Starting phenix.real_space_refine on Sun Jul 5 04:03:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xkr_33265/07_2026/7xkr_33265.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkr_33265/07_2026/7xkr_33265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xkr_33265/07_2026/7xkr_33265.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xkr_33265/07_2026/7xkr_33265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xkr_33265/07_2026/7xkr_33265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkr_33265/07_2026/7xkr_33265.map" model { file = "/net/cci-nas-00/data/ceres_data/7xkr_33265/07_2026/7xkr_33265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkr_33265/07_2026/7xkr_33265.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 79 5.16 5 C 15900 2.51 5 N 4397 2.21 5 O 4849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25246 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" 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: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 987 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.19, per 1000 atoms: 0.21 Number of scatterers: 25246 At special positions: 0 Unit cell: (130.24, 123.2, 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 79 16.00 P 16 15.00 Mg 5 11.99 O 4849 8.00 N 4397 7.00 C 15900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.3 seconds 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 23 sheets defined 48.3% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.528A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.867A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 186 through 189 removed outlier: 3.515A pdb=" N GLN A 189 " --> pdb=" O GLN A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.545A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.597A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.621A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.979A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.504A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 393 removed outlier: 4.177A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 removed outlier: 4.855A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 398 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.639A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.556A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.503A pdb=" N LEU A 487 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.728A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.580A 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 215 Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.743A pdb=" N ASP B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.619A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.665A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.896A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) 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: 3.609A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.705A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 4.013A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.530A pdb=" N LYS B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 465 Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.688A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.502A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.634A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.535A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.864A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.623A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.861A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.723A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.723A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.578A pdb=" N GLY C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 394 removed outlier: 3.783A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.705A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.631A 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 468 removed outlier: 3.532A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.512A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 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 244 removed outlier: 3.653A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN D 243 " --> pdb=" O PHE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.935A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.686A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.514A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 379 Processing helix chain 'D' and resid 380 through 387 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.633A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 442 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.679A pdb=" N PHE D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.727A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 244 removed outlier: 3.589A pdb=" N ARG E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.763A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.785A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.754A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.680A pdb=" N ARG E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.872A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.519A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 