Starting phenix.real_space_refine on Mon Sep 14 03:18:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6voo_21271/09_2026/6voo_21271.cif Found real_map, /net/cci-nas-00/data/ceres_data/6voo_21271/09_2026/6voo_21271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6voo_21271/09_2026/6voo_21271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6voo_21271/09_2026/6voo_21271.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6voo_21271/09_2026/6voo_21271.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6voo_21271/09_2026/6voo_21271.cif" model { file = "/net/cci-nas-00/data/ceres_data/6voo_21271/09_2026/6voo_21271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6voo_21271/09_2026/6voo_21271.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 104 5.16 5 C 17295 2.51 5 N 4754 2.21 5 O 5382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 173 residue(s): 0.02s 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: 27551 Number of models: 1 Model: "" Number of chains: 15 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: "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: "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: "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: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2502 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} 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: "B" 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: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 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: 6.24, per 1000 atoms: 0.23 Number of scatterers: 27551 At special positions: 0 Unit cell: (171.639, 137.943, 131.625, 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 104 16.00 P 16 15.00 O 5382 8.00 N 4754 7.00 C 17295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6570 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 21 sheets defined 47.1% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 3.825A pdb=" N GLU A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.873A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix removed outlier: 3.874A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.795A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.624A pdb=" N ALA A 286 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.696A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.851A pdb=" N SER A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.900A pdb=" N ALA A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 404 through 421 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.547A pdb=" N TYR A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.627A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 505 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.727A pdb=" N ILE B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.595A 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 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.880A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.610A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.525A pdb=" N ALA B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.903A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.562A pdb=" N GLY B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.529A pdb=" N THR B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.661A pdb=" N SER B 363 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 373 through 397 removed outlier: 4.913A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.552A pdb=" N THR B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.823A pdb=" N GLU B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.744A pdb=" N ASN B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 469 through 480 removed outlier: 3.889A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 removed outlier: 4.174A pdb=" N LEU B 503 " --> pdb=" O GLU B 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 removed outlier: 4.390A pdb=" N SER C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.999A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.609A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) 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 372 removed outlier: 4.134A pdb=" N ALA C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 394 removed outlier: 3.955A pdb=" N LYS C 378 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 400 removed