Starting phenix.real_space_refine on Mon Sep 14 02:33:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6voi_21265/09_2026/6voi_21265.cif Found real_map, /net/cci-nas-00/data/ceres_data/6voi_21265/09_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_21265/09_2026/6voi_21265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6voi_21265/09_2026/6voi_21265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6voi_21265/09_2026/6voi_21265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6voi_21265/09_2026/6voi_21265.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6voi_21265/09_2026/6voi_21265.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6voi_21265/09_2026/6voi_21265.cif" } 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-2.2.1-6174/lib/python3.11/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: 6.28, per 1000 atoms: 0.23 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 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: 0.80 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: 4.88 Time building geometry restraints manager: 3.07 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: 16202 27.14 - 54.29: 777 54.29 - 81.43: 60 81.43 - 108.57: 13 108.57 - 135.71: 3 Dihedral angle restraints: 17055 sinusoidal: 6816 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 17052 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.100 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 15.123 135.715 10480 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/Z covalent geometry : bond 0.00507 / 0.28 (27879) covalent geometry : angle 0.94588 / 0.60 (37781) SS BOND : bond 0.01407 / 0.74 ( 1) SS BOND : angle 1.90182 / 1.27 ( 2) hydrogen bonds : bond 0.15365 / 10.44 ( 1206) hydrogen bonds : angle 7.24105 / 5.06 ( 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 : 1.042 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: 0.2003 time to fit residues: 234.1262 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 : 1.086 ------------------------------------------------------------------------------- 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... 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 = 0.3487 r_free = 0.3487 target = 0.139303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126972 restraints weight = 37415.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.126884 restraints weight = 37615.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126983 restraints weight = 32985.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.127028 restraints weight = 29415.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.127086 restraints weight = 29316.749| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1530 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= 0.176 Angle : 0.727 9.204 37783 Z= 0.374 Chirality : 0.047 0.240 4446 Planarity : 0.005 0.068 4912 Dihedral : 7.379 123.209 3898 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.84 % Favored : 91.90 % Rotamer: Outliers : 0.07 % Allowed : 6.19 % Favored : 93.75 % 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: -2.72 (0.13), residues: 3557 helix: -0.57 (0.13), residues: 1422 sheet: -3.47 (0.20), residues: 448 loop : -2.41 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 140 TYR 0.015 0.002 TYR g 94 PHE 0.031 0.002 PHE B 292 TRP 0.003 0.001 TRP e 15 HIS 0.005 0.001 HIS F 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (27879) covalent geometry : angle 0.72731 / 0.37 (37781) SS BOND : bond 0.01986 / 1.05 ( 1) SS BOND : angle 0.99728 / 0.66 ( 2) hydrogen bonds : bond 0.04575 / 3.11 ( 1206) hydrogen bonds : angle 5.62428 / 3.92 ( 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 655 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 653 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.6734 (t0) cc_final: 0.6433 (t0) REVERT: A 219 MET cc_start: 0.8579 (tpp) cc_final: 0.8299 (tpp) REVERT: A 447 ASP cc_start: 0.6844 (t0) cc_final: 0.6295 (t0) REVERT: C 14 ARG cc_start: 0.5312 (mmm160) cc_final: 0.5024 (mpt-90) REVERT: C 49 MET cc_start: 0.7909 (mtm) cc_final: 0.7696 (mtt) REVERT: C 348 ASP cc_start: 0.7155 (m-30) cc_final: 0.6769 (m-30) REVERT: C 386 GLU cc_start: 0.7795 (tp30) cc_final: 0.7583 (tp30) REVERT: C 425 GLN cc_start: 0.7355 (tt0) cc_final: 0.7154 (tt0) REVERT: C 440 THR cc_start: 0.9270 (m) cc_final: 0.9024 (m) REVERT: B 34 GLN cc_start: 0.8389 (tt0) cc_final: 0.8125 (tt0) REVERT: D 83 ASP cc_start: 0.7553 (m-30) cc_final: 0.7352 (m-30) REVERT: D 178 LYS cc_start: 0.7986 (ttpp) cc_final: 0.7577 (ttpp) REVERT: D 247 MET cc_start: 0.7741 (ttp) cc_final: 0.7517 (ttp) REVERT: E 20 LEU cc_start: 0.6972 (mt) cc_final: 0.6744 (tp) REVERT: E 39 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7783 (mmmm) REVERT: E 89 MET cc_start: 0.8652 (mtt) cc_final: 