Starting phenix.real_space_refine on Fri Mar 6 02:47:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6voi_21265/03_2026/6voi_21265.cif Found real_map, /net/cci-nas-00/data/ceres_data/6voi_21265/03_2026/6voi_21265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6voi_21265/03_2026/6voi_21265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6voi_21265/03_2026/6voi_21265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6voi_21265/03_2026/6voi_21265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6voi_21265/03_2026/6voi_21265.map" } resolution = 4.03 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= 0.003 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 105 5.16 5 C 17265 2.51 5 N 4745 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 175 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27497 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3854 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 17, 'TRANS': 484} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2508 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain: "e" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.16, per 1000 atoms: 0.22 Number of scatterers: 27497 At special positions: 0 Unit cell: (131.04, 145.6, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 14 15.00 O 5368 8.00 N 4745 7.00 C 17265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.05 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6572 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 32 sheets defined 46.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.766A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 4.026A pdb=" N GLN A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.539A pdb=" N GLN A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 3.821A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.540A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.655A pdb=" N LEU A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.586A pdb=" N THR A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.503A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.786A pdb=" N ALA A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 371 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 398 removed outlier: 3.859A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 removed outlier: 3.916A pdb=" N ALA A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 4.220A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 4.561A pdb=" N LEU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 4.465A pdb=" N TYR A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.793A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 505 removed outlier: 3.881A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.623A pdb=" N ILE C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.733A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.891A pdb=" N TYR C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR C 222 " --> pdb=" O MET C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 222' Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.506A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.978A pdb=" N ALA C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 393 removed outlier: 4.386A pdb=" N GLY C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 422 removed outlier: 3.732A pdb=" N GLU C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 443 removed outlier: 4.200A pdb=" N MET C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 483 through 503 Processing helix chain 'B' and resid 9 through 19 removed outlier: 4.344A pdb=" N GLY B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.938A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.591A pdb=" N ALA B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.600A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.622A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 396 removed outlier: 4.536A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.840A pdb=" N GLY B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 453 through 469 removed outlier: 4.299A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 removed outlier: 4.242A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 179 through 189 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 227 through 231 removed outlier: 4.310A pdb=" N LYS D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 264 removed outlier: 3.875A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 289 removed outlier: 3.587A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 311 Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.891A pdb=" N ASP D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP D 333 " --> pdb=" O PRO D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 333' Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.164A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 359 removed outlier: 4.155A pdb=" N ALA D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 401 removed outlier: 3.523A pdb=" N VAL D 380 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU D 382 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N GLU D 383 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N HIS D 384 " --> pdb=" O VAL D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 409 through 413 removed outlier: 3.547A pdb=" N LEU D 413 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 450 through 463 removed outlier: 4.186A pdb=" N ARG D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 475 removed outlier: 4.130A pdb=" N PHE D 474 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D 475 " --> pdb=" O GLU D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 470 through 475' Processing helix chain 'D' and resid 479 through 494 Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 177 through 192 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 242 through 265 removed outlier: 3.520A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 290 removed outlier: 3.960A pdb=" N PHE E 278 " --> pdb=" O ASN E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.703A pdb=" N ASP E 332 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 333' Processing helix chain 'E' and resid 336 through 344 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 381 through 402 Processing helix chain 'E' and resid 408 through 413 removed outlier: 4.118A pdb=" N GLU E 412 " --> pdb=" O LEU E 408 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 413 " --> pdb=" O GLY E 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 408 through 413' Processing helix chain 'E' and resid 417 through 431 Processing helix chain 'E' and resid 450 through 464 removed outlier: 3.771A pdb=" N GLY E 464 