227 through 243 removed outlier: 3.599A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 243 " --> pdb=" O PHE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.899A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 322 through 325 Processing helix chain 'F' and resid 332 through 338 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 393 through 410 removed outlier: 3.631A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.586A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 removed outlier: 3.636A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 41 Processing helix chain 'G' and resid 42 through 58 Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.968A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.561A pdb=" N ARG G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 162 removed outlier: 4.362A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 284 removed outlier: 4.605A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.693A pdb=" N LEU G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 130 removed outlier: 3.656A pdb=" N ARG H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.939A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.210A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.413A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.242A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.851A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.766A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.401A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.143A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.247A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.542A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.204A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS D 153 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR D 329 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY D 155 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.614A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.363A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.465A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.744A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.288A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 137 removed outlier: 8.009A pdb=" N ILE G 134 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.365A pdb=" N GLU G 204 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 41 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS H 5 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE H 77 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER H 7 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL H 6 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU H 17 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL H 8 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AC5, first strand: chain 'H' and resid 48 through 49 removed outlier: 3.718A pdb=" N SER H 48 " --> pdb=" O VAL H 63 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3444 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8576 1.34 - 1.46: 5068 1.46 - 1.58: 11842 1.58 - 1.70: 22 1.70 - 1.82: 158 Bond restraints: 25666 Sorted by residual: bond pdb=" CA LEU A 402 " pdb=" CB LEU A 402 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.35e-02 5.49e+03 2.44e+00 bond pdb=" CG PRO F 342 " pdb=" CD PRO F 342 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.63e+00 bond pdb=" N PRO G 132 " pdb=" CA PRO G 132 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" C4 ADP F 602 " pdb=" C5 ADP F 602 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" N ILE F 292 " pdb=" CA ILE F 292 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.02e+00 ... (remaining 25661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 34199 1.64 - 3.29: 504 3.29 - 4.93: 75 4.93 - 6.58: 19 6.58 - 8.22: 3 Bond angle restraints: 34800 Sorted by residual: angle pdb=" N VAL C 366 " pdb=" CA VAL C 366 " pdb=" C VAL C 366 " ideal model delta sigma weight residual 111.77 107.35 4.42 1.04e+00 9.25e-01 1.81e+01 angle pdb=" N ASP A 401 " pdb=" CA ASP A 401 " pdb=" C ASP A 401 " ideal model delta sigma weight residual 112.13 106.95 5.18 1.37e+00 5.33e-01 1.43e+01 angle pdb=" N VAL E 275 " pdb=" CA VAL E 275 " pdb=" C VAL E 275 " ideal model delta sigma weight residual 111.91 108.66 3.25 8.90e-01 1.26e+00 1.34e+01 angle pdb=" CA ARG C 164 " pdb=" CB ARG C 164 " pdb=" CG ARG C 164 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C TYR A 329 " pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta sigma weight residual 120.33 122.96 -2.63 8.00e-01 1.56e+00 1.08e+01 ... (remaining 34795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 14870 22.02 - 44.03: 587 44.03 - 66.05: 75 66.05 - 88.07: 37 88.07 - 110.08: 3 Dihedral angle restraints: 15572 sinusoidal: 6278 harmonic: 9294 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 -170.08 110.08 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" O1B ADP F 602 " pdb=" O3A ADP F 602 " pdb=" PB ADP F 602 " pdb=" PA ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 -154.72 94.72 1 2.00e+01 2.50e-03 2.60e+01 dihedral pdb=" C5' ADP F 602 " pdb=" O5' ADP F 602 " pdb=" PA ADP F 602 " pdb=" O2A ADP F 602 " ideal model delta