optimal weight: 0.6980 chunk 40 optimal weight: 0.0970 chunk 71 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3327 r_free = 0.3327 target = 0.083191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.067638 restraints weight = 61907.105| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.40 r_work: 0.2912 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24651 Z= 0.089 Angle : 0.473 7.969 33427 Z= 0.246 Chirality : 0.043 0.152 3852 Planarity : 0.004 0.062 4362 Dihedral : 6.925 88.977 3546 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 1.01 % Allowed : 10.12 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3115 helix: 1.68 (0.15), residues: 1248 sheet: 0.93 (0.23), residues: 523 loop : -0.24 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 401 PHE 0.017 0.001 PHE C 494 TYR 0.014 0.001 TYR A 461 ARG 0.003 0.000 ARG C 383 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 1132) hydrogen bonds : angle 4.43121 ( 3234) covalent geometry : bond 0.00188 (24651) covalent geometry : angle 0.47316 (33427) *********************** 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 185 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 2.932 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8173 (tpt) cc_final: 0.7953 (tpp) REVERT: B 172 GLN cc_start: 0.7357 (mm-40) cc_final: 0.7148 (mm-40) REVERT: B 245 MET cc_start: 0.8471 (ttm) cc_final: 0.8088 (mtt) REVERT: B 395 PHE cc_start: 0.6561 (t80) cc_final: 0.6087 (t80) REVERT: B 466 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7191 (mm-40) REVERT: C 476 ARG cc_start: 0.8524 (ttp-110) cc_final: 0.8245 (mtm-85) REVERT: D 87 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8623 (m) REVERT: E 131 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: F 5 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8207 (mtp-110) REVERT: G 113 TYR cc_start: 0.6042 (p90) cc_final: 0.5430 (p90) outliers start: 26 outliers final: 16 residues processed: 177 average time/residue: 0.3452 time to fit residues: 101.6706 Evaluate side-chains 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL 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 C residue 314 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 221 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.078685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.062884 restraints weight = 64052.908| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.63 r_work: 0.2793 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1472 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= 0.201 Angle : 0.569 8.518 33427 Z= 0.296 Chirality : 0.046 0.305 3852 Planarity : 0.005 0.054 4362 Dihedral : 7.097 93.306 3546 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 1.40 % Allowed : 10.94 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3115 helix: 1.51 (0.15), residues: 1239 sheet: 0.80 (0.23), residues: 510 loop : -0.37 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 470 PHE 0.016 0.001 PHE B 494 TYR 0.031 0.002 TYR B 389 ARG 0.005 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1132) hydrogen bonds : angle 4.62853 ( 3234) covalent geometry : bond 0.00481 (24651) covalent geometry : angle 0.56874 (33427) *********************** 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 172 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 2.961 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8468 (tpt) cc_final: 0.8226 (tpp) REVERT: B 245 MET cc_start: 0.8785 (ttm) cc_final: 0.8371 (mtt) REVERT: B 395 PHE cc_start: 0.6550 (t80) cc_final: 0.6146 (t80) REVERT: B 466 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7192 (mm-40) REVERT: C 88 VAL cc_start: 0.9301 (OUTLIER) cc_final: 0.9066 (p) REVERT: C 476 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8422 (mtm-85) REVERT: D 87 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8681 (m) REVERT: E 131 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: F 5 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8166 (mtp-110) REVERT: G 113 TYR cc_start: 0.5967 (p90) cc_final: 0.5356 (p90) REVERT: G 189 LEU cc_start: 0.7010 (mm) cc_final: 0.6673 (mt) outliers start: 36 outliers final: 26 residues processed: 164 average time/residue: 0.3772 time to fit residues: 104.1548 Evaluate side-chains 164 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE 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 A residue 450 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 314 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 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 280 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 293 THR 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 174 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 9 optimal weight: 3.9990 chunk 243 optimal weight: 0.7980 chunk 208 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 269 optimal weight: 0.3980 chunk 144 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3263 r_free = 0.3263 target = 0.080179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.064210 restraints weight = 63276.274| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.61 r_work: 0.2828 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24651 Z= 0.126 Angle : 0.507 8.778 33427 Z= 0.264 Chirality : 0.044 0.305 3852 Planarity : 0.004 0.069 4362 Dihedral : 6.965 91.163 3546 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.36 % Allowed : 11.10 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3115 helix: 1.58 (0.15), residues: 1247 sheet: 0.75 (0.23), residues: 523 loop : -0.30 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 470 PHE 0.014 0.001 PHE G 160 TYR 0.022 0.001 TYR B 389 ARG 0.003 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 1132) hydrogen bonds : angle 4.50491 ( 3234) covalent geometry : bond 0.00295 (24651) covalent geometry : angle 0.50721 (33427) *********************** 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 170 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 2.562 Fit side-chains revert: symmetry clash REVERT: B 172 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7330 (mm-40) REVERT: B 191 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7585 (mtp) REVERT: B 245 MET cc_start: 0.8616 (ttm) cc_final: 0.8234 (mtt) REVERT: B 395 PHE cc_start: 0.6541 (t80) cc_final: 0.6137 (t80) REVERT: B 466 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7194 (mm-40) REVERT: C 88 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9158 (p) REVERT: C 476 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8384 (mtm-85) REVERT: D 87 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8725 (m) REVERT: E 131 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: F 5 ARG cc_start: 0.8768 (ttm-80) cc_final: 0.8230 (mtp-110) REVERT: G 113 TYR cc_start: 0.6101 (p90) cc_final: 0.5478 (p90) REVERT: G 189 LEU cc_start: 0.6856 (mm) cc_final: 0.6551 (mt) outliers start: 35 outliers final: 27 residues processed: 166 average time/residue: 0.3190 time to fit residues: 88.9185 Evaluate side-chains 164 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE 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 A residue 450 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 314 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 