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 474 Processing helix chain 'E' and resid 479 through 495 removed outlier: 4.246A pdb=" N LYS E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 179 through 193 removed outlier: 4.988A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 226 through 230 removed outlier: 3.784A pdb=" N SER F 230 " --> pdb=" O ILE F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 247 removed outlier: 3.540A pdb=" N ARG F 246 " --> pdb=" O PRO F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 Processing helix chain 'F' and resid 276 through 290 removed outlier: 4.065A pdb=" N GLY F 282 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY F 290 " --> pdb=" O SER F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 329 through 333 Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 341 through 346 removed outlier: 4.025A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 4.116A pdb=" N LYS F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 409 removed outlier: 4.750A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 413 removed outlier: 4.070A pdb=" N LEU F 413 " --> pdb=" O LEU F 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 410 through 413' Processing helix chain 'F' and resid 416 through 431 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 450 through 463 removed outlier: 3.565A pdb=" N LEU F 460 " --> pdb=" O ARG F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 475 Processing helix chain 'F' and resid 479 through 496 removed outlier: 3.776A pdb=" N LYS F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 89 Processing helix chain 'd' and resid 91 through 107 Processing helix chain 'd' and resid 108 through 116 removed outlier: 4.211A pdb=" N TYR d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 4.033A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 Processing helix chain 'd' and resid 236 through 249 removed outlier: 4.279A pdb=" N GLN d 240 " --> pdb=" O SER d 236 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU d 249 " --> pdb=" O ALA d 245 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 100 Proline residue: g 84 - end of helix removed outlier: 3.691A pdb=" N TYR g 94 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 111 removed outlier: 3.953A pdb=" N LYS g 111 " --> pdb=" O PRO g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 151 removed outlier: 4.042A pdb=" N MET g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 169 Processing helix chain 'g' and resid 187 through 204 removed outlier: 3.693A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 362 removed outlier: 3.715A pdb=" N ILE g 291 " --> pdb=" O ASP g 287 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix removed outlier: 3.736A pdb=" N SER g 311 " --> pdb=" O ALA g 307 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN g 361 " --> pdb=" O VAL g 357 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA g 362 " --> pdb=" O ALA g 358 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 104 removed outlier: 4.032A pdb=" N ARG e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 131 removed outlier: 3.909A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER e 129 " --> pdb=" O ARG e 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR e 131 " --> pdb=" O GLU e 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 5.958A pdb=" N VAL A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N HIS A 43 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASN A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU A 67 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 7.380A pdb=" N LEU A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.415A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 35 removed outlier: 6.655A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.084A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 319 through 321 removed outlier: 3.547A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 193 through 196 removed outlier: 6.231A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 198 through 199 removed outlier: 6.519A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 62 through 67 removed outlier: 4.239A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 31 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU B 67 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 65 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE D 92 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA D 46 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN D 45 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE D 23 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 97 through 98 removed outlier: 4.053A pdb=" N ARG B 128 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 109 removed outlier: 5.759A pdb=" N ILE B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR B 228 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA B 198 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP B 262 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 197 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 315 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 341 through 342 Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB6, first strand: chain 'E' and resid 25 through 27 removed outlier: 6.660A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 99 through 100 Processing sheet with id=AB8, first strand: chain 'E' and resid 148 through 149 removed outlier: 4.383A pdb=" N TYR E 162 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'E' and resid 197 through 200 Processing sheet with id=AC2, first strand: chain 'E' and resid 202 through 204 removed outlier: 6.640A pdb=" N GLY E 237 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 23 through 27 removed outlier: 5.928A pdb=" N ILE F 23 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AC5, first strand: chain 'F' and resid 148 through 149 removed outlier: 4.324A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 269 through 273 removed outlier: 7.144A pdb=" N LEU F 270 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ALA F 326 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE F 272 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS F 167 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR F 350 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY F 169 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU F 352 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE F 171 " --> pdb=" O LEU F 352 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 200 through 202 Processing sheet with id=AC8, first strand: chain 'd' and resid 177 through 178 Processing sheet with id=AC9, first strand: chain 'd' and resid 