sinusoidal sigma weight residual -60.00 -139.62 79.63 1 2.00e+01 2.50e-03 1.97e+01 ... (remaining 15569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2550 0.032 - 0.065: 968 0.065 - 0.097: 290 0.097 - 0.129: 190 0.129 - 0.162: 14 Chirality restraints: 4012 Sorted by residual: chirality pdb=" CA ARG H 71 " pdb=" N ARG H 71 " pdb=" C ARG H 71 " pdb=" CB ARG H 71 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB VAL C 366 " pdb=" CA VAL C 366 " pdb=" CG1 VAL C 366 " pdb=" CG2 VAL C 366 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE E 109 " pdb=" N ILE E 109 " pdb=" C ILE E 109 " pdb=" CB ILE E 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 4009 not shown) Planarity restraints: 4538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 206 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO G 207 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 207 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 207 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.17e+00 pdb=" N PRO C 110 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 315 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO E 316 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.020 5.00e-02 4.00e+02 ... (remaining 4535 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 128 2.59 - 3.16: 20755 3.16 - 3.74: 37872 3.74 - 4.32: 54430 4.32 - 4.90: 92381 Nonbonded interactions: 205566 Sorted by model distance: nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 2.012 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.052 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.064 2.170 nonbonded pdb="MG MG E 501 " pdb=" O2B ATP E 502 " model vdw 2.070 2.170 ... (remaining 205561 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 2 through 470) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 24.690 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 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 0.034 25666 Z= 0.124 Angle : 0.535 8.221 34800 Z= 0.301 Chirality : 0.042 0.162 4012 Planarity : 0.003 0.055 4538 Dihedral : 12.535 110.082 9620 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.15), residues: 3241 helix: 2.20 (0.15), residues: 1272 sheet: 1.23 (0.22), residues: 571 loop : 0.55 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 103 TYR 0.024 0.001 TYR H 16 PHE 0.013 0.001 PHE F 257 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (25666) covalent geometry : angle 0.53519 / 0.30 (34800) hydrogen bonds : bond 0.17186 / 11.93 ( 1209) hydrogen bonds : angle 6.68771 / 4.76 ( 3444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.061 Fit side-chains REVERT: H 108 GLN cc_start: 0.8487 (mm110) cc_final: 0.7977 (mm-40) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.7583 time to fit residues: 142.2602 Evaluate side-chains 127 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 20 ASN F 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.055874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.039374 restraints weight = 65997.192| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 2.73 r_work: 0.2384 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2258 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9325 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 25666 Z= 0.361 Angle : 0.684 8.623 34800 Z= 0.358 Chirality : 0.052 0.187 4012 Planarity : 0.005 0.049 4538 Dihedral : 5.969 103.269 3572 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.60 % Allowed : 5.05 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.15), residues: 3241 helix: 1.61 (0.15), residues: 1296 sheet: 0.78 (0.21), residues: 581 loop : 0.23 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 164 TYR 0.019 0.002 TYR H 16 PHE 0.020 0.002 PHE E 125 HIS 0.009 0.002 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00883 / 0.36 (25666) covalent geometry : angle 0.68442 / 0.36 (34800) hydrogen bonds : bond 0.06566 / 4.39 ( 1209) hydrogen bonds : angle 5.36113 / 3.77 ( 3444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.132 Fit side-chains REVERT: B 350 PHE cc_start: 0.8735 (m-10) cc_final: 0.8510 (m-10) REVERT: H 84 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7873 (mtt-85) REVERT: H 108 GLN cc_start: 0.8499 (mm110) cc_final: 0.8051 (mm110) REVERT: H 112 ASP cc_start: 0.8995 (m-30) cc_final: 0.8726 (m-30) outliers start: 16 outliers final: 7 residues processed: 133 average time/residue: 0.7064 time to fit residues: 108.0700 Evaluate side-chains 126 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 91 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 273 optimal weight: 0.4980 chunk 187 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.042695 restraints weight = 65207.645| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 2.73 r_work: 0.2486 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9251 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25666 Z= 0.102 Angle : 0.497 9.920 34800 Z= 0.253 Chirality : 0.043 0.145 4012 Planarity : 0.004 0.049 4538 Dihedral : 5.255 81.214 3572 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.71 % Allowed : 5.84 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.15), residues: 3241 helix: 1.95 (0.15), residues: 1295 sheet: 0.88 (0.21), residues: 583 loop : 0.30 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 