0.8215 (mtp) REVERT: E 155 VAL cc_start: 0.9098 (t) cc_final: 0.8804 (t) REVERT: E 206 THR cc_start: 0.8594 (m) cc_final: 0.8056 (m) REVERT: E 247 MET cc_start: 0.7717 (ttp) cc_final: 0.7459 (ttp) REVERT: E 310 GLN cc_start: 0.7950 (mt0) cc_final: 0.7739 (mt0) REVERT: E 313 ILE cc_start: 0.8775 (mm) cc_final: 0.8422 (mt) REVERT: E 325 GLN cc_start: 0.8405 (mt0) cc_final: 0.7706 (mt0) REVERT: F 184 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6736 (tm-30) REVERT: F 216 MET cc_start: 0.7981 (mmp) cc_final: 0.7551 (mmm) REVERT: F 368 LEU cc_start: 0.9013 (mt) cc_final: 0.8803 (mt) REVERT: F 475 TYR cc_start: 0.8612 (t80) cc_final: 0.8335 (t80) REVERT: d 239 LYS cc_start: 0.5891 (mttt) cc_final: 0.5383 (ttpt) REVERT: g 155 TYR cc_start: 0.6433 (p90) cc_final: 0.6120 (p90) outliers start: 2 outliers final: 1 residues processed: 655 average time/residue: 0.1811 time to fit residues: 190.3971 Evaluate side-chains 502 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 501 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 0.7980 chunk 338 optimal weight: 0.7980 chunk 267 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 277 optimal weight: 0.4980 chunk 222 optimal weight: 1.9990 chunk 266 optimal weight: 0.0010 chunk 313 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** 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** g 228 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.141730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134829 restraints weight = 37219.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.128539 restraints weight = 65432.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.127929 restraints weight = 54970.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128435 restraints weight = 43480.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.129009 restraints weight = 33241.396| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27880 Z= 0.150 Angle : 0.697 11.710 37783 Z= 0.354 Chirality : 0.046 0.247 4446 Planarity : 0.005 0.066 4912 Dihedral : 7.167 121.692 3898 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.62 % Favored : 92.16 % Rotamer: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % 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: -2.18 (0.13), residues: 3557 helix: -0.04 (0.13), residues: 1428 sheet: -3.26 (0.20), residues: 462 loop : -2.14 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG g 256 TYR 0.022 0.002 TYR A 445 PHE 0.026 0.002 PHE B 292 TRP 0.002 0.001 TRP e 57 HIS 0.011 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (27879) covalent geometry : angle 0.69700 / 0.35 (37781) SS BOND : bond 0.02606 / 1.37 ( 1) SS BOND : angle 1.61185 / 1.07 ( 2) hydrogen bonds : bond 0.04210 / 2.87 ( 1206) hydrogen bonds : angle 5.30751 / 3.70 ( 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 654 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 652 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.6703 (t0) cc_final: 0.6465 (t0) REVERT: A 215 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6517 (pt0) REVERT: A 219 MET cc_start: 0.8490 (tpp) cc_final: 0.8260 (tpp) REVERT: A 413 ARG cc_start: 0.7163 (tpp80) cc_final: 0.6799 (tpp80) REVERT: A 447 ASP cc_start: 0.6832 (t0) cc_final: 0.6200 (t0) REVERT: C 14 ARG cc_start: 0.5293 (mmm160) cc_final: 0.4915 (mpt-90) REVERT: C 386 GLU cc_start: 0.7830 (tp30) cc_final: 0.7452 (tt0) REVERT: C 440 THR cc_start: 0.9222 (m) cc_final: 0.9017 (m) REVERT: C 451 LEU cc_start: 0.7800 (mt) cc_final: 0.7575 (mt) REVERT: B 34 GLN cc_start: 0.8361 (tt0) cc_final: 0.8069 (tt0) REVERT: D 247 MET cc_start: 0.7675 (ttp) cc_final: 0.7350 (ttp) REVERT: E 39 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7763 (mmmm) REVERT: E 89 MET cc_start: 0.8707 (mtt) cc_final: 0.8146 (mtp) REVERT: E 112 ASN cc_start: 0.7860 (p0) cc_final: 0.7659 (p0) REVERT: E 206 THR cc_start: 0.8282 (m) cc_final: 0.7957 (m) REVERT: E 313 ILE cc_start: 0.8668 (mm) cc_final: 0.8348 (mt) REVERT: E 325 GLN cc_start: 0.8396 (mt0) cc_final: 0.7908 (mt0) REVERT: E 488 MET cc_start: 0.6968 (ppp) cc_final: 0.6749 (ppp) REVERT: F 71 ASN cc_start: 0.7371 (t0) cc_final: 0.7164 (t0) REVERT: F 216 MET cc_start: 0.8162 (mmp) cc_final: 0.7692 (mmm) REVERT: F 374 MET cc_start: 0.8515 (mmt) cc_final: 0.8149 (tpp) REVERT: d 131 GLU cc_start: 0.7860 (tt0) cc_final: 0.7633 (tt0) REVERT: d 239 LYS cc_start: 0.5944 (mttt) cc_final: 0.5412 (ttpt) REVERT: g 264 LEU cc_start: 0.9172 (tp) cc_final: 0.8856 (tt) REVERT: e 37 HIS cc_start: 0.6965 (t-90) cc_final: 0.6744 (t-90) outliers start: 2 outliers final: 1 residues processed: 654 average time/residue: 0.1852 time to fit residues: 194.9518 Evaluate side-chains 502 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 501 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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: 0.9990 chunk 104 optimal weight: 0.3980 chunk 323 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 350 optimal weight: 0.9990 chunk 315 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 242 optimal weight: 0.0870 chunk 213 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.141972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.135176 restraints weight = 37059.