outlier: 4.508A pdb=" N GLN C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 400 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 418 Processing helix chain 'C' and resid 419 through 422 Processing helix chain 'C' and resid 430 through 444 Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 469 through 479 removed outlier: 4.141A pdb=" N GLN C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 503 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'D' and resid 205 through 220 Processing helix chain 'D' and resid 242 through 263 removed outlier: 3.765A pdb=" N ARG D 246 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 289 removed outlier: 3.581A pdb=" N VAL D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 311 removed outlier: 3.598A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 336 through 346 removed outlier: 4.544A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 359 Processing helix chain 'D' and resid 381 through 401 Processing helix chain 'D' and resid 401 through 408 Processing helix chain 'D' and resid 409 through 413 removed outlier: 3.758A pdb=" N GLU D 412 " --> pdb=" O GLY D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 450 through 463 Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 480 through 494 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 178 through 193 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 242 through 263 removed outlier: 5.359A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 290 removed outlier: 3.811A pdb=" N PHE E 278 " --> pdb=" O ASN E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 removed outlier: 3.681A pdb=" N LEU E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 333 Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 381 through 408 removed outlier: 5.098A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 removed outlier: 3.595A pdb=" N LEU E 413 " --> pdb=" O LEU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 450 through 463 Processing helix chain 'E' and resid 470 through 474 removed outlier: 3.684A pdb=" N ALA E 473 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 496 removed outlier: 3.731A pdb=" N SER E 494 " --> pdb=" O LEU E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 178 through 190 Processing helix chain 'F' and resid 205 through 219 removed outlier: 3.507A pdb=" N GLY F 209 " --> pdb=" O ARG F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.508A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 287 removed outlier: 3.730A pdb=" N GLY F 282 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 313 removed outlier: 3.789A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 336 through 344 removed outlier: 4.151A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 358 Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 401 Processing helix chain 'F' and resid 401 through 407 removed outlier: 3.525A pdb=" N ILE F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 432 removed outlier: 3.542A pdb=" N LEU F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER F 432 " --> pdb=" O GLU F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 462 Processing helix chain 'F' and resid 470 through 475 removed outlier: 3.531A pdb=" N TYR F 475 " --> pdb=" O GLN F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 496 Processing helix chain 'd' and resid 73 through 89 removed outlier: 4.013A pdb=" N THR d 89 " --> pdb=" O VAL d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 107 removed outlier: 3.711A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 116 removed outlier: 4.172A pdb=" N TYR d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 137 removed outlier: 3.531A pdb=" N VAL d 128 " --> pdb=" O ASN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 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 173 removed outlier: 4.328A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL d 168 " --> pdb=" O GLU d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 203 Processing helix chain 'd' and resid 237 through 249 Processing helix chain 'g' and resid 43 through 99 Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 132 through 152 removed outlier: 3.945A pdb=" N LYS g 150 " --> pdb=" O ALA g 146 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 171 Processing helix chain 'g' and resid 188 through 204 removed outlier: 3.658A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 