103 TYR 0.008 0.001 TYR E 238 PHE 0.013 0.001 PHE E 125 HIS 0.003 0.000 HIS G 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (25666) covalent geometry : angle 0.49678 / 0.25 (34800) hydrogen bonds : bond 0.04140 / 2.75 ( 1209) hydrogen bonds : angle 4.84005 / 3.41 ( 3444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 PHE cc_start: 0.8678 (m-10) cc_final: 0.8469 (m-10) REVERT: C 262 ASP cc_start: 0.7920 (m-30) cc_final: 0.7679 (t0) REVERT: E 10 MET cc_start: 0.8991 (mtp) cc_final: 0.8747 (mtm) REVERT: H 34 ILE cc_start: 0.9357 (mp) cc_final: 0.9021 (pp) REVERT: H 59 GLN cc_start: 0.8790 (tp40) cc_final: 0.8523 (tp-100) REVERT: H 84 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7940 (mmt90) REVERT: H 103 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7493 (mtm-85) REVERT: H 108 GLN cc_start: 0.8523 (mm110) cc_final: 0.8006 (mm110) REVERT: H 112 ASP cc_start: 0.8961 (m-30) cc_final: 0.8655 (m-30) outliers start: 19 outliers final: 7 residues processed: 144 average time/residue: 0.7198 time to fit residues: 118.9513 Evaluate side-chains 131 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 132 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 53 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 270 optimal weight: 0.0370 chunk 192 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.058582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.042151 restraints weight = 64676.575| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 2.72 r_work: 0.2473 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2348 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9262 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25666 Z= 0.121 Angle : 0.503 10.129 34800 Z= 0.256 Chirality : 0.044 0.188 4012 Planarity : 0.004 0.054 4538 Dihedral : 5.038 64.980 3572 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.09 % Allowed : 6.51 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.15), residues: 3241 helix: 2.05 (0.15), residues: 1294 sheet: 0.90 (0.21), residues: 576 loop : 0.30 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 164 TYR 0.010 0.001 TYR H 16 PHE 0.014 0.001 PHE E 125 HIS 0.003 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (25666) covalent geometry : angle 0.50297 / 0.26 (34800) hydrogen bonds : bond 0.04298 / 2.86 ( 1209) hydrogen bonds : angle 4.71930 / 3.33 ( 3444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 PHE cc_start: 0.8650 (m-10) cc_final: 0.8415 (m-10) REVERT: C 262 ASP cc_start: 0.8028 (m-30) cc_final: 0.7794 (t0) REVERT: E 10 MET cc_start: 0.9040 (mtp) cc_final: 0.8783 (mtm) REVERT: H 34 ILE cc_start: 0.9387 (mp) cc_final: 0.9056 (pp) REVERT: H 51 ARG cc_start: 0.7440 (mmt-90) cc_final: 0.7236 (mmp-170) REVERT: H 84 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8071 (mmt90) REVERT: H 108 GLN cc_start: 0.8541 (mm110) cc_final: 0.7968 (mm110) REVERT: H 112 ASP cc_start: 0.8962 (m-30) cc_final: 0.8611 (m-30) outliers start: 29 outliers final: 14 residues processed: 142 average time/residue: 0.7153 time to fit residues: 116.5247 Evaluate side-chains 138 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 295 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 246 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.056047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.039529 restraints weight = 65053.203| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 2.71 r_work: 0.2390 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2264 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9329 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 25666 Z= 0.298 Angle : 0.610 8.845 34800 Z= 0.316 Chirality : 0.049 0.195 4012 Planarity : 0.004 0.061 4538 Dihedral : 5.520 73.976 3572 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.16 % Allowed : 7.23 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.15), residues: 3241 helix: 1.74 (0.15), residues: 1302 sheet: 0.69 (0.21), residues: 565 loop : 0.10 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 103 TYR 0.012 0.001 TYR F 427 PHE 0.019 0.002 PHE F 125 HIS 0.007 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.30 (25666) covalent geometry : angle 0.60968 / 0.32 (34800) hydrogen bonds : bond 0.05933 / 3.96 ( 1209) hydrogen bonds : angle 5.01287 / 3.52 ( 3444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8848 (pt0) cc_final: 0.8320 (pt0) REVERT: B 350 PHE cc_start: 0.8777 (m-10) cc_final: 0.8546 (m-10) REVERT: E 10 MET cc_start: 0.9204 (mtp) cc_final: 0.8941 (mtm) REVERT: H 84 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8129 (mmt90) REVERT: H 108 GLN cc_start: 0.8609 (mm110) cc_final: 0.8029 (mm110) REVERT: H 112 ASP cc_start: 0.9002 (m-30) cc_final: 0.8591 (m-30) outliers start: 31 outliers final: 18 residues processed: 145 average time/residue: 0.7660 time to fit residues: 127.0969 Evaluate side-chains 140 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 91 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 257 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.057877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.041444 restraints weight = 64986.098| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 2.70 r_work: 0.2450 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2325 