D residue 390 ASP 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 171 LEU Chi-restraints excluded: chain E residue 183 SER 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 293 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 90 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 300 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.079808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.064321 restraints weight = 63468.613| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.42 r_work: 0.2834 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24651 Z= 0.148 Angle : 0.522 8.858 33427 Z= 0.271 Chirality : 0.045 0.308 3852 Planarity : 0.004 0.071 4362 Dihedral : 6.937 91.972 3546 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 1.48 % Allowed : 11.29 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 3115 helix: 1.56 (0.15), residues: 1245 sheet: 0.74 (0.23), residues: 511 loop : -0.32 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 470 PHE 0.015 0.001 PHE C 494 TYR 0.021 0.001 TYR B 389 ARG 0.003 0.000 ARG D 333 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 1132) hydrogen bonds : angle 4.52111 ( 3234) covalent geometry : bond 0.00354 (24651) covalent geometry : angle 0.52156 (33427) *********************** 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 172 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 2.827 Fit side-chains revert: symmetry clash REVERT: B 172 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7294 (mm-40) REVERT: B 191 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7734 (mtp) REVERT: B 245 MET cc_start: 0.8743 (ttm) cc_final: 0.8368 (mtt) REVERT: B 395 PHE cc_start: 0.6456 (t80) cc_final: 0.5957 (t80) REVERT: B 466 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7251 (mm-40) REVERT: C 88 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9200 (p) REVERT: C 476 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.8514 (mtm-85) REVERT: D 87 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8726 (m) REVERT: E 131 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: F 5 ARG cc_start: 0.8939 (ttm-80) cc_final: 0.8402 (mtp-110) REVERT: F 469 MET cc_start: 0.6806 (mtm) cc_final: 0.6590 (mtp) REVERT: G 113 TYR cc_start: 0.6179 (p90) cc_final: 0.5544 (p90) REVERT: G 189 LEU cc_start: 0.6882 (mm) cc_final: 0.6552 (mt) outliers start: 38 outliers final: 32 residues processed: 165 average time/residue: 0.3240 time to fit residues: 90.0434 Evaluate side-chains 169 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 ASN 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 A residue 450 VAL 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 B residue 451 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 314 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 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 171 LEU Chi-restraints excluded: chain E residue 183 SER 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 168 ILE Chi-restraints excluded: chain F residue 293 THR 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 174 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 250 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 278 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.079870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.064003 restraints weight = 63493.751| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.60 r_work: 0.2822 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24651 Z= 0.147 Angle : 0.521 9.521 33427 Z= 0.271 Chirality : 0.045 0.300 3852 Planarity : 0.004 0.075 4362 Dihedral : 6.908 92.436 3546 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 1.36 % Allowed : 11.49 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 3115 helix: 1.56 (0.15), residues: 1246 sheet: 0.74 (0.23), residues: 511 loop : -0.32 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 470 PHE 0.014 0.001 PHE C 494 TYR 0.019 0.001 TYR B 389 ARG 0.003 0.000 ARG D 333 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 1132) hydrogen bonds : angle 4.51593 ( 3234) covalent geometry : bond 0.00350 (24651) covalent geometry : angle 0.52108 (33427) ********************** 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 169 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 2.835 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8409 (tpt) cc_final: 0.7940 (tpt) REVERT: B 172 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7267 (mm-40) REVERT: B 191 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7617 (mtp) REVERT: B 245 MET cc_start: 0.8650 (ttm) cc_final: 0.8263 (mtt) REVERT: B 395 PHE cc_start: 0.6410 (t80) cc_final: 0.5962 (t80) REVERT: B 466 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7210 (mm-40) REVERT: C 88 VAL cc_start: 0.9371 (OUTLIER) cc_final: 0.9154 (p) REVERT: C 476 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8424 (mtm-85) REVERT: D 87 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8682 (m) REVERT: E 131 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: F 5 ARG cc_start: 0.8768 (ttm-80) cc_final: 0.8234 (mtp-110) REVERT: G 113 TYR cc_start: 0.6098 (p90) cc_final: 0.5480 (p90) REVERT: G 189 LEU cc_start: 0.6854 (mm) cc_final: 0.6526 (mt) outliers start: 35 outliers final: 31 residues processed: 164 average time/residue: 0.3226 time to fit residues: 88.7635 Evaluate side-chains 168 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 ASN 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 A residue 450 VAL 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 B residue 451 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 314 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 D residue 390 ASP 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 171 LEU Chi-restraints excluded: chain E residue 183 SER 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 168 ILE Chi-restraints excluded: chain F residue 293 THR 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 174 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 66 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 199 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 132 optimal weight: 0.1980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.080750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.065314 restraints weight = 62926.375| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.42 r_work: 0.2855 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24651 Z= 0.113 Angle : 0.494 9.877 33427 Z= 0.256 Chirality : 0.044 0.297 3852 Planarity : 0.004 0.075 4362 Dihedral : 6.754 87.442 3546 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 11.49 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3115 helix: 1.67 (0.15), residues: 1246 sheet: 0.81 (0.23), residues: 513 loop : -0.22 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 470 PHE 0.015 0.001 PHE C 494 TYR 0.020 0.001 TYR B 389 ARG 0.002 0.000 ARG E 405 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 1132) hydrogen bonds : angle 4.43283 ( 3234) covalent geometry : bond 0.00264 (24651) covalent geometry : angle 0.49387 (33427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11899.07 seconds wall clock time: 212 minutes 2.59 seconds (12722.59 seconds total)