246 through 251 removed outlier: 3.555A pdb=" N ALA g 249 " --> pdb=" O CYS g 246 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA g 250 " --> pdb=" O VAL g 247 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU g 251 " --> pdb=" O ASP g 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 246 through 251' Processing helix chain 'g' and resid 287 through 363 removed outlier: 3.841A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix Processing helix chain 'e' and resid 88 through 106 removed outlier: 3.731A pdb=" N ALA e 92 " --> pdb=" O ASP e 88 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE e 98 " --> pdb=" O GLN e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 130 removed outlier: 3.605A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR e 124 " --> pdb=" O ARG e 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.084A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU F 90 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.738A pdb=" N CYS A 194 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 167 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU A 345 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 169 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 67 removed outlier: 4.135A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA D 46 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN D 45 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 removed outlier: 4.620A pdb=" N ARG B 128 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.076A pdb=" N ILE B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 261 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 167 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 90 through 93 removed outlier: 6.978A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL d 233 " --> pdb=" O ILE d 223 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET d 235 " --> pdb=" O PHE d 221 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE d 221 " --> pdb=" O MET d 235 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 90 through 93 removed outlier: 6.774A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.639A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.731A pdb=" N ILE C 199 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU C 345 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE C 169 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB2, first strand: chain 'D' and resid 110 through 111 removed outlier: 3.597A pdb=" N ALA D 233 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 273 " --> pdb=" O GLY D 200 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE D 168 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL D 327 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU D 170 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AB4, first strand: chain 'E' and resid 110 through 111 removed outlier: 6.231A pdb=" N PHE E 111 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N GLN E 238 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL E 268 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE E 324 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU E 270 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ALA E 326 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE E 272 " --> pdb=" O ALA E 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 148 through 149 removed outlier: 4.463A pdb=" N TYR E 162 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'F' and resid 110 through 111 removed outlier: 3.573A pdb=" N TYR F 236 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL F 198 " --> pdb=" O PHE F 271 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE F 168 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL F 327 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU F 170 " --> pdb=" O VAL F 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'g' and resid 157 through 159 removed outlier: 6.293A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 256 through 259 Processing sheet with id=AC1, first strand: chain 'e' and resid 13 through 15 removed outlier: 6.912A pdb=" N VAL e 7 " --> pdb=" O ILE e 14 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS e 6 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY e 65 " --> pdb=" O VAL e 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 22 through 24 removed outlier: 3.903A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 48 through 52 1369 hydrogen bonds defined for protein. 