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25666 Z= 0.128 Angle : 0.512 9.557 34800 Z= 0.262 Chirality : 0.044 0.146 4012 Planarity : 0.004 0.061 4538 Dihedral : 5.191 67.115 3572 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.46 % Allowed : 7.49 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3241 helix: 1.99 (0.15), residues: 1288 sheet: 0.75 (0.22), residues: 570 loop : 0.15 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG D 333 TYR 0.013 0.001 TYR H 16 PHE 0.014 0.001 PHE E 125 HIS 0.003 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (25666) covalent geometry : angle 0.51199 / 0.26 (34800) hydrogen bonds : bond 0.04440 / 2.95 ( 1209) hydrogen bonds : angle 4.76088 / 3.35 ( 3444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8273 (mm-40) REVERT: B 350 PHE cc_start: 0.8731 (m-10) cc_final: 0.8518 (m-10) REVERT: D 59 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8767 (m) REVERT: E 10 MET cc_start: 0.9068 (mtp) cc_final: 0.8817 (mtm) REVERT: E 340 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8981 (pp) REVERT: F 10 MET cc_start: 0.8856 (mtm) cc_final: 0.8558 (mtm) REVERT: H 26 LYS cc_start: 0.7247 (tppt) cc_final: 0.6982 (tppt) REVERT: H 108 GLN cc_start: 0.8602 (mm110) cc_final: 0.8016 (mm110) REVERT: H 112 ASP cc_start: 0.8983 (m-30) cc_final: 0.8607 (m-30) outliers start: 39 outliers final: 19 residues processed: 152 average time/residue: 0.7440 time to fit residues: 130.0722 Evaluate side-chains 145 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 9 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 230 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 284 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 ASN H 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.040628 restraints weight = 65147.842| |-----------------------------------------------------------------------------| r_work (start): 0.2549 rms_B_bonded: 2.70 r_work: 0.2402 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2271 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9301 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25666 Z= 0.185 Angle : 0.542 10.308 34800 Z= 0.278 Chirality : 0.045 0.154 4012 Planarity : 0.004 0.064 4538 Dihedral : 5.226 65.806 3572 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.27 % Allowed : 7.90 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.15), residues: 3241 helix: 1.95 (0.15), residues: 1292 sheet: 0.72 (0.22), residues: 570 loop : 0.11 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 333 TYR 0.018 0.001 TYR H 16 PHE 0.016 0.001 PHE F 257 HIS 0.005 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (25666) covalent geometry : angle 0.54234 / 0.28 (34800) hydrogen bonds : bond 0.04933 / 3.29 ( 1209) hydrogen bonds : angle 4.80358 / 3.38 ( 3444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 350 PHE cc_start: 0.8767 (m-10) cc_final: 0.8558 (m-10) REVERT: E 10 MET cc_start: 0.9173 (mtp) cc_final: 0.8925 (mtm) REVERT: E 340 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9040 (pp) REVERT: F 10 MET cc_start: 0.8893 (mtm) cc_final: 0.8607 (mtm) REVERT: H 26 LYS cc_start: 0.7215 (tppt) cc_final: 0.6952 (tppt) REVERT: H 108 GLN cc_start: 0.8600 (mm110) cc_final: 0.8020 (mm110) REVERT: H 112 ASP cc_start: 0.9002 (m-30) cc_final: 0.8625 (m-30) outliers start: 34 outliers final: 20 residues processed: 152 average time/residue: 0.7381 time to fit residues: 128.9622 Evaluate side-chains 144 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 188 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN E 381 GLN F 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.039841 restraints weight = 65401.374| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 2.69 r_work: 0.2405 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2281 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9312 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25666 Z= 0.239 Angle : 0.581 10.837 34800 Z= 0.299 Chirality : 0.047 0.172 4012 Planarity : 0.004 0.068 4538 Dihedral : 5.410 71.286 3572 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 7.97 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.15), residues: 3241 helix: 1.84 (0.15), residues: 1297 sheet: 0.64 (0.21), residues: 570 loop : 0.04 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 333 TYR 0.018 0.001 TYR H 16 PHE 0.017 0.002 PHE F 257 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.24 (25666) covalent geometry : angle 0.58118 / 0.30 (34800) hydrogen bonds : bond 0.05453 / 3.64 ( 1209) hydrogen bonds : angle 4.91405 / 3.46 ( 3444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: B 350 PHE cc_start: 0.8749 (m-10) cc_final: 0.8544 (m-10) REVERT: E 10 MET cc_start: 0.9174 (mtp) cc_final: 0.8921 (mtm) REVERT: F 10 MET cc_start: 0.8893 (mtm) cc_final: 0.8602 (mtm) REVERT: H 4 ILE cc_start: 0.6254 (tp) cc_final: 0.5974 (tt) REVERT: H 26 LYS cc_start: 0.7225 (tppt) cc_final: 0.6949 (tppt) REVERT: H 84 ARG cc_start: 0.8080 (mmt90) cc_final: 0.7755 (mmt90) REVERT: H 103 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7595 (mtm-85) outliers start: 33 outliers final: 21 residues processed: 146 average time/residue: 0.7456 time to fit residues: 124.5531 Evaluate side-chains 142 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 212 