212 through 213 removed outlier: 6.572A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 156 through 159 removed outlier: 3.581A pdb=" N ILE g 158 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL g 226 " --> pdb=" O TYR g 214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'g' and resid 254 through 259 removed outlier: 3.555A pdb=" N THR g 265 " --> pdb=" O THR g 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'e' and resid 12 through 19 removed outlier: 7.104A pdb=" N VAL e 7 " --> pdb=" O ILE e 14 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN e 16 " --> pdb=" O LEU e 5 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU e 5 " --> pdb=" O ASN e 16 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU e 18 " --> pdb=" O LEU e 3 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU e 3 " --> pdb=" O GLU e 18 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE e 74 " --> pdb=" O ASN e 4 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'e' and resid 21 through 23 removed outlier: 3.565A pdb=" N GLU e 21 " --> pdb=" O ARG e 52 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG e 50 " --> pdb=" O ILE e 23 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'e' and resid 47 through 48 removed outlier: 3.909A pdb=" N GLY e 47 " --> pdb=" O LEU e 62 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU e 62 " --> pdb=" O GLY e 47 " (cutoff:3.500A) 1206 hydrogen bonds defined for protein. 3486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.97 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9313 1.34 - 1.46: 5491 1.46 - 1.58: 12854 1.58 - 1.71: 23 1.71 - 1.83: 198 Bond restraints: 27879 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.04e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.65e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C5 ATP D 601 " pdb=" C6 ATP D 601 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.26e+01 ... (remaining 27874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 37592 4.51 - 9.03: 175 9.03 - 13.54: 6 13.54 - 18.06: 2 18.06 - 22.57: 6 Bond angle restraints: 37781 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.30 22.57 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.15 21.72 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.33 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 121.51 18.36 1.00e+00 1.00e+00 3.37e+02 ... (remaining 37776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.14: 16290 27.14 - 54.29: 805 54.29 - 81.43: 67 81.43 - 108.57: 14 108.57 - 135.71: 3 Dihedral angle restraints: 17179 sinusoidal: 6940 harmonic: 10239 Sorted by residual: dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -130.96 -49.04 0 5.00e+00 4.00e-02 9.62e+01 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual 180.00 -133.84 -46.16 0 5.00e+00 4.00e-02 8.52e+01 dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual 180.00 -139.18 -40.82 0 5.00e+00 4.00e-02 6.67e+01 ... (remaining 17176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3461 0.054 - 0.108: 835 0.108 - 0.161: 130 0.161 - 0.215: 16 0.215 - 0.269: 4 Chirality restraints: 4446 Sorted by residual: chirality pdb=" CB ILE g 239 " pdb=" CA ILE g 239 " pdb=" CG1 ILE g 239 " pdb=" CG2 ILE g 239 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE e 31 " pdb=" CA ILE e 31 " pdb=" CG1 ILE e 31 " pdb=" CG2 ILE e 31 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE e 69 " pdb=" CA ILE e 69 " pdb=" CG1 ILE e 69 " pdb=" CG2 ILE e 69 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4443 not shown) Planarity restraints: 4912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 176 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C LYS B 176 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS B 176 " -0.020 2.00e-02 2.50e+03 pdb=" N THR B 177 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG g 83 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO g 84 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO g 84 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO g 84 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 241 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO D 242 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 242 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 242 " 0.033 5.00e-02 4.00e+02 ... (remaining 4909 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 792 2.69 - 3.25: 29148 3.25 - 3.80: 44571 3.80 - 4.35: 58526 4.35 - 4.90: 96912 Nonbonded interactions: 229949 Sorted by model distance: nonbonded pdb=" O ALA F 295 " pdb=" N GLY F 297 " model vdw 2.142 3.120 nonbonded pdb=" O ILE A 193 " pdb=" OG1 THR A 257 " model vdw 2.153 3.040 nonbonded pdb=" O LEU A 53 " pdb=" OG1 THR A 92 " model vdw 2.159 3.040 nonbonded pdb=" O ALA E 295 " pdb=" N GLY E 297 " model vdw 2.199 3.120 nonbonded pdb=" OG1 THR d 181 " pdb=" OG1 THR d 222 " model vdw 2.203 3.040 ... (remaining 229944 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 6 through 503 or resid 600)) selection = (chain 'B' and resid 6 through 600) selection = (chain 'C' and (resid 6 through 503 or resid 600)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.900 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.005 0.084 27880 Z= 0.284 Angle : 0.946 22.569 37783 Z= 0.602 Chirality : 0.048 0.269 4446 Planarity : 0.005 0.063 4912 Dihedral : 15.346 135.715 10604 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.73 % Favored : 91.96 % Rotamer: Outliers : 0.24 % Allowed : 7.68 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.86 (0.12), residues: 3557 helix: -1.75 (0.11), residues: 1421 sheet: -3.82 (0.18), residues: 451 loop : -2.90 (0.13), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 140 TYR 0.013 0.001 TYR g 94 PHE 0.019 0.002 PHE B 472 TRP 0.006 0.001 TRP e 15 HIS 0.004 0.001 HIS F 345 Details of bonding type rmsd covalent geometry : bond 0.00507 (27879) covalent geometry : angle 0.94588 (37781) SS BOND : bond 0.01407 ( 1) SS BOND : angle 1.90182 ( 2) hydrogen bonds : bond 0.15365 ( 1206) hydrogen bonds : angle 7.24105 ( 3486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 752 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 191 ASN cc_start: 0.7230 (t0) cc_final: 0.6834 (t0) REVERT: A 237 TYR cc_start: 0.8916 (t80) cc_final: 0.8713 (t80) REVERT: A 389 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8405 (tm-30) REVERT: C 14 ARG cc_start: 0.5852 (mmm160) cc_final: 0.5234 (mpt-90) REVERT: C 237 TYR cc_start: 0.8766 (t80) cc_final: 0.8528 (t80) REVERT: C 251 MET cc_start: 0.7923 (ttp) cc_final: 0.7510 (ttp) REVERT: C 300 GLU cc_start: 0.8592 (tt0) cc_final: 0.8382 (tp30) REVERT: C 314 MET cc_start: 0.8597 (ttp) cc_final: 0.8374 (ttt) REVERT: C 348 ASP cc_start: 0.7481 (m-30) cc_final: 