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.128933 restraints weight = 64775.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128244 restraints weight = 62220.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.128822 restraints weight = 46637.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.129496 restraints weight = 33504.669| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2331 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= 0.152 Angle : 0.687 9.936 37783 Z= 0.348 Chirality : 0.046 0.256 4446 Planarity : 0.005 0.055 4912 Dihedral : 7.056 120.756 3898 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.07 % Favored : 91.76 % Rotamer: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % 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: -1.90 (0.14), residues: 3557 helix: 0.19 (0.13), residues: 1435 sheet: -3.15 (0.21), residues: 456 loop : -1.99 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 109 TYR 0.042 0.002 TYR A 445 PHE 0.024 0.002 PHE B 292 TRP 0.003 0.001 TRP e 15 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (27879) covalent geometry : angle 0.68682 / 0.35 (37781) SS BOND : bond 0.01411 / 0.74 ( 1) SS BOND : angle 1.20024 / 0.80 ( 2) hydrogen bonds : bond 0.04048 / 2.76 ( 1206) hydrogen bonds : angle 5.18692 / 3.61 ( 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 628 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 626 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6736 (m-80) cc_final: 0.6302 (m-10) REVERT: A 215 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6536 (pt0) REVERT: A 262 ASP cc_start: 0.8078 (t70) cc_final: 0.7675 (t70) REVERT: A 413 ARG cc_start: 0.7084 (tpp80) cc_final: 0.6726 (tpp80) REVERT: A 447 ASP cc_start: 0.6699 (t0) cc_final: 0.6050 (t0) REVERT: C 14 ARG cc_start: 0.5328 (mmm160) cc_final: 0.4922 (mpt-90) REVERT: C 451 LEU cc_start: 0.7856 (mt) cc_final: 0.7595 (mt) REVERT: B 34 GLN cc_start: 0.8420 (tt0) cc_final: 0.8173 (tt0) REVERT: B 164 GLN cc_start: 0.9102 (pp30) cc_final: 0.8792 (pp30) REVERT: B 314 MET cc_start: 0.8734 (ttm) cc_final: 0.8509 (ttp) REVERT: D 247 MET cc_start: 0.7682 (ttp) cc_final: 0.7264 (ttp) REVERT: D 306 MET cc_start: 0.8496 (tpp) cc_final: 0.8261 (tpp) REVERT: E 39 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7696 (mmmm) REVERT: E 98 LEU cc_start: 0.8918 (mp) cc_final: 0.8710 (mt) REVERT: E 148 ILE cc_start: 0.8043 (mm) cc_final: 0.7755 (mm) REVERT: E 206 THR cc_start: 0.8178 (m) cc_final: 0.7932 (m) REVERT: E 313 ILE cc_start: 0.8629 (mm) cc_final: 0.8403 (mt) REVERT: F 71 ASN cc_start: 0.7535 (t0) cc_final: 0.7304 (t0) REVERT: F 184 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6637 (tm-30) REVERT: F 216 MET cc_start: 0.8091 (mmp) cc_final: 0.7717 (mmm) REVERT: F 343 PHE cc_start: 0.8299 (m-10) cc_final: 0.7910 (m-80) REVERT: d 239 LYS cc_start: 0.5925 (mttt) cc_final: 0.5319 (ttpt) REVERT: g 264 LEU cc_start: 0.9016 (tp) cc_final: 0.8741 (tt) outliers start: 2 outliers final: 1 residues processed: 627 average time/residue: 0.1792 time to fit residues: 182.6137 Evaluate side-chains 495 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 494 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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: 0.6980 chunk 90 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 240 optimal weight: 0.9980 chunk 147 optimal weight: 0.0770 chunk 315 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 389 GLN C 164 GLN C 434 GLN B 148 GLN B 423 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN d 144 ASN e 102 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.143075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.136409 restraints weight = 36747.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.130071 restraints weight = 63926.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.129171 restraints weight = 50229.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129242 restraints weight = 48176.