3963 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: 6.14 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4830 1.32 - 1.44: 6493 1.44 - 1.57: 16390 1.57 - 1.69: 26 1.69 - 1.81: 197 Bond restraints: 27936 Sorted by residual: bond pdb=" C4 ATP D 502 " pdb=" C5 ATP D 502 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.05e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.68e+01 ... (remaining 27931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.83: 37742 4.83 - 9.66: 111 9.66 - 14.49: 7 14.49 - 19.32: 3 19.32 - 24.15: 2 Bond angle restraints: 37865 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 115.72 24.15 1.00e+00 1.00e+00 5.83e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 122.14 17.73 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 124.07 15.80 1.00e+00 1.00e+00 2.50e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 122.09 14.74 1.00e+00 1.00e+00 2.17e+02 ... (remaining 37860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.00: 16292 28.00 - 56.00: 687 56.00 - 84.00: 71 84.00 - 112.00: 15 112.00 - 140.00: 1 Dihedral angle restraints: 17066 sinusoidal: 6830 harmonic: 10236 Sorted by residual: 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 -135.50 -44.50 0 5.00e+00 4.00e-02 7.92e+01 dihedral pdb=" CA LEU g 129 " pdb=" C LEU g 129 " pdb=" N CYS g 130 " pdb=" CA CYS g 130 " ideal model delta harmonic sigma weight residual 180.00 137.65 42.35 0 5.00e+00 4.00e-02 7.17e+01 dihedral pdb=" CA LYS g 116 " pdb=" C LYS g 116 " pdb=" N LYS g 117 " pdb=" CA LYS g 117 " ideal model delta harmonic sigma weight residual 180.00 144.24 35.76 0 5.00e+00 4.00e-02 5.12e+01 ... (remaining 17063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4001 0.083 - 0.165: 437 0.165 - 0.248: 12 0.248 - 0.331: 0 0.331 - 0.413: 1 Chirality restraints: 4451 Sorted by residual: chirality pdb=" C9 TTX D 501 " pdb=" C10 TTX D 501 " pdb=" C8 TTX D 501 " pdb=" N3 TTX D 501 " both_signs ideal model delta sigma weight residual False -2.28 -2.69 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB VAL F 380 " pdb=" CA VAL F 380 " pdb=" CG1 VAL F 380 " pdb=" CG2 VAL F 380 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ASN D 479 " pdb=" N ASN D 479 " pdb=" C ASN D 479 " pdb=" CB ASN D 479 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4448 not shown) Planarity restraints: 4918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 176 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LYS B 176 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS B 176 " -0.022 2.00e-02 2.50e+03 pdb=" N THR B 177 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 178 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS F 178 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS F 178 " -0.021 2.00e-02 2.50e+03 pdb=" N THR F 179 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU g 296 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.62e+00 pdb=" N PRO g 297 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO g 297 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO g 297 " -0.033 5.00e-02 4.00e+02 ... (remaining 4915 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1056 2.71 - 3.26: 28306 3.26 - 3.80: 46181 3.80 - 4.35: 60431 4.35 - 4.90: 100661 Nonbonded interactions: 236635 Sorted by model distance: nonbonded pdb=" OG1 THR C 228 " pdb=" OD1 ASP C 230 " model vdw 2.159 3.040 nonbonded pdb=" OH TYR C 464 " pdb=" OE1 GLU C 496 " model vdw 2.186 3.040 nonbonded pdb=" O ALA F 295 " pdb=" N GLY F 297 " model vdw 2.187 3.120 nonbonded pdb=" O ALA C 218 " pdb=" OG1 THR C 222 " model vdw 2.218 3.040 nonbonded pdb=" O ILE C 475 " pdb=" OG1 THR C 479 " model vdw 2.218 3.040 ... (remaining 236630 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 601)) selection = (chain 'B' and resid 6 through 601) selection = (chain 'C' and (resid 6 through 503 or resid 601)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 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: 0.060 Process input model: 26.610 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.006 0.093 27936 Z= 0.315 Angle : 0.857 24.149 37865 Z= 0.529 Chirality : 0.050 0.413 4451 Planarity : 0.005 0.059 4918 Dihedral : 15.270 140.000 10496 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.21 % Favored : 93.64 % Rotamer: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.76 (0.12), residues: 3556 helix: -1.18 (0.12), residues: 1482 sheet: -2.05 (0.18), residues: 629 loop : -2.29 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 107 TYR 0.018 0.002 TYR B 457 PHE 0.036 0.002 PHE C 482 TRP 0.007 0.001 TRP e 15 HIS 0.005 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.31 (27936) covalent geometry : angle 0.85750 / 0.53 (37865) hydrogen bonds : bond 0.15384 / 10.14 ( 1360) hydrogen bonds : angle 6.94865 / 4.86 ( 3963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 736 time to evaluate : 1.079 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 63 ILE cc_start: 0.8286 (mt) cc_final: 0.7989 (mt) REVERT: A 290 ASP cc_start: 0.7611 (p0) cc_final: 0.7316 (p0) REVERT: A 330 TYR cc_start: 0.8181 (t80) cc_final: 0.7861 (t80) REVERT: B 20 TYR cc_start: 0.6032 (t80) cc_final: 0.5774 (t80) REVERT: B 58 GLU cc_start: 0.7066 (tt0) cc_final: 0.6796 (tp30) REVERT: B 260 ILE cc_start: 0.8964 (mt) cc_final: 0.8668 (mt) REVERT: B 359 ASN cc_start: 0.7846 (t0) cc_final: 0.7262 (t0) REVERT: B 378 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7454 (mtmt) REVERT: B 419 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6560 (mp0) REVERT: B 453 GLN cc_start: 0.8000 (mt0) cc_final: 0.7573 (mt0) REVERT: B 474 GLU cc_start: 0.6840 (tp30) cc_final: 0.6388 (mm-30) REVERT: B 498 MET cc_start: 0.7030 (tpt) cc_final: 0.4959 (tmm) REVERT: C 90 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7563 (pptt) REVERT: C 155 ASP cc_start: 0.8324 (m-30) cc_final: 0.8113 (m-30) REVERT: C 402 ASP cc_start: 0.7463 (p0) cc_final: 0.6989 (p0) REVERT: C 456 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7820 (tppt) REVERT: D 22 ARG cc_start: 0.7776 (mmt-90) cc_final: 0.7540 (mpt180) REVERT: D 32 ASP cc_start: 0.8019 (p0) cc_final: 0.7761 (p0) REVERT: D 59 MET cc_start: 0.5518 (mpp) cc_final: 0.5272 (mpp) REVERT: D 92 ILE cc_start: 0.8169 (mt) cc_final: 0.7891 (pt) REVERT: D 229 GLU cc_start: 0.7583 (pp20) cc_final: 0.7287 (pp20) REVERT: D 231 LYS cc_start: 0.8222 (mptt) cc_final: 0.7940 (mtmt) REVERT: D 258 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7874 (mt-10) REVERT: D 306 MET cc_start: 0.7974 (tpp) cc_final: 0.7755 (tpp) REVERT: D 401 LEU cc_start: 0.8452 (pp) cc_final: 0.8127 (pp) REVERT: E 31 LEU cc_start: 0.8210 (mt) cc_final: 0.7835 (mt) REVERT: E 184 GLU cc_start: 0.7618 (tp30) cc_final: 0.7357 (tp30) REVERT: E 275 ILE cc_start: 0.8661 (tp) cc_final: 0.8439 (tt) REVERT: E 292 MET cc_start: 0.7955 (ttm) cc_final: 0.7543 (ttm) REVERT: E 328 TYR cc_start: 0.8228 (t80) cc_final: 0.7992 (t80) REVERT: E 397 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7094 (tpp-160) REVERT: E 398 TYR cc_start: 0.8265 (t80) cc_final: 0.7821 (t80) REVERT: F 66 GLN cc_start: 0.7962 (mm110) cc_final: 0.7630 (mm-40) REVERT: F 71 ASN cc_start: 0.6925 (t0) cc_final: 0.6574 (t0) REVERT: F 241 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7456 (mm-30) REVERT: F 248 ARG cc_start: 0.7129 (mmt-90) cc_final: 0.6814 (mmt-90) REVERT: g 71 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8105 (mtpt) REVERT: g 113 ARG cc_start: 0.5101 (ttp-170) cc_final: 0.4535 (ttp-170) REVERT: g 139 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6746 (mtmt) REVERT: g 163 LYS cc_start: 0.8165 (mmpt) cc_final: 0.7853 (mmtm) REVERT: g 178 ARG cc_start: 0.7060 (tpp80) cc_final: 0.6604 (tpp80) REVERT: g 211 GLU cc_start: 0.6964 (pm20) cc_final: 0.6478 (pm20) REVERT: g 214 TYR cc_start: 0.8303 (p90) cc_final: 0.7625 (p90) REVERT: g 306 ARG cc_start: 0.7651 (tpt-90) cc_final: 0.6940 (tpp-160) REVERT: g 309 GLN cc_start: 0.7807 (mt0) cc_final: 0.7209 (mt0) REVERT: g 353 ILE cc_start: 0.8867 (mt) cc_final: 0.8302 (pt) REVERT: e 4 ASN cc_start: 0.3766 (t0) cc_final: 0.3466 (t0) REVERT: e 110 ARG cc_start: 0.5655 (ptm-80) cc_final: 0.5356 (ptm-80) REVERT: e 125 ARG cc_start: 0.7076 (ttm170) cc_final: 0.6673 (ttp80) outliers start: 1 outliers final: 1 residues processed: 737 average time/residue: 0.2296 time to fit residues: 251.3953 Evaluate side-chains 618 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 617 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 237 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN A 190 GLN A 201 GLN A 351 ASN A 408 GLN A 410 GLN A 415 GLN A 423 GLN A 434 GLN A 468 ASN B 71 ASN B 148 GLN B 186 ASN B 208 GLN B 425 GLN B 453 GLN B 497 GLN C 34 GLN C 186 ASN C 342 GLN C 415 