0.6956 (m-30) REVERT: C 449 LEU cc_start: 0.7993 (mt) cc_final: 0.7690 (tp) REVERT: B 110 ASN cc_start: 0.8522 (t0) cc_final: 0.8224 (t0) REVERT: B 157 MET cc_start: 0.7650 (mpp) cc_final: 0.7324 (mpp) REVERT: B 164 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 422 LYS cc_start: 0.7437 (pttp) cc_final: 0.7058 (ptmt) REVERT: B 489 LEU cc_start: 0.6955 (pp) cc_final: 0.6638 (pp) REVERT: B 495 GLN cc_start: 0.5786 (mm110) cc_final: 0.5583 (tm-30) REVERT: D 79 MET cc_start: 0.8966 (mmp) cc_final: 0.8256 (mmm) REVERT: D 121 LEU cc_start: 0.8598 (pp) cc_final: 0.7917 (pt) REVERT: D 178 LYS cc_start: 0.7819 (ttpp) cc_final: 0.7618 (ttpp) REVERT: D 256 MET cc_start: 0.8153 (ttm) cc_final: 0.7709 (mtt) REVERT: D 283 SER cc_start: 0.8492 (t) cc_final: 0.8091 (p) REVERT: E 20 LEU cc_start: 0.7291 (mt) cc_final: 0.6940 (tt) REVERT: E 39 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7786 (mmmm) REVERT: E 64 GLU cc_start: 0.8248 (pp20) cc_final: 0.7816 (pp20) REVERT: E 89 MET cc_start: 0.8639 (mtt) cc_final: 0.8164 (mtp) REVERT: E 155 VAL cc_start: 0.9199 (t) cc_final: 0.8996 (t) REVERT: E 191 LYS cc_start: 0.8361 (tptm) cc_final: 0.8122 (ttpt) REVERT: E 206 THR cc_start: 0.8679 (m) cc_final: 0.7904 (m) REVERT: E 214 MET cc_start: 0.7840 (mmt) cc_final: 0.7278 (tpp) REVERT: E 218 GLU cc_start: 0.6611 (pt0) cc_final: 0.6285 (pt0) REVERT: E 238 GLN cc_start: 0.7035 (mt0) cc_final: 0.6536 (mp10) REVERT: E 306 MET cc_start: 0.8478 (tmm) cc_final: 0.7235 (tmm) REVERT: E 310 GLN cc_start: 0.8005 (mt0) cc_final: 0.7620 (mt0) REVERT: E 313 ILE cc_start: 0.8542 (mm) cc_final: 0.8221 (mt) REVERT: F 63 CYS cc_start: 0.8227 (m) cc_final: 0.7905 (m) REVERT: F 184 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6679 (tm-30) REVERT: F 386 GLU cc_start: 0.7870 (tp30) cc_final: 0.7650 (tp30) REVERT: F 399 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7934 (ttmm) REVERT: d 72 ASP cc_start: 0.6324 (m-30) cc_final: 0.6064 (m-30) REVERT: d 92 LEU cc_start: 0.5172 (tp) cc_final: 0.4858 (pt) REVERT: d 169 PHE cc_start: 0.7366 (t80) cc_final: 0.7087 (t80) REVERT: d 171 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8340 (ttmm) REVERT: d 208 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7717 (ttp-110) REVERT: d 239 LYS cc_start: 0.5689 (mttt) cc_final: 0.4945 (ttpt) REVERT: g 100 LEU cc_start: 0.7092 (pp) cc_final: 0.6828 (pp) REVERT: g 136 MET cc_start: 0.8050 (tpt) cc_final: 0.7603 (ttp) REVERT: g 139 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6494 (mptt) REVERT: g 144 ARG cc_start: 0.6377 (mmm160) cc_final: 0.5665 (tpp80) REVERT: g 263 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7198 (ttmt) REVERT: e 20 LYS cc_start: 0.6083 (tptp) cc_final: 0.5697 (ttpt) REVERT: e 37 HIS cc_start: 0.7308 (t-90) cc_final: 0.6910 (t-90) REVERT: e 63 MET cc_start: 0.4653 (mmm) cc_final: 0.4279 (mmp) REVERT: e 91 GLU cc_start: 0.6898 (tp30) cc_final: 0.5947 (pm20) outliers start: 7 outliers final: 3 residues processed: 757 average time/residue: 0.1936 time to fit residues: 225.0881 Evaluate side-chains 523 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 520 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 497 GLN A 504 GLN C 186 ASN B 34 GLN B 201 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN d 163 ASN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 331 ASN g 342 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.139497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132682 restraints weight = 37342.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.130216 restraints weight = 61597.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.128582 restraints weight = 59989.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.128446 restraints weight = 62622.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.128943 restraints weight = 43037.751| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27880 Z= 0.178 Angle : 0.726 9.282 37783 Z= 0.373 Chirality : 0.046 0.237 4446 Planarity : 0.005 0.069 4912 Dihedral : 8.770 123.336 4022 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.87 % Favored : 91.88 % Rotamer: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.74 (0.13), residues: 3557 helix: -0.59 (0.13), residues: 1424 sheet: -3.47 (0.20), residues: 448 loop : -2.42 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 140 TYR 0.015 0.002 TYR g 94 PHE 0.031 0.002 PHE B 292 TRP 0.002 0.001 TRP e 15 HIS 0.004 0.001 HIS F 345 Details of bonding type rmsd covalent geometry : bond 0.00413 (27879) covalent geometry : angle 0.72603 (37781) SS BOND : bond 0.02179 ( 1) SS BOND : angle 1.59552 ( 2) hydrogen bonds : bond 0.04604 ( 1206) hydrogen bonds : angle 5.63561 ( 3486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 651 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.6711 (t0) cc_final: 0.6410 (t0) REVERT: A 219 MET cc_start: 0.8584 (tpp) cc_final: 0.8304 (tpp) REVERT: A 447 ASP cc_start: 0.6779 (t0) cc_final: 0.6231 (t0) REVERT: C 348 ASP cc_start: 0.7151 (m-30) cc_final: 0.6778 (m-30) REVERT: C 440 THR cc_start: 0.9259 (m) cc_final: 0.9042 (m) REVERT: B 34 GLN cc_start: 0.8395 (tt0) cc_final: 0.8136 (tt0) REVERT: D 83 ASP cc_start: 0.7587 (m-30) cc_final: 0.7377 (m-30) REVERT: D 178 LYS cc_start: 0.7999 (ttpp) cc_final: 0.7572 (ttpp) REVERT: D 247 MET cc_start: 0.7737 (ttp) cc_final: 0.7438 (ttp) REVERT: E 20 LEU cc_start: 0.6958 (mt) cc_final: 0.6706 (tp) REVERT: E 39 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7783 (mmmm) REVERT: E 89 MET cc_start: 0.8661 (mtt) cc_final: 0.8229 (mtp) REVERT: E 155 VAL cc_start: 0.9094 (t) cc_final: 0.8789 (t) REVERT: E 206 THR cc_start: 0.8593 (m) cc_final: 0.8061 (m) REVERT: E 247 MET cc_start: 0.7707 (ttp) cc_final: 0.7444 (ttp) REVERT: E 310 GLN cc_start: 0.7950 (mt0) cc_final: 0.7742 (mt0) REVERT: E 313 ILE cc_start: 0.8770 (mm) cc_final: 0.8416 (mt) REVERT: E 325 GLN cc_start: 0.8404 (mt0) cc_final: 0.7704 (mt0) REVERT: F 184 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6735 (tm-30) REVERT: F 216 MET cc_start: 0.7965 (mmp) cc_final: 0.7548 (mmm) REVERT: F 368 LEU cc_start: 0.9020 (mt) cc_final: 0.8804 (mt) REVERT: F 475 TYR cc_start: 0.8609 (t80) cc_final: 0.8330 (t80) REVERT: d 239 LYS cc_start: 0.5872 (mttt) cc_final: 0.5485 (ttpt) REVERT: g 155 TYR cc_start: 0.6398 (p90) cc_final: 0.6094 (p90) outliers start: 2 outliers final: 1 residues processed: 653 average time/residue: 0.1779 time to fit residues: 184.5098 Evaluate side-chains 503 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 502 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 66 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 338 optimal weight: 0.8980 chunk 267 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 chunk 263 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN C 43 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN F 71 ASN F 402 GLN d 144 ASN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 GLN g 228 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.128413 restraints weight = 37308.