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.129506 restraints weight = 36786.828| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 0.085 27880 Z= 0.153 Angle : 0.693 10.628 37783 Z= 0.348 Chirality : 0.046 0.234 4446 Planarity : 0.005 0.064 4912 Dihedral : 6.970 118.849 3898 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.87 % Favored : 91.93 % Rotamer: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % 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: -1.67 (0.14), residues: 3557 helix: 0.34 (0.14), residues: 1446 sheet: -2.96 (0.21), residues: 460 loop : -1.85 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 416 TYR 0.023 0.001 TYR A 445 PHE 0.024 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/Z covalent geometry : bond 0.00357 / 0.15 (27879) covalent geometry : angle 0.69252 / 0.35 (37781) SS BOND : bond 0.01401 / 0.74 ( 1) SS BOND : angle 1.72543 / 1.15 ( 2) hydrogen bonds : bond 0.03922 / 2.69 ( 1206) hydrogen bonds : angle 5.06958 / 3.52 ( 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 620 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 619 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6719 (m-80) cc_final: 0.6298 (m-10) REVERT: A 342 GLN cc_start: 0.9016 (pm20) cc_final: 0.8796 (pm20) REVERT: A 389 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7933 (tp40) REVERT: A 425 GLN cc_start: 0.6895 (pt0) cc_final: 0.6074 (pp30) REVERT: C 14 ARG cc_start: 0.5412 (mmm160) cc_final: 0.4949 (mpt-90) REVERT: C 386 GLU cc_start: 0.7756 (tp30) cc_final: 0.7474 (tt0) REVERT: C 451 LEU cc_start: 0.7877 (mt) cc_final: 0.7458 (mt) REVERT: B 34 GLN cc_start: 0.8391 (tt0) cc_final: 0.8118 (tt0) REVERT: B 164 GLN cc_start: 0.9129 (pp30) cc_final: 0.8788 (pp30) REVERT: B 436 MET cc_start: 0.6526 (tpp) cc_final: 0.6117 (tpt) REVERT: D 49 VAL cc_start: 0.9320 (t) cc_final: 0.9073 (t) REVERT: D 149 PHE cc_start: 0.6046 (t80) cc_final: 0.5705 (t80) REVERT: D 247 MET cc_start: 0.7462 (ttp) cc_final: 0.7056 (ttp) REVERT: D 428 GLU cc_start: 0.7703 (pp20) cc_final: 0.7428 (pp20) REVERT: E 39 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7712 (mmmm) REVERT: E 112 ASN cc_start: 0.7967 (p0) cc_final: 0.7659 (p0) REVERT: E 206 THR cc_start: 0.8515 (m) cc_final: 0.7572 (m) REVERT: E 306 MET cc_start: 0.8771 (tpp) cc_final: 0.8541 (tpp) REVERT: F 71 ASN cc_start: 0.7420 (t0) cc_final: 0.7170 (t0) REVERT: F 216 MET cc_start: 0.8068 (mmp) cc_final: 0.7570 (mmm) REVERT: F 343 PHE cc_start: 0.8220 (m-10) cc_final: 0.7903 (m-80) REVERT: d 239 LYS cc_start: 0.6022 (mttt) cc_final: 0.5517 (ttpt) REVERT: g 264 LEU cc_start: 0.9166 (tp) cc_final: 0.8935 (tt) outliers start: 1 outliers final: 0 residues processed: 619 average time/residue: 0.1788 time to fit residues: 179.7954 Evaluate side-chains 479 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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: 1.9990 chunk 118 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 207 optimal weight: 0.2980 chunk 163 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 chunk 346 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN C 148 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 GLN e 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.142561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.136008 restraints weight = 37062.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.129394 restraints weight = 62943.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.128706 restraints weight = 60516.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.129419 restraints weight = 45764.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.129834 restraints weight = 34718.210| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27880 Z= 0.159 Angle : 0.696 11.237 37783 Z= 0.349 Chirality : 0.046 0.252 4446 Planarity : 0.005 0.059 4912 Dihedral : 6.915 116.485 3898 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.04 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -1.57 (0.14), residues: 3557 helix: 0.42 (0.14), residues: 1441 sheet: -2.90 (0.21), residues: 472 loop : -1.78 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 83 TYR 0.044 0.002 TYR A 445 PHE 0.023 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/Z covalent geometry : bond 0.00374 / 0.16 (27879) covalent geometry : angle 0.69601 / 0.35 (37781) SS BOND : bond 0.00997 / 0.52 ( 1) SS BOND : angle 0.86463 / 0.58 ( 2) hydrogen bonds : bond 0.03874 / 2.67 ( 1206) hydrogen bonds : angle 5.04396 / 3.50 ( 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 618 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6703 (m-80) cc_final: 0.6401 (m-10) REVERT: A 215 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6686 (pt0) REVERT: A 342 GLN cc_start: 0.9028 (pm20) cc_final: 0.8807 (pm20) REVERT: A 425 GLN cc_start: 0.6867 (pt0) cc_final: 0.5996 (pp30) REVERT: A 447 ASP cc_start: 0.6755 (t0) cc_final: 0.6253 (t0) REVERT: C 14 ARG cc_start: 0.5389 (mmm160) cc_final: 0.4933 (mpt-90) REVERT: B 34 GLN cc_start: 0.8447 (tt0) cc_final: 0.8196 (tt0) REVERT: B 164 GLN cc_start: 0.9111 (pp30) cc_final: 0.8802 (pp30) REVERT: B 436 MET cc_start: 0.6358 (tpp) cc_final: 0.6109 (tpt) REVERT: D 49 VAL cc_start: 0.9323 (t) cc_final: 0.9087 (t) REVERT: D 149 PHE cc_start: 0.6058 (t80) cc_final: 0.5613 (t80) REVERT: D 247 MET cc_start: 0.7605 (ttp) cc_final: 0.7137 (ttp) REVERT: D 309 LEU cc_start: 0.8875 (mt) cc_final: 0.8671 (mp) REVERT: E 39 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7703 (mmmm) REVERT: E 48 ILE cc_start: 0.8807 (pt) cc_final: 0.8601 (pt) REVERT: E 112 ASN cc_start: 0.7991 (p0) cc_final: 0.7582 (p0) REVERT: E 206 THR cc_start: 0.8497 (m) cc_final: 0.7666 (m) REVERT: E 313 ILE cc_start: 0.8735 (mt) cc_final: 0.8458 (mt) REVERT: F 71 ASN cc_start: 0.7574 (t0) cc_final: 0.7272 (t0) REVERT: F 86 THR cc_start: 0.7568 (m) cc_final: 0.7326 (m) REVERT: F 119 ASP cc_start: 0.8373 (p0) cc_final: 0.8116 (p0) REVERT: F 184 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6535 (tm-30) REVERT: F 216 MET cc_start: 0.8101 (mmp) cc_final: 0.7585 (mmm) REVERT: F 343 PHE cc_start: 0.8279 (m-10) cc_final: 0.7921 (m-80) REVERT: F 415 GLU cc_start: 0.6448 (mm-30) cc_final: 0.5029 (tp30) REVERT: F 488 MET cc_start: 0.6595 (tpt) cc_final: 0.6155 (tpt) REVERT: d 155 ILE cc_start: 0.7909 (tp) cc_final: 0.7667 (tp) REVERT: d 239 LYS cc_start: 0.6016 (mttt) cc_final: 0.5717 (ttpt) REVERT: g 264 LEU cc_start: 0.9130 (tp) cc_final: 0.8876 (tt) REVERT: e 37 HIS cc_start: 0.7065 (t-90) cc_final: 0.6862 (t-90) REVERT: e 102 ASN cc_start: 0.4063 (m-40) cc_final: 0.3849 (t0) outliers start: 0 outliers final: 0 residues processed: 618 average time/residue: 0.1743 time to fit residues: 176.1803 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 : 0.984 ------------------------------------------------------------------------------- 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: 0.5980 chunk 335 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 63 optimal weight: 0.0050 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 294 optimal weight: 0.9980 chunk 315 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN F 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.143961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.138170 restraints weight = 36716.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.133578 restraints weight = 47882.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.131871 restraints weight = 38072.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.132029 restraints weight = 38002.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.132144 restraints weight = 32978.202| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27880 Z= 0.148 Angle : 0.690 11.411 37783 Z= 0.345 Chirality : 0.046 0.252 4446 Planarity : 0.004 0.057 4912 Dihedral : 6.803 112.649 3898 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.79 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -1.45 (0.14), residues: 3557 helix: 0.51 (0.14), residues: 1440 sheet: -2.78 (0.21), residues: 474 loop : -1.71 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 109 TYR 0.018 0.001 TYR g 155 PHE 0.024 0.002 PHE g 133 TRP 0.004 0.001 TRP e 15 HIS 0.009 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (27879) covalent geometry : angle 0.68966 / 0.35 (37781) SS BOND : bond 0.01320 / 0.69 ( 1) SS BOND : angle 1.40466 / 0.94 ( 2) hydrogen bonds : bond 0.03799 / 2.61 ( 1206) hydrogen bonds : angle 4.97601 / 3.46 ( 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 606 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6793 (m-80) cc_final: 0.6424 (m-10) REVERT: A 215 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6623 (pt0) REVERT: A 342 GLN cc_start: 0.9004 (pm20) cc_final: 0.8785 (pm20) REVERT: A 425 GLN cc_start: 0.6822 (pt0) cc_final: 0.6003 (pp30) REVERT: A 447 ASP cc_start: 0.6622 (t0) cc_final: 0.6180 (t0) REVERT: C 14 ARG cc_start: 0.5413 (mmm160) cc_final: 0.4964 (mpt-90) REVERT: B 34 GLN cc_start: 0.8430 (tt0) cc_final: 0.8164 (tt0) REVERT: B 164 GLN cc_start: 0.9107 (pp30) cc_final: 0.8796 (pp30) REVERT: B 376 MET cc_start: 0.7495 (ttt) cc_final: 0.7104 (ttt) REVERT: D 49 VAL cc_start: 0.9279 (t) cc_final: 0.8999 (t) REVERT: D 247 MET cc_start: 0.7568 (ttp) cc_final: 0.7100 (ttp) REVERT: E 39 LYS cc_start: 0.7928 (mmtm) cc_final: 0.7686 (mmmm) REVERT: E 112 ASN cc_start: 0.7936 (p0) cc_final: 0.7456 (p0) REVERT: E 206 THR cc_start: 0.8381 (m) cc_final: 0.7663 (m) REVERT: E 313 ILE cc_start: 0.8803 (mt) cc_final: 0.8502 (mt) REVERT: F 71 ASN cc_start: 0.7669 (t0) cc_final: 0.7374 (t0) REVERT: F 216 MET cc_start: 0.8118 (mmp) cc_final: 0.7688 (mmm) REVERT: F 415 GLU cc_start: 0.6487 (mm-30) cc_final: 0.4952 (tp30) REVERT: F 488 MET cc_start: 0.6578 (tpt) cc_final: 0.6110 (tpt) REVERT: d 117 ASN cc_start: 0.7340 (t0) cc_final: 0.7004 (t0) REVERT: d 155 ILE cc_start: 0.7935 (tp) cc_final: 0.7624 (tp) REVERT: d 208 ARG cc_start: 0.7273 (ttp-110) cc_final: 0.7018 (mtm110) REVERT: d 239 LYS cc_start: 0.5930 (mttt) cc_final: 0.5580 (ttpt) REVERT: e 1 MET cc_start: 0.4397 (ppp) cc_final: 0.4188 (ppp) REVERT: e 37 HIS cc_start: 0.7068 (t-90) cc_final: 0.6837 (t-90) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.1762 time to fit residues: 174.5883 Evaluate side-chains 480 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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: 0.0020 chunk 128 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 311 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 389 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN e 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.144415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.138237 restraints weight = 36957.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.131750 restraints weight = 64003.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.130896 restraints weight = 62531.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.131564 restraints weight = 47868.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.131906 restraints weight = 36452.230| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27880 Z= 0.153 Angle : 0.705 16.842 37783 Z= 0.354 Chirality : 0.046 0.289 4446 Planarity : 0.005 0.061 4912 Dihedral : 6.713 109.494 3898 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.10 % Favored : 91.73 % Rotamer: Outliers : 0.03 % Allowed : 1.33 % Favored : 98.64 % 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: -1.41 (0.14), residues: 3557 helix: 0.55 (0.14), residues: 1444 sheet: -2.76 (0.21), residues: 495 loop : -1.67 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG g 48 TYR 0.026 0.002 TYR A 445 PHE 0.024 0.001 PHE B 292 TRP 0.004 0.001 TRP e 15 HIS 0.009 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (27879) covalent geometry : angle 0.70529 / 0.35 (37781) SS BOND : bond 0.01205 / 0.63 ( 1) SS BOND : angle 1.52523 / 1.02 ( 2) hydrogen bonds : bond 0.03809 / 2.62 ( 1206) hydrogen bonds : angle 4.94625 / 3.43 ( 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: 1 poor density : 593 time to evaluate : 1.018 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: A 215 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6592 (pt0) REVERT: A 413 ARG cc_start: 0.7037 (tpp80) cc_final: 0.6704 (tpp80) REVERT: A 425 GLN cc_start: 0.6775 (pt0) cc_final: 0.6014 (pp30) REVERT: A 447 ASP cc_start: 0.6499 (t0) cc_final: 0.6066 (t0) REVERT: C 14 ARG cc_start: 0.5361 (mmm160) cc_final: 0.5144 (mpt-90) REVERT: C 53 LEU cc_start: 0.8950 (pp) cc_final: 0.8627 (pp) REVERT: B 34 GLN cc_start: 0.8405 (tt0) cc_final: 0.8172 (tt0) REVERT: B 95 ILE cc_start: 0.8849 (mp) cc_final: 0.8610 (mt) REVERT: B 164 GLN cc_start: 0.9075 (pp30) cc_final: 0.8787 (pp30) REVERT: D 25 GLN cc_start: 0.8412 (tt0) cc_final: 0.8209 (tt0) REVERT: D 49 VAL cc_start: 0.9318 (t) cc_final: 0.9040 (t) REVERT: D 247 MET cc_start: 0.7486 (ttp) cc_final: 0.7007 (ttp) REVERT: D 343 PHE cc_start: 0.8699 (m-80) cc_final: 0.8444 (m-80) REVERT: D 428 GLU cc_start: 0.7767 (pp20) cc_final: 0.7469 (pp20) REVERT: E 39 LYS cc_start: 0.7937 (mmtm) cc_final: 0.7679 (mmmm) REVERT: E 59 MET cc_start: 0.6593 (mpp) cc_final: 0.6295 (mpp) REVERT: E 313 ILE cc_start: 0.8835 (mt) cc_final: 0.8531 (mt) REVERT: E 416 GLU cc_start: 0.7180 (pp20) cc_final: 0.6963 (pp20) REVERT: F 71 ASN cc_start: 0.7652 (t0) cc_final: 0.7393 (t0) REVERT: F 216 MET cc_start: 0.8141 (mmp) cc_final: 0.7688 (mmm) REVERT: F 415 GLU cc_start: 0.6428 (mm-30) cc_final: 0.5118 (tp30) REVERT: F 488 MET cc_start: 0.6545 (tpt) cc_final: 0.6222 (tpt) REVERT: d 117 ASN cc_start: 0.7315 (t0) cc_final: 0.7028 (t0) REVERT: d 155 ILE cc_start: 0.7926 (tp) cc_final: 0.7619 (tp) REVERT: d 239 LYS cc_start: 0.5961 (mttt) cc_final: 0.5461 (ttpt) REVERT: g 264 LEU cc_start: 0.9157 (tp) cc_final: 0.8956 (tt) outliers start: 1 outliers final: 0 residues processed: 594 average time/residue: 0.1773 time to fit residues: 171.4465 Evaluate side-chains 481 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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: 0.6980 chunk 301 optimal weight: 0.8980 chunk 338 optimal weight: 0.8980 chunk 281 optimal weight: 0.0470 chunk 243 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 245 optimal weight: 4.9990 chunk 232 optimal weight: 0.0040 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN C 201 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN F 376 GLN F 402 GLN d 199 GLN e 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.145944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.138846 restraints weight = 36788.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.133432 restraints weight = 63604.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.132716 restraints weight = 43166.