GLN C 423 GLN D 25 GLN D 60 ASN D 67 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN D 402 GLN E 45 ASN E 66 GLN E 225 GLN F 25 GLN F 71 ASN F 120 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN F 376 GLN F 489 ASN d 147 ASN g 76 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN g 346 GLN ** g 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124626 restraints weight = 35794.214| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.76 r_work: 0.3339 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27936 Z= 0.202 Angle : 0.669 12.493 37865 Z= 0.344 Chirality : 0.046 0.183 4451 Planarity : 0.005 0.064 4918 Dihedral : 6.601 130.786 3914 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.91 % Favored : 93.98 % Rotamer: Outliers : 1.60 % Allowed : 13.09 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.13), residues: 3556 helix: 0.03 (0.13), residues: 1497 sheet: -1.62 (0.19), residues: 645 loop : -1.84 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 94 TYR 0.017 0.002 TYR C 464 PHE 0.020 0.001 PHE D 458 TRP 0.006 0.001 TRP e 15 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (27936) covalent geometry : angle 0.66902 / 0.34 (37865) hydrogen bonds : bond 0.04867 / 3.36 ( 1360) hydrogen bonds : angle 5.41953 / 3.76 ( 3963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 634 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8678 (p) cc_final: 0.8129 (m) REVERT: A 141 ARG cc_start: 0.8296 (ttt90) cc_final: 0.8015 (ttm170) REVERT: A 266 LYS cc_start: 0.7410 (mttp) cc_final: 0.7137 (mttp) REVERT: B 20 TYR cc_start: 0.6102 (t80) cc_final: 0.5831 (t80) REVERT: B 41 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7872 (mtt-85) REVERT: B 68 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7967 (mt-10) REVERT: B 77 MET cc_start: 0.8309 (mmm) cc_final: 0.8064 (mmp) REVERT: B 260 ILE cc_start: 0.9055 (mt) cc_final: 0.8801 (mp) REVERT: B 359 ASN cc_start: 0.8291 (t0) cc_final: 0.7807 (t0) REVERT: B 378 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7616 (mtmt) REVERT: B 387 LEU cc_start: 0.7926 (mt) cc_final: 0.7638 (mt) REVERT: B 450 GLU cc_start: 0.6643 (mp0) cc_final: 0.6235 (mp0) REVERT: B 453 GLN cc_start: 0.8064 (mt0) cc_final: 0.7491 (mt0) REVERT: B 498 MET cc_start: 0.6946 (tpt) cc_final: 0.4954 (tmm) REVERT: C 85 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7586 (tm-30) REVERT: C 90 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7810 (pptt) REVERT: C 155 ASP cc_start: 0.8421 (m-30) cc_final: 0.8210 (m-30) REVERT: C 321 GLU cc_start: 0.8021 (tt0) cc_final: 0.7749 (tt0) REVERT: C 402 ASP cc_start: 0.7464 (p0) cc_final: 0.7032 (p0) REVERT: C 456 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8036 (tppt) REVERT: D 20 LEU cc_start: 0.7702 (mt) cc_final: 0.7455 (tp) REVERT: D 22 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.8032 (mpt180) REVERT: D 59 MET cc_start: 0.6072 (mpp) cc_final: 0.5724 (mpp) REVERT: D 92 ILE cc_start: 0.8500 (mt) cc_final: 0.8296 (pt) REVERT: D 134 ARG cc_start: 0.8123 (ptm-80) cc_final: 0.7414 (ptp-110) REVERT: D 216 MET cc_start: 0.8307 (mmm) cc_final: 0.8087 (mtt) REVERT: D 231 LYS cc_start: 0.8564 (mptt) cc_final: 0.8282 (mtpt) REVERT: D 311 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7946 (mm-30) REVERT: D 366 ASP cc_start: 0.8289 (t0) cc_final: 0.7891 (t0) REVERT: D 369 ASP cc_start: 0.7146 (m-30) cc_final: 0.6889 (m-30) REVERT: E 31 LEU cc_start: 0.8315 (mt) cc_final: 0.7928 (mt) REVERT: E 47 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8461 (pp) REVERT: E 162 TYR cc_start: 0.8043 (m-10) cc_final: 0.7817 (m-10) REVERT: E 184 GLU cc_start: 0.8262 (tp30) cc_final: 0.8057 (tp30) REVERT: E 328 TYR cc_start: 0.8563 (t80) cc_final: 0.8319 (t80) REVERT: E 333 ASP cc_start: 0.7967 (p0) cc_final: 0.7675 (p0) REVERT: E 378 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7211 (ptt-90) REVERT: E 382 GLU cc_start: 0.7132 (tp30) cc_final: 0.6866 (tp30) REVERT: E 397 ARG cc_start: 0.7925 (tpp80) cc_final: 0.7532 (tpp-160) REVERT: E 398 TYR cc_start: 0.8581 (t80) cc_final: 0.8236 (t80) REVERT: F 22 ARG cc_start: 0.8409 (mmt90) cc_final: 0.8090 (mmm-85) REVERT: F 64 GLU cc_start: 0.8277 (tt0) cc_final: 0.8021 (tt0) REVERT: F 71 ASN cc_start: 0.7431 (t0) cc_final: 0.6999 (t0) REVERT: F 214 MET cc_start: 0.8178 (mmt) cc_final: 0.7936 (mmm) REVERT: F 248 ARG cc_start: 0.7947 (mmt-90) cc_final: 0.7728 (mmt-90) REVERT: F 359 LYS