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.127994 restraints weight = 44215.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.128245 restraints weight = 35754.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.128813 restraints weight = 29441.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.128795 restraints weight = 27714.067| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27880 Z= 0.157 Angle : 0.702 11.185 37783 Z= 0.356 Chirality : 0.046 0.250 4446 Planarity : 0.005 0.066 4912 Dihedral : 8.558 121.901 4022 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.90 % Favored : 91.88 % Rotamer: Outliers : 0.10 % Allowed : 6.05 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.19 (0.13), residues: 3557 helix: -0.05 (0.13), residues: 1427 sheet: -3.24 (0.20), residues: 461 loop : -2.16 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 284 TYR 0.026 0.002 TYR A 445 PHE 0.027 0.002 PHE B 292 TRP 0.002 0.001 TRP e 57 HIS 0.010 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00356 (27879) covalent geometry : angle 0.70153 (37781) SS BOND : bond 0.01445 ( 1) SS BOND : angle 1.21898 ( 2) hydrogen bonds : bond 0.04236 ( 1206) hydrogen bonds : angle 5.31676 ( 3486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 643 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.6717 (t0) cc_final: 0.6487 (t0) REVERT: A 215 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6513 (pt0) REVERT: A 219 MET cc_start: 0.8475 (tpp) cc_final: 0.8232 (tpp) REVERT: A 413 ARG cc_start: 0.7170 (tpp80) cc_final: 0.6789 (tpp80) REVERT: A 447 ASP cc_start: 0.6790 (t0) cc_final: 0.6170 (t0) REVERT: C 386 GLU cc_start: 0.7850 (tp30) cc_final: 0.7459 (tt0) REVERT: C 399 PHE cc_start: 0.7887 (m-10) cc_final: 0.7677 (m-10) REVERT: C 440 THR cc_start: 0.9223 (m) cc_final: 0.9019 (m) REVERT: C 451 LEU cc_start: 0.7774 (mt) cc_final: 0.7565 (mt) REVERT: B 34 GLN cc_start: 0.8399 (tt0) cc_final: 0.8078 (tt0) REVERT: D 79 MET cc_start: 0.9151 (mmt) cc_final: 0.8849 (mmt) REVERT: D 247 MET cc_start: 0.7665 (ttp) cc_final: 0.7390 (ttp) REVERT: E 39 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7732 (mmmm) REVERT: E 89 MET cc_start: 0.8725 (mtt) cc_final: 0.8185 (mtp) REVERT: E 112 ASN cc_start: 0.7901 (p0) cc_final: 0.7572 (p0) REVERT: E 313 ILE cc_start: 0.8698 (mm) cc_final: 0.8355 (mt) REVERT: E 325 GLN cc_start: 0.8477 (mt0) cc_final: 0.7963 (mt0) REVERT: F 184 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6685 (tm-30) REVERT: F 216 MET cc_start: 0.8092 (mmp) cc_final: 0.7615 (mmm) REVERT: F 374 MET cc_start: 0.8543 (mmt) cc_final: 0.8182 (tpp) REVERT: d 131 GLU cc_start: 0.7824 (tt0) cc_final: 0.7588 (tt0) REVERT: d 239 LYS cc_start: 0.5975 (mttt) cc_final: 0.5475 (ttpt) REVERT: g 144 ARG cc_start: 0.7065 (mmm160) cc_final: 0.6576 (tpp80) REVERT: g 264 LEU cc_start: 0.9238 (tp) cc_final: 0.8998 (tt) outliers start: 3 outliers final: 1 residues processed: 645 average time/residue: 0.1729 time to fit residues: 178.8422 Evaluate side-chains 504 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 503 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 290 optimal weight: 0.0370 chunk 104 optimal weight: 3.9990 chunk 323 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 242 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127650 restraints weight = 37326.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.127302 restraints weight = 39908.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.127520 restraints weight = 33676.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127670 restraints weight = 29249.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.127864 restraints weight = 27534.583| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27880 Z= 0.180 Angle : 0.713 10.458 37783 Z= 0.362 Chirality : 0.046 0.267 4446 Planarity : 0.005 0.054 4912 Dihedral : 8.487 121.597 4022 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.49 % Favored : 91.28 % Rotamer: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.94 (0.14), residues: 3557 helix: 0.15 (0.13), residues: 1434 sheet: -3.20 (0.20), residues: 462 loop : -1.98 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG g 256 TYR 0.040 0.002 TYR A 445 PHE 0.025 0.002 PHE B 292 TRP 0.003 0.001 TRP e 15 HIS 0.011 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00415 (27879) covalent geometry : angle 0.71256 (37781) SS BOND : bond 0.01860 ( 1) SS BOND : angle 1.27959 ( 2) hydrogen bonds : bond 0.04136 ( 1206) hydrogen bonds : angle 5.24295 ( 3486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 625 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6735 (m-80) cc_final: 0.6275 (m-10) REVERT: A 262 ASP cc_start: 0.8040 (t70) cc_final: 0.7610 (t70) REVERT: A 342 GLN cc_start: 0.9021 (pm20) cc_final: 0.8779 (pm20) REVERT: A 413 ARG cc_start: 0.7118 (tpp80) cc_final: 0.6747 (tpp80) REVERT: A 447 ASP cc_start: 0.6725 (t0) cc_final: 0.6074 (t0) REVERT: C 49 MET cc_start: 0.7304 (mtt) cc_final: 0.6848 (mtp) REVERT: C 386 GLU cc_start: 0.7854 (tp30) cc_final: 0.7542 (tt0) REVERT: C 440 THR cc_start: 0.9232 (m) cc_final: 0.9019 (m) REVERT: C 451 LEU cc_start: 0.7800 (mt) cc_final: 0.7534 (mt) REVERT: B 34 GLN cc_start: 0.8469 (tt0) cc_final: 0.8189 (tt0) REVERT: B 164 GLN cc_start: 0.9119 (pp30) cc_final: 0.8830 (pp30) REVERT: B 314 MET cc_start: 0.8784 (ttm) cc_final: 0.8570 (ttp) REVERT: B 436 MET cc_start: 0.6463 (tpp) cc_final: 0.6204 (tpt) REVERT: D 79 MET cc_start: 0.9180 (mmt) cc_final: 0.8802 (mmt) REVERT: D 247 MET cc_start: 0.7736 (ttp) cc_final: 0.7410 (ttp) REVERT: D 306 MET cc_start: 0.8522 (tpp) cc_final: 0.8302 (tpp) REVERT: D 385 TYR cc_start: 0.8382 (t80) cc_final: 0.8043 (t80) REVERT: E 39 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7706 (mmmm) REVERT: E 112 ASN cc_start: 0.7906 (p0) cc_final: 0.7689 (p0) REVERT: E 148 ILE cc_start: 0.7983 (mm) cc_final: 0.7749 (mm) REVERT: E 206 THR cc_start: 0.8676 (m) cc_final: 0.7778 (m) REVERT: E 313 ILE cc_start: 0.8716 (mm) cc_final: 0.8431 (mt) REVERT: E 361 ILE cc_start: 0.7732 (mm) cc_final: 0.7311 (tt) REVERT: F 184 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6534 (tm-30) REVERT: F 216 MET cc_start: 0.8086 (mmp) cc_final: 0.7541 (mmm) REVERT: F 343 PHE cc_start: 0.8314 (m-10) cc_final: 0.7968 (m-80) REVERT: d 239 LYS cc_start: 0.5975 (mttt) cc_final: 0.5323 (ttpt) REVERT: g 264 LEU cc_start: 0.9052 (tp) cc_final: 0.8727 (tt) REVERT: e 37 HIS cc_start: 0.6960 (t-90) cc_final: 0.6723 (t-90) outliers start: 1 outliers final: 1 residues processed: 626 average time/residue: 0.1677 time to fit residues: 169.4136 Evaluate side-chains 499 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 498 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 293 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 259 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 260 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 315 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN C 164 GLN C 434 GLN B 423 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN d 144 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.142143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130014 restraints weight = 36935.