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.132798 restraints weight = 39250.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.133066 restraints weight = 32599.474| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 27880 Z= 0.138 Angle : 0.695 15.541 37783 Z= 0.349 Chirality : 0.046 0.281 4446 Planarity : 0.004 0.059 4912 Dihedral : 6.615 108.304 3898 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.68 % Favored : 92.16 % Rotamer: Outliers : 0.03 % Allowed : 0.68 % Favored : 99.29 % 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: -1.30 (0.14), residues: 3557 helix: 0.67 (0.14), residues: 1436 sheet: -2.70 (0.21), residues: 509 loop : -1.61 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 429 TYR 0.029 0.001 TYR A 445 PHE 0.032 0.002 PHE D 171 TRP 0.005 0.001 TRP e 15 HIS 0.008 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (27879) covalent geometry : angle 0.69470 / 0.35 (37781) SS BOND : bond 0.00255 / 0.13 ( 1) SS BOND : angle 2.85588 / 1.90 ( 2) hydrogen bonds : bond 0.03758 / 2.58 ( 1206) hydrogen bonds : angle 4.90678 / 3.39 ( 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 600 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 599 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6584 (pt0) REVERT: A 413 ARG cc_start: 0.7046 (tpp80) cc_final: 0.6676 (tpp80) REVERT: A 425 GLN cc_start: 0.6665 (pt0) cc_final: 0.5935 (pp30) REVERT: A 447 ASP cc_start: 0.6587 (t0) cc_final: 0.6123 (t0) REVERT: C 14 ARG cc_start: 0.5201 (mmm160) cc_final: 0.4893 (mpt-90) REVERT: C 53 LEU cc_start: 0.8914 (pp) cc_final: 0.8561 (pp) REVERT: C 149 THR cc_start: 0.8818 (p) cc_final: 0.8615 (p) REVERT: C 425 GLN cc_start: 0.7311 (tt0) cc_final: 0.7007 (tt0) REVERT: B 34 GLN cc_start: 0.8404 (tt0) cc_final: 0.8187 (tt0) REVERT: B 95 ILE cc_start: 0.8837 (mp) cc_final: 0.8584 (mt) REVERT: B 164 GLN cc_start: 0.9108 (pp30) cc_final: 0.8794 (pp30) REVERT: D 49 VAL cc_start: 0.9311 (t) cc_final: 0.9073 (t) REVERT: D 247 MET cc_start: 0.7330 (ttp) cc_final: 0.6882 (ttp) REVERT: D 306 MET cc_start: 0.8594 (tpp) cc_final: 0.8357 (tpp) REVERT: D 428 GLU cc_start: 0.7757 (pp20) cc_final: 0.7410 (pp20) REVERT: E 39 LYS cc_start: 0.7812 (mmtm) cc_final: 0.7462 (mmmm) REVERT: E 90 GLU cc_start: 0.7885 (tt0) cc_final: 0.7617 (tt0) REVERT: E 98 LEU cc_start: 0.8808 (mp) cc_final: 0.8594 (mt) REVERT: E 109 ARG cc_start: 0.7648 (mtm-85) cc_final: 0.7054 (mtm-85) REVERT: E 313 ILE cc_start: 0.8751 (mt) cc_final: 0.8520 (mt) REVERT: E 353 SER cc_start: 0.8892 (t) cc_final: 0.8485 (p) REVERT: F 71 ASN cc_start: 0.7661 (t0) cc_final: 0.7410 (t0) REVERT: F 86 THR cc_start: 0.7255 (p) cc_final: 0.6512 (p) REVERT: F 216 MET cc_start: 0.8095 (mmp) cc_final: 0.7644 (mmm) REVERT: F 415 GLU cc_start: 0.6371 (mm-30) cc_final: 0.5043 (tp30) REVERT: d 117 ASN cc_start: 0.7254 (t0) cc_final: 0.6917 (t0) REVERT: d 155 ILE cc_start: 0.7862 (tp) cc_final: 0.7599 (tp) REVERT: d 239 LYS cc_start: 0.6048 (mttt) cc_final: 0.5646 (ttpt) REVERT: g 264 LEU cc_start: 0.9187 (tp) cc_final: 0.8850 (tt) REVERT: e 1 MET cc_start: 0.4543 (ppp) cc_final: 0.4189 (ppp) REVERT: e 37 HIS cc_start: 0.7101 (t-90) cc_final: 0.6858 (t-90) outliers start: 1 outliers final: 1 residues processed: 599 average time/residue: 0.1735 time to fit residues: 169.7064 Evaluate side-chains 474 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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: 0.8980 chunk 254 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 338 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 41 optimal weight: 0.0270 chunk 96 optimal weight: 0.7980 chunk 210 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 346 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN B 434 GLN B 443 ASN ** 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 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.145605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.138755 restraints weight = 36643.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.133307 restraints weight = 60262.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.131904 restraints weight = 45566.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.132170 restraints weight = 41490.