cc_start: 0.8394 (ptpp) cc_final: 0.8012 (mtmm) REVERT: F 428 GLU cc_start: 0.7977 (tt0) cc_final: 0.7513 (tt0) REVERT: d 112 TYR cc_start: 0.6172 (t80) cc_final: 0.5892 (t80) REVERT: g 71 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8411 (mtpt) REVERT: g 139 LYS cc_start: 0.7559 (ttmt) cc_final: 0.7177 (mtmt) REVERT: g 163 LYS cc_start: 0.8452 (mmpt) cc_final: 0.8204 (mmtm) REVERT: g 211 GLU cc_start: 0.7183 (pm20) cc_final: 0.6783 (pm20) REVERT: g 214 TYR cc_start: 0.8372 (p90) cc_final: 0.7742 (p90) REVERT: g 260 LYS cc_start: 0.6637 (tppt) cc_final: 0.6407 (ttpp) REVERT: g 306 ARG cc_start: 0.8252 (tpt-90) cc_final: 0.7502 (tpp-160) REVERT: g 353 ILE cc_start: 0.8822 (mt) cc_final: 0.8400 (pt) REVERT: e 60 LEU cc_start: 0.6219 (tt) cc_final: 0.5465 (mm) REVERT: e 117 LEU cc_start: 0.7326 (tp) cc_final: 0.6846 (tt) REVERT: e 125 ARG cc_start: 0.7075 (ttm170) cc_final: 0.6639 (ttp80) outliers start: 47 outliers final: 28 residues processed: 657 average time/residue: 0.2257 time to fit residues: 221.4041 Evaluate side-chains 630 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 600 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 378 ARG Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 287 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 175 optimal weight: 0.9980 chunk 110 optimal weight: 0.3980 chunk 162 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 326 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 201 GLN A 212 ASN C 28 ASN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126976 restraints weight = 35713.385| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.72 r_work: 0.3293 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27936 Z= 0.163 Angle : 0.625 11.061 37865 Z= 0.319 Chirality : 0.045 0.189 4451 Planarity : 0.004 0.052 4918 Dihedral : 6.313 122.502 3914 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.26 % Favored : 94.63 % Rotamer: Outliers : 2.52 % Allowed : 15.43 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.92 (0.14), residues: 3556 helix: 0.68 (0.13), residues: 1488 sheet: -1.36 (0.19), residues: 641 loop : -1.57 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 104 TYR 0.018 0.001 TYR C 464 PHE 0.025 0.001 PHE B 390 TRP 0.004 0.001 TRP e 15 HIS 0.006 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (27936) covalent geometry : angle 0.62503 / 0.32 (37865) hydrogen bonds : bond 0.04370 / 3.01 ( 1360) hydrogen bonds : angle 5.10096 / 3.54 ( 3963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 621 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8609 (mp) cc_final: 0.8331 (mp) REVERT: A 141 ARG cc_start: 0.8274 (ttt90) cc_final: 0.8066 (ttt-90) REVERT: A 266 LYS cc_start: 0.7308 (mttp) cc_final: 0.6974 (mttp) REVERT: B 20 TYR cc_start: 0.6052 (t80) cc_final: 0.5800 (t80) REVERT: B 41 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7816 (mtt-85) REVERT: B 68 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7829 (mt-10) REVERT: B 260 ILE cc_start: 0.9064 (mt) cc_final: 0.8771 (mp) REVERT: B 355 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6338 (tpt170) REVERT: B 359 ASN cc_start: 0.8267 (t0) cc_final: 0.7710 (t0) REVERT: B 378 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7452 (mtmt) REVERT: B 384 LYS cc_start: 0.7060 (tmtt) cc_final: 0.6783 (tptt) REVERT: B 387 LEU cc_start: 0.7958 (mt) cc_final: 0.7568 (mt) REVERT: B 450 GLU cc_start: 0.6716 (mp0) cc_final: 0.6344 (tp30) REVERT: B 498 MET cc_start: 0.6930 (tpt) cc_final: 0.4870 (tmm) REVERT: C 85 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7690 (tm-30) REVERT: C 90 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7716 (pptt) REVERT: C 321 GLU cc_start: 0.8025 (tt0) cc_final: 0.7729 (tt0) REVERT: C 402 ASP cc_start: 0.7596 (p0) cc_final: 0.7185 (p0) REVERT: C 456 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7890 (tppt) REVERT: C 483 THR cc_start: 0.7309 (m) cc_final: 0.7063 (p) REVERT: D 22 ARG cc_start: 0.8278 (mmt-90) cc_final: 0.7952 (mpt180) REVERT: D 59 MET cc_start: 0.6025 (mpp) cc_final: 0.5667 (mpp) REVERT: D 92 ILE cc_start: 0.8545 (mt) cc_final: 0.8273 (pt) REVERT: D 262 ASP cc_start: 0.8333 (m-30) cc_final: 0.8032 (m-30) REVERT: D 311 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8013 (mm-30) REVERT: D 369 ASP cc_start: 0.7162 (m-30) cc_final: 0.6903 (m-30) REVERT: D 401 LEU cc_start: 0.8306 (pp) cc_final: 0.7434 (mt) REVERT: D 481 ASP