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.129651 restraints weight = 38067.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.129698 restraints weight = 33937.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.129874 restraints weight = 30355.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.129977 restraints weight = 27985.779| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27880 Z= 0.157 Angle : 0.699 10.495 37783 Z= 0.352 Chirality : 0.046 0.270 4446 Planarity : 0.005 0.063 4912 Dihedral : 8.314 119.184 4022 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.82 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.70 (0.14), residues: 3557 helix: 0.30 (0.14), residues: 1443 sheet: -2.95 (0.21), residues: 454 loop : -1.86 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 87 TYR 0.023 0.002 TYR A 445 PHE 0.025 0.002 PHE B 292 TRP 0.003 0.001 TRP e 15 HIS 0.010 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00366 (27879) covalent geometry : angle 0.69909 (37781) SS BOND : bond 0.01640 ( 1) SS BOND : angle 1.79152 ( 2) hydrogen bonds : bond 0.03964 ( 1206) hydrogen bonds : angle 5.11057 ( 3486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6708 (m-80) cc_final: 0.6253 (m-10) REVERT: A 342 GLN cc_start: 0.9060 (pm20) cc_final: 0.8788 (pm20) REVERT: A 425 GLN cc_start: 0.6900 (pt0) cc_final: 0.6040 (pp30) REVERT: A 447 ASP cc_start: 0.6554 (t0) cc_final: 0.6099 (t0) REVERT: C 49 MET cc_start: 0.7183 (mtt) cc_final: 0.6873 (mtp) REVERT: C 440 THR cc_start: 0.9188 (m) cc_final: 0.8952 (m) REVERT: C 451 LEU cc_start: 0.7798 (mt) cc_final: 0.7566 (mt) REVERT: B 34 GLN cc_start: 0.8445 (tt0) cc_final: 0.8160 (tt0) REVERT: B 164 GLN cc_start: 0.9147 (pp30) cc_final: 0.8825 (pp30) REVERT: D 79 MET cc_start: 0.9163 (mmt) cc_final: 0.8813 (mmt) REVERT: D 149 PHE cc_start: 0.6092 (t80) cc_final: 0.5732 (t80) REVERT: D 247 MET cc_start: 0.7548 (ttp) cc_final: 0.7193 (ttp) REVERT: D 428 GLU cc_start: 0.7750 (pp20) cc_final: 0.7411 (pp20) REVERT: E 39 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7666 (mmmm) REVERT: E 306 MET cc_start: 0.8841 (tpp) cc_final: 0.8618 (tpp) REVERT: E 313 ILE cc_start: 0.8638 (mm) cc_final: 0.8388 (mt) REVERT: F 86 THR cc_start: 0.7550 (m) cc_final: 0.7336 (m) REVERT: F 184 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6549 (tm-30) REVERT: F 216 MET cc_start: 0.8079 (mmp) cc_final: 0.7602 (mmm) REVERT: F 343 PHE cc_start: 0.8208 (m-10) cc_final: 0.7899 (m-80) REVERT: d 239 LYS cc_start: 0.6162 (mttt) cc_final: 0.5705 (ttpt) REVERT: g 335 LYS cc_start: 0.7669 (mtpt) cc_final: 0.7463 (mtpt) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.1663 time to fit residues: 169.5144 Evaluate side-chains 489 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 105 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 346 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN E 240 ASN ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.141211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.134762 restraints weight = 37210.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.128312 restraints weight = 62431.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.127534 restraints weight = 52106.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.127728 restraints weight = 45250.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.128163 restraints weight = 34402.525| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27880 Z= 0.173 Angle : 0.710 10.990 37783 Z= 0.359 Chirality : 0.047 0.264 4446 Planarity : 0.005 0.058 4912 Dihedral : 8.222 115.906 4022 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.35 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.59 (0.14), residues: 3557 helix: 0.40 (0.14), residues: 1441 sheet: -2.94 (0.21), residues: 474 loop : -1.78 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 429 TYR 0.019 0.002 TYR g 155 PHE 0.024 0.002 PHE B 292 TRP 0.003 0.001 TRP e 15 HIS 0.009 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00408 (27879) covalent geometry : angle 0.71028 (37781) SS BOND : bond 0.00957 ( 1) SS BOND : angle 1.39587 ( 2) hydrogen bonds : bond 0.03956 ( 1206) hydrogen bonds : angle 5.06262 ( 3486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 621 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6751 (m-80) cc_final: 0.6386 (m-10) REVERT: A 342 GLN cc_start: 0.9091 (pm20) cc_final: 0.8842 (pm20) REVERT: A 425 GLN cc_start: 0.7096 (pt0) cc_final: 0.6198 (pp30) REVERT: C 49 MET cc_start: 0.7254 (mtt) cc_final: 0.6967 (mtp) REVERT: B 34 GLN cc_start: 0.8490 (tt0) cc_final: 0.8197 (tt0) REVERT: B 164 GLN cc_start: 0.9100 (pp30) cc_final: 0.8812 (pp30) REVERT: D 79 MET cc_start: 0.9160 (mmt) cc_final: 0.8822 (mmt) REVERT: D 247 MET cc_start: 0.7558 (ttp) cc_final: 0.7252 (ttp) REVERT: E 112 ASN cc_start: 0.7973 (p0) cc_final: 0.7594 (p0) REVERT: E 148 ILE cc_start: 0.7884 (mm) cc_final: 0.7651 (mm) REVERT: E 313 ILE cc_start: 0.8691 (mm) cc_final: 0.8449 (mt) REVERT: F 184 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6516 (tm-30) REVERT: F 218 GLU cc_start: 0.6925 (pp20) cc_final: 0.6588 (pp20) REVERT: F 318 GLU cc_start: 0.7284 (tp30) cc_final: 0.7018 (tp30) REVERT: F 343 PHE cc_start: 0.8224 (m-10) cc_final: 0.7920 (m-80) REVERT: F 415 GLU cc_start: 0.6530 (mm-30) cc_final: 0.5086 (tp30) REVERT: F 488 MET cc_start: 0.6528 (tpt) cc_final: 0.6208 (tpt) REVERT: d 239 LYS cc_start: 0.6079 (mttt) cc_final: 0.5549 (ttpt) REVERT: g 240 CYS cc_start: 0.6136 (p) cc_final: 0.5895 (p) REVERT: e 37 HIS cc_start: 0.7106 (t-90) cc_final: 0.6886 (t-90) outliers start: 0 outliers final: 0 residues processed: 621 average time/residue: 0.1662 time to fit residues: 167.7532 Evaluate side-chains 484 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 82 optimal weight: 0.0020 chunk 335 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 294 optimal weight: 0.8980 chunk 315 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN A 504 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN F 71 ASN F 402 GLN d 144 ASN e 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.142655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135580 restraints weight = 36957.