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 chunk 321 optimal weight: 0.8980 chunk 292 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 316 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.057537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.041094 restraints weight = 64928.421| |-----------------------------------------------------------------------------| r_work (start): 0.2559 rms_B_bonded: 2.71 r_work: 0.2413 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2283 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9288 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25666 Z= 0.139 Angle : 0.531 11.992 34800 Z= 0.269 Chirality : 0.044 0.156 4012 Planarity : 0.004 0.070 4538 Dihedral : 5.199 67.505 3572 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.97 % Allowed : 8.39 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.15), residues: 3241 helix: 1.97 (0.15), residues: 1294 sheet: 0.68 (0.22), residues: 570 loop : 0.09 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 333 TYR 0.015 0.001 TYR H 16 PHE 0.015 0.001 PHE E 125 HIS 0.004 0.001 HIS E 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (25666) covalent geometry : angle 0.53080 / 0.27 (34800) hydrogen bonds : bond 0.04558 / 3.03 ( 1209) hydrogen bonds : angle 4.76606 / 3.36 ( 3444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: B 350 PHE cc_start: 0.8759 (m-10) cc_final: 0.8552 (m-10) REVERT: D 59 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8792 (m) REVERT: E 10 MET cc_start: 0.9106 (mtp) cc_final: 0.8862 (mtm) REVERT: F 10 MET cc_start: 0.8870 (mtm) cc_final: 0.8594 (mtm) REVERT: H 4 ILE cc_start: 0.6207 (tp) cc_final: 0.5941 (tt) REVERT: H 26 LYS cc_start: 0.7212 (tppt) cc_final: 0.6959 (tppt) REVERT: H 84 ARG cc_start: 0.8416 (mmt90) cc_final: 0.7756 (mmt90) REVERT: H 108 GLN cc_start: 0.8658 (mm110) cc_final: 0.8078 (mm-40) REVERT: H 112 ASP cc_start: 0.8981 (m-30) cc_final: 0.8612 (m-30) outliers start: 26 outliers final: 20 residues processed: 144 average time/residue: 0.6979 time to fit residues: 115.1936 Evaluate side-chains 141 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 22 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.058038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.041626 restraints weight = 64929.134| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 2.71 r_work: 0.2452 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2326 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9280 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25666 Z= 0.126 Angle : 0.514 11.867 34800 Z= 0.261 Chirality : 0.044 0.155 4012 Planarity : 0.004 0.071 4538 Dihedral : 5.050 64.366 3572 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.82 % Allowed : 8.65 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.15), residues: 3241 helix: 2.04 (0.15), residues: 1298 sheet: 0.76 (0.22), residues: 556 loop : 0.14 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 333 TYR 0.015 0.001 TYR H 16 PHE 0.015 0.001 PHE E 125 HIS 0.005 0.001 HIS H 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (25666) covalent geometry : angle 0.51386 / 0.26 (34800) hydrogen bonds : bond 0.04311 / 2.86 ( 1209) hydrogen bonds : angle 4.69151 / 3.31 ( 3444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: B 350 PHE cc_start: 0.8737 (m-10) cc_final: 0.8529 (m-10) REVERT: D 59 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8786 (m) REVERT: E 10 MET cc_start: 0.9084 (mtp) cc_final: 0.8839 (mtm) REVERT: F 10 MET cc_start: 0.8857 (mtm) cc_final: 0.8568 (mtm) REVERT: H 26 LYS cc_start: 0.7247 (tppt) cc_final: 0.7021 (tppt) REVERT: H 84 ARG cc_start: 0.8568 (mmt90) cc_final: 0.8224 (mmt90) REVERT: H 108 GLN cc_start: 0.8658 (mm110) cc_final: 0.8058 (mm-40) REVERT: H 112 ASP cc_start: 0.8972 (m-30) cc_final: 0.8608 (m-30) outliers start: 22 outliers final: 19 residues processed: 138 average time/residue: 0.7187 time to fit residues: 114.0895 Evaluate side-chains 138 residues out of total 2671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 287 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 273 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.039806 restraints weight = 65406.462| |-----------------------------------------------------------------------------| r_work (start): 0.2536 rms_B_bonded: 2.69 r_work: 0.2391 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2264 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9319 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25666 Z= 0.241 Angle : 0.585 12.498 34800 Z= 0.300 Chirality : 0.047 0.172 4012 Planarity : 0.004 0.071 4538 Dihedral : 5.358 67.532 3572 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.01 % Allowed : 8.42 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.15), residues: 3241 helix: 1.89 (0.15), residues: 1292 sheet: 0.59 (0.21), residues: 575 loop : 0.02 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 333 TYR 0.015 0.001 TYR H 16 PHE 0.018 0.002 PHE F 257 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.24 (25666) covalent geometry : angle 0.58481 / 0.30 (34800) hydrogen bonds : bond 0.05457 / 3.64 ( 1209) hydrogen bonds : angle 4.89669 / 3.44 ( 3444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7575.84 seconds wall clock time: 130 minutes 3.39 seconds (7803.39 seconds total)