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132604 restraints weight = 33532.317| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27880 Z= 0.148 Angle : 0.705 15.052 37783 Z= 0.354 Chirality : 0.046 0.290 4446 Planarity : 0.005 0.059 4912 Dihedral : 6.572 108.302 3898 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.07 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -1.27 (0.14), residues: 3557 helix: 0.67 (0.14), residues: 1431 sheet: -2.68 (0.21), residues: 509 loop : -1.56 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 14 TYR 0.029 0.001 TYR F 475 PHE 0.023 0.002 PHE D 171 TRP 0.005 0.001 TRP e 15 HIS 0.008 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (27879) covalent geometry : angle 0.70517 / 0.35 (37781) SS BOND : bond 0.01139 / 0.60 ( 1) SS BOND : angle 2.10090 / 1.40 ( 2) hydrogen bonds : bond 0.03770 / 2.60 ( 1206) hydrogen bonds : angle 4.91618 / 3.40 ( 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 596 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 1.018 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: A 215 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6552 (pt0) REVERT: A 314 MET cc_start: 0.8352 (ttp) cc_final: 0.8018 (ttp) REVERT: A 413 ARG cc_start: 0.7028 (tpp80) cc_final: 0.6709 (tpp80) REVERT: A 425 GLN cc_start: 0.6743 (pt0) cc_final: 0.6068 (pp30) REVERT: C 14 ARG cc_start: 0.5220 (mmm160) cc_final: 0.4895 (mpt-90) REVERT: C 53 LEU cc_start: 0.8858 (pp) cc_final: 0.8545 (pp) REVERT: C 221 TYR cc_start: 0.8929 (p90) cc_final: 0.8626 (p90) REVERT: C 399 PHE cc_start: 0.8077 (m-10) cc_final: 0.7873 (m-10) REVERT: C 425 GLN cc_start: 0.7357 (tt0) cc_final: 0.7098 (tt0) REVERT: B 34 GLN cc_start: 0.8456 (tt0) cc_final: 0.8190 (tt0) REVERT: B 77 MET cc_start: 0.8395 (mmt) cc_final: 0.8139 (mmt) REVERT: B 95 ILE cc_start: 0.8852 (mp) cc_final: 0.8616 (mt) REVERT: B 164 GLN cc_start: 0.9090 (pp30) cc_final: 0.8785 (pp30) REVERT: D 49 VAL cc_start: 0.9328 (t) cc_final: 0.9058 (t) REVERT: D 247 MET cc_start: 0.7343 (ttp) cc_final: 0.6902 (ttp) REVERT: D 269 LEU cc_start: 0.8427 (mp) cc_final: 0.8175 (mp) REVERT: D 306 MET cc_start: 0.8541 (tpp) cc_final: 0.8332 (tpp) REVERT: D 343 PHE cc_start: 0.8657 (m-80) cc_final: 0.8205 (m-80) REVERT: E 89 MET cc_start: 0.8625 (mtt) cc_final: 0.8334 (mtt) REVERT: E 90 GLU cc_start: 0.7849 (tt0) cc_final: 0.7629 (tt0) REVERT: E 183 MET cc_start: 0.7969 (tpp) cc_final: 0.7693 (tpp) REVERT: E 313 ILE cc_start: 0.8749 (mt) cc_final: 0.8507 (mt) REVERT: F 86 THR cc_start: 0.7551 (p) cc_final: 0.7078 (p) REVERT: F 216 MET cc_start: 0.8132 (mmp) cc_final: 0.7652 (mmm) REVERT: F 415 GLU cc_start: 0.6324 (mm-30) cc_final: 0.5023 (tp30) REVERT: F 476 LEU cc_start: 0.8327 (mm) cc_final: 0.8121 (mm) REVERT: d 117 ASN cc_start: 0.7268 (t0) cc_final: 0.6873 (t0) REVERT: d 155 ILE cc_start: 0.7865 (tp) cc_final: 0.7582 (tp) REVERT: d 208 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6951 (ptp90) REVERT: d 239 LYS cc_start: 0.6065 (mttt) cc_final: 0.5760 (ttpt) REVERT: g 264 LEU cc_start: 0.9185 (tp) cc_final: 0.8671 (tt) REVERT: g 315 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6607 (tm-30) REVERT: e 1 MET cc_start: 0.4579 (ppp) cc_final: 0.4226 (ppp) REVERT: e 37 HIS cc_start: 0.7097 (t-90) cc_final: 0.6836 (t-90) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 0.1716 time to fit residues: 166.4694 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 : 1.258 ------------------------------------------------------------------------------- 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: 0.7980 chunk 150 optimal weight: 0.5980 chunk 279 optimal weight: 0.3980 chunk 245 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 323 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 389 GLN A 398 GLN B 186 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN F 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.146270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.139386 restraints weight = 36448.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.134003 restraints weight = 61107.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.132821 restraints weight = 49887.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.133055 restraints weight = 41848.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.134109 restraints weight = 33014.493| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27880 Z= 0.149 Angle : 0.717 15.263 37783 Z= 0.359 Chirality : 0.046 0.392 4446 Planarity : 0.005 0.065 4912 Dihedral : 6.534 108.562 3898 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.32 % Rotamer: Outliers : 0.07 % Allowed : 0.37 % Favored : 99.56 % 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: -1.22 (0.14), residues: 3557 helix: 0.75 (0.14), residues: 1422 sheet: -2.70 (0.20), residues: 517 loop : -1.54 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 172 TYR 0.029 0.001 TYR A 20 PHE 0.028 0.002 PHE D 171 TRP 0.005 0.001 TRP e 15 HIS 0.008 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (27879) covalent geometry : angle 0.71684 / 0.36 (37781) SS BOND : bond 0.00941 / 0.50 ( 1) SS BOND : angle 1.83530 / 1.22 ( 2) hydrogen bonds : bond 0.03766 / 2.59 ( 1206) hydrogen bonds : angle 4.93402 / 3.42 ( 3486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4714.55 seconds wall clock time: 82 minutes 33.39 seconds (4953.39 seconds total)