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.129620 restraints weight = 65362.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.128809 restraints weight = 49680.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129283 restraints weight = 41199.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.130362 restraints weight = 31182.002| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27880 Z= 0.157 Angle : 0.700 11.451 37783 Z= 0.352 Chirality : 0.046 0.269 4446 Planarity : 0.005 0.056 4912 Dihedral : 8.067 112.793 4022 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.96 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.14), residues: 3557 helix: 0.48 (0.14), residues: 1440 sheet: -2.83 (0.21), residues: 480 loop : -1.70 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 378 TYR 0.020 0.001 TYR g 155 PHE 0.023 0.002 PHE B 292 TRP 0.004 0.001 TRP e 15 HIS 0.009 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00368 (27879) covalent geometry : angle 0.69996 (37781) SS BOND : bond 0.00829 ( 1) SS BOND : angle 1.07486 ( 2) hydrogen bonds : bond 0.03841 ( 1206) hydrogen bonds : angle 5.01791 ( 3486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 599 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6754 (m-80) cc_final: 0.6455 (m-10) REVERT: A 447 ASP cc_start: 0.6535 (t70) cc_final: 0.6169 (t0) REVERT: C 49 MET cc_start: 0.7384 (mtt) cc_final: 0.7109 (mtp) REVERT: B 34 GLN cc_start: 0.8435 (tt0) cc_final: 0.8185 (tt0) REVERT: B 164 GLN cc_start: 0.9079 (pp30) cc_final: 0.8831 (pp30) REVERT: D 79 MET cc_start: 0.9142 (mmt) cc_final: 0.8808 (mmt) REVERT: D 247 MET cc_start: 0.7451 (ttp) cc_final: 0.7098 (ttp) REVERT: E 112 ASN cc_start: 0.8011 (p0) cc_final: 0.7589 (p0) REVERT: E 206 THR cc_start: 0.8355 (m) cc_final: 0.7652 (m) REVERT: E 313 ILE cc_start: 0.8683 (mm) cc_final: 0.8425 (mt) REVERT: F 216 MET cc_start: 0.8141 (mmp) cc_final: 0.7747 (mmm) REVERT: F 218 GLU cc_start: 0.6914 (pp20) cc_final: 0.6644 (pp20) REVERT: F 415 GLU cc_start: 0.6561 (mm-30) cc_final: 0.5152 (tp30) REVERT: F 488 MET cc_start: 0.6424 (tpt) cc_final: 0.6155 (tpt) REVERT: d 117 ASN cc_start: 0.7330 (t0) cc_final: 0.6963 (t0) REVERT: d 208 ARG cc_start: 0.7306 (ttp-110) cc_final: 0.7024 (mtm110) REVERT: d 239 LYS cc_start: 0.6147 (mttt) cc_final: 0.5703 (ttpt) REVERT: g 264 LEU cc_start: 0.8804 (tt) cc_final: 0.8582 (tt) REVERT: e 37 HIS cc_start: 0.7156 (t-90) cc_final: 0.6905 (t-90) outliers start: 0 outliers final: 0 residues processed: 599 average time/residue: 0.1612 time to fit residues: 157.3562 Evaluate side-chains 473 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 148 optimal weight: 5.9990 chunk 64 optimal weight: 0.0870 chunk 128 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 223 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 GLN e 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.143034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135696 restraints weight = 37046.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.130135 restraints weight = 68914.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.129324 restraints weight = 46832.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.129731 restraints weight = 40430.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.130002 restraints weight = 33491.101| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27880 Z= 0.158 Angle : 0.710 11.612 37783 Z= 0.356 Chirality : 0.046 0.237 4446 Planarity : 0.005 0.062 4912 Dihedral : 7.939 110.115 4022 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.21 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.44 (0.14), residues: 3557 helix: 0.50 (0.14), residues: 1441 sheet: -2.80 (0.20), residues: 515 loop : -1.63 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG g 48 TYR 0.027 0.002 TYR A 445 PHE 0.024 0.002 PHE B 292 TRP 0.005 0.001 TRP e 15 HIS 0.009 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00371 (27879) covalent geometry : angle 0.70976 (37781) SS BOND : bond 0.02470 ( 1) SS BOND : angle 1.49229 ( 2) hydrogen bonds : bond 0.03812 ( 1206) hydrogen bonds : angle 4.98697 ( 3486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6685 (pt0) REVERT: A 447 ASP cc_start: 0.6664 (t70) cc_final: 0.6286 (t0) REVERT: B 34 GLN cc_start: 0.8428 (tt0) cc_final: 0.8156 (tt0) REVERT: B 164 GLN cc_start: 0.9071 (pp30) cc_final: 0.8826 (pp30) REVERT: B 410 GLN cc_start: 0.5783 (tp40) cc_final: 0.5563 (tp40) REVERT: D 79 MET cc_start: 0.9140 (mmt) cc_final: 0.8767 (mmt) REVERT: D 109 ARG cc_start: 0.7577 (mmm160) cc_final: 0.7340 (mmm160) REVERT: D 247 MET cc_start: 0.7309 (ttp) cc_final: 0.7000 (ttp) REVERT: D 428 GLU cc_start: 0.7849 (pp20) cc_final: 0.7494 (pp20) REVERT: E 59 MET cc_start: 0.6707 (mpp) cc_final: 0.6225 (mpp) REVERT: E 79 MET cc_start: 0.8234 (mpp) cc_final: 0.7259 (mpp) REVERT: E 112 ASN cc_start: 0.8002 (p0) cc_final: 0.7494 (p0) REVERT: E 183 MET cc_start: 0.8084 (tpp) cc_final: 0.7761 (tpp) REVERT: E 206 THR cc_start: 0.8264 (m) cc_final: 0.7544 (m) REVERT: E 416 GLU cc_start: 0.7215 (pp20) cc_final: 0.6953 (pp20) REVERT: F 119 ASP cc_start: 0.8353 (p0) cc_final: 0.7445 (p0) REVERT: F 216 MET cc_start: 0.8191 (mmp) cc_final: 0.7696 (mmm) REVERT: F 374 MET cc_start: 0.8549 (mmt) cc_final: 0.8258 (tpp) REVERT: F 415 GLU cc_start: 0.6606 (mm-30) cc_final: 0.5158 (tp30) REVERT: F 488 MET cc_start: 0.6426 (tpt) cc_final: 0.6097 (tpt) REVERT: d 117 ASN cc_start: 0.7325 (t0) cc_final: 0.6935 (t0) REVERT: d 239 LYS cc_start: 0.6084 (mttt) cc_final: 0.5618 (ttpt) REVERT: e 37 HIS cc_start: 0.7159 (t-90) cc_final: 0.6890 (t-90) outliers start: 0 outliers final: 0 residues processed: 594 average time/residue: 0.1624 time to fit residues: 156.4555 Evaluate side-chains 469 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 27 optimal weight: 0.0030 chunk 301 optimal weight: 0.5980 chunk 338 optimal weight: 0.5980 chunk 281 optimal weight: 3.9990 chunk 243 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.144193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.137353 restraints weight = 36897.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.131473 restraints weight = 65911.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.130817 restraints weight = 47859.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.131198 restraints weight = 36725.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.131911 restraints weight = 29489.114| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27880 Z= 0.150 Angle : 0.707 12.033 37783 Z= 0.355 Chirality : 0.046 0.264 4446 Planarity : 0.005 0.058 4912 Dihedral : 7.864 108.992 4022 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.68 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.14), residues: 3557 helix: 0.53 (0.14), residues: 1441 sheet: -2.72 (0.21), residues: 514 loop : -1.62 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG g 48 TYR 0.030 0.001 TYR A 445 PHE 0.029 0.002 PHE D 171 TRP 0.006 0.001 TRP e 15 HIS 0.015 0.001 HIS g 228 Details of bonding type rmsd covalent geometry : bond 0.00353 (27879) covalent geometry : angle 0.70627 (37781) SS BOND : bond 0.02758 ( 1) SS BOND : angle 3.64408 ( 2) hydrogen bonds : bond 0.03804 ( 1206) hydrogen bonds : angle 4.94514 ( 3486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6650 (pt0) REVERT: A 425 GLN cc_start: 0.6877 (pt0) cc_final: 0.5963 (pp30) REVERT: C 221 TYR cc_start: 0.8966 (p90) cc_final: 0.8659 (p90) REVERT: B 34 GLN cc_start: 0.8433 (tt0) cc_final: 0.8192 (tt0) REVERT: B 164 GLN cc_start: 0.9072 (pp30) cc_final: 0.8836 (pp30) REVERT: D 79 MET cc_start: 0.9127 (mmt) cc_final: 0.8771 (mmt) REVERT: E 59 MET cc_start: 0.6674 (mpp) cc_final: 0.6258 (mpp) REVERT: E 206 THR cc_start: 0.8246 (m) cc_final: 0.7598 (m) REVERT: E 416 GLU cc_start: 0.7136 (pp20) cc_final: 0.6936 (pp20) REVERT: F 216 MET cc_start: 0.8078 (mmp) cc_final: 0.7595 (mmm) REVERT: F 374 MET cc_start: 0.8555 (mmt) cc_final: 0.8252 (tpp) REVERT: F 415 GLU cc_start: 0.6501 (mm-30) cc_final: 0.5145 (tp30) REVERT: d 117 ASN cc_start: 0.7281 (t0) cc_final: 0.6964 (t0) REVERT: d 239 LYS cc_start: 0.6139 (mttt) cc_final: 0.5784 (ttpt) REVERT: g 264 LEU cc_start: 0.8701 (tt) cc_final: 0.8352 (tt) REVERT: g 323 MET cc_start: 0.7925 (mmt) cc_final: 0.7556 (mmt) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.1624 time to fit residues: 155.6218 Evaluate side-chains 474 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 312 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 338 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 210 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS e 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.142020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134784 restraints weight = 37099.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.129278 restraints weight = 67412.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.128334 restraints weight = 47027.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128819 restraints weight = 39287.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.129100 restraints weight = 32402.881| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27880 Z= 0.182 Angle : 0.734 14.931 37783 Z= 0.370 Chirality : 0.047 0.203 4446 Planarity : 0.005 0.058 4912 Dihedral : 7.929 108.771 4022 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.43 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.14), residues: 3557 helix: 0.43 (0.14), residues: 1447 sheet: -2.71 (0.20), residues: 525 loop : -1.65 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG d 208 TYR 0.019 0.002 TYR g 155 PHE 0.025 0.002 PHE B 292 TRP 0.005 0.001 TRP e 15 HIS 0.008 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00434 (27879) covalent geometry : angle 0.73372 (37781) SS BOND : bond 0.01492 ( 1) SS BOND : angle 2.71166 ( 2) hydrogen bonds : bond 0.03891 ( 1206) hydrogen bonds : angle 5.00043 ( 3486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 MET cc_start: 0.8397 (ttp) cc_final: 0.8065 (ttp) REVERT: A 413 ARG cc_start: 0.7201 (tpp80) cc_final: 0.6923 (tpp80) REVERT: A 425 GLN cc_start: 0.6969 (pt0) cc_final: 0.6061 (pp30) REVERT: C 221 TYR cc_start: 0.8954 (p90) cc_final: 0.8585 (p90) REVERT: C 387 LEU cc_start: 0.8712 (mt) cc_final: 0.7933 (tt) REVERT: B 34 GLN cc_start: 0.8486 (tt0) cc_final: 0.8188 (tt0) REVERT: B 95 ILE cc_start: 0.8987 (mp) cc_final: 0.8773 (mt) REVERT: B 157 MET cc_start: 0.7752 (mpp) cc_final: 0.7524 (mpp) REVERT: B 164 GLN cc_start: 0.9079 (pp30) cc_final: 0.8855 (pp30) REVERT: B 410 GLN cc_start: 0.5688 (tp40) cc_final: 0.5426 (tp40) REVERT: D 79 MET cc_start: 0.9144 (mmt) cc_final: 0.8676 (mmt) REVERT: D 247 MET cc_start: 0.7306 (ttp) cc_final: 0.7041 (ttp) REVERT: D 343 PHE cc_start: 0.8705 (m-80) cc_final: 0.8325 (m-80) REVERT: E 313 ILE cc_start: 0.8894 (mt) cc_final: 0.8647 (mt) REVERT: F 216 MET cc_start: 0.8178 (mmp) cc_final: 0.7618 (mmm) REVERT: F 374 MET cc_start: 0.8588 (mmt) cc_final: 0.8304 (tpp) REVERT: F 415 GLU cc_start: 0.6447 (mm-30) cc_final: 0.5133 (tp30) REVERT: d 117 ASN cc_start: 0.7308 (t0) cc_final: 0.6938 (t0) REVERT: d 239 LYS cc_start: 0.6098 (mttt) cc_final: 0.5735 (ttpt) REVERT: e 37 HIS cc_start: 0.7207 (t-90) cc_final: 0.6894 (t-90) REVERT: e 91 GLU cc_start: 0.6493 (tp30) cc_final: 0.6020 (tp30) outliers start: 0 outliers final: 0 residues processed: 571 average time/residue: 0.1637 time to fit residues: 152.0187 Evaluate side-chains 471 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 45 optimal weight: 0.6980 chunk 150 optimal weight: 0.0980 chunk 279 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 323 optimal weight: 0.0070 chunk 160 optimal weight: 0.0370 chunk 261 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN d 170 ASN g 99 GLN e 72 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.154313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.138240 restraints weight = 350892.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.142032 restraints weight = 226578.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.140578 restraints weight = 176605.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.140792 restraints weight = 190268.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.140823 restraints weight = 182832.731| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27880 Z= 0.136 Angle : 0.705 13.986 37783 Z= 0.352 Chirality : 0.045 0.198 4446 Planarity : 0.005 0.059 4912 Dihedral : 7.796 110.749 4022 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.34 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.29 (0.14), residues: 3557 helix: 0.63 (0.14), residues: 1430 sheet: -2.70 (0.21), residues: 509 loop : -1.55 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG d 154 TYR 0.033 0.001 TYR B 237 PHE 0.031 0.002 PHE D 149 TRP 0.008 0.001 TRP e 15 HIS 0.010 0.001 HIS g 228 Details of bonding type rmsd covalent geometry : bond 0.00314 (27879) covalent geometry : angle 0.70471 (37781) SS BOND : bond 0.01123 ( 1) SS BOND : angle 2.53266 ( 2) hydrogen bonds : bond 0.03702 ( 1206) hydrogen bonds : angle 4.92995 ( 3486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4299.72 seconds wall clock time: 75 minutes 10.71 seconds (4510.71 seconds total)