cc_start: 0.7801 (p0) cc_final: 0.7592 (p0) REVERT: E 47 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8404 (pp) REVERT: E 145 LYS cc_start: 0.7953 (tptt) cc_final: 0.7585 (tptt) REVERT: E 184 GLU cc_start: 0.8278 (tp30) cc_final: 0.7985 (tp30) REVERT: E 333 ASP cc_start: 0.7934 (p0) cc_final: 0.7660 (p0) REVERT: E 397 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7442 (tpp-160) REVERT: E 398 TYR cc_start: 0.8487 (t80) cc_final: 0.8187 (t80) REVERT: F 22 ARG cc_start: 0.8412 (mmt90) cc_final: 0.7989 (mmm-85) REVERT: F 44 TYR cc_start: 0.8513 (m-10) cc_final: 0.8094 (m-10) REVERT: F 64 GLU cc_start: 0.8265 (tt0) cc_final: 0.7994 (tt0) REVERT: F 71 ASN cc_start: 0.7515 (t0) cc_final: 0.7083 (t0) REVERT: F 214 MET cc_start: 0.8053 (mmt) cc_final: 0.7763 (mmm) REVERT: F 248 ARG cc_start: 0.7960 (mmt-90) cc_final: 0.7631 (mmt-90) REVERT: F 359 LYS cc_start: 0.8391 (ptpp) cc_final: 0.8060 (mtmm) REVERT: F 428 GLU cc_start: 0.7959 (tt0) cc_final: 0.7491 (tt0) REVERT: d 103 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6283 (mt) REVERT: d 176 GLU cc_start: 0.5458 (mm-30) cc_final: 0.5174 (mp0) REVERT: g 76 GLN cc_start: 0.6956 (tt0) cc_final: 0.6524 (tt0) REVERT: g 139 LYS cc_start: 0.7325 (ttmt) cc_final: 0.6921 (mtmt) REVERT: g 163 LYS cc_start: 0.8241 (mmpt) cc_final: 0.7938 (mmtm) REVERT: g 214 TYR cc_start: 0.8207 (p90) cc_final: 0.7550 (p90) REVERT: g 353 ILE cc_start: 0.8807 (mt) cc_final: 0.8311 (pt) REVERT: e 60 LEU cc_start: 0.6178 (tt) cc_final: 0.5518 (mm) REVERT: e 110 ARG cc_start: 0.5451 (ptm-80) cc_final: 0.5160 (ptm-80) REVERT: e 125 ARG cc_start: 0.7033 (ttm170) cc_final: 0.6573 (ttp80) outliers start: 74 outliers final: 46 residues processed: 664 average time/residue: 0.2217 time to fit residues: 221.5975 Evaluate side-chains 646 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 597 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 231 LYS Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 287 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 174 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 221 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN B 201 GLN C 28 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 325 ASN ** g 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124500 restraints weight = 35780.240| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.70 r_work: 0.3350 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27936 Z= 0.170 Angle : 0.626 10.978 37865 Z= 0.319 Chirality : 0.045 0.202 4451 Planarity : 0.004 0.054 4918 Dihedral : 6.228 118.305 3914 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 2.86 % Allowed : 16.28 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.67 (0.14), residues: 3556 helix: 0.88 (0.13), residues: 1492 sheet: -1.26 (0.20), residues: 654 loop : -1.42 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 425 TYR 0.021 0.002 TYR d 112 PHE 0.016 0.001 PHE E 441 TRP 0.002 0.001 TRP e 15 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (27936) covalent geometry : angle 0.62638 / 0.32 (37865) hydrogen bonds : bond 0.04271 / 2.95 ( 1360) hydrogen bonds : angle 4.99885 / 3.47 ( 3963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 622 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.7335 (mttp) cc_final: 0.7048 (mttp) REVERT: B 20 TYR cc_start: 0.6065 (t80) cc_final: 0.5825 (t80) REVERT: B 41 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7982 (mtt-85) REVERT: B 68 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8012 (mt-10) REVERT: B 77 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7793 (mmp) REVERT: B 94 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7798 (mtm110) REVERT: B 260 ILE cc_start: 0.9036 (mt) cc_final: 0.8753 (mp) REVERT: B 359 ASN cc_start: 0.8236 (t0) cc_final: 0.7797 (t0) REVERT: B 378 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7564 (mtmt) REVERT: B 384 LYS cc_start: 0.7095 (tmtt) cc_final: 0.6873 (tptt) REVERT: B 387 LEU cc_start: 0.8130 (mt) cc_final: 0.7708 (mt) REVERT: B 450 GLU cc_start: 0.6517 (mp0) cc_final: 0.6234 (tp30) REVERT: B 489 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5638 (pp) REVERT: B 498 MET cc_start: 0.6880 (tpt) cc_final: 0.4898 (tmm) REVERT: C 85 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7713 (tm-30) REVERT: C 155 ASP cc_start: 0.8305 (m-30) cc_final: 0.7980 (m-30) REVERT: C 262 ASP cc_start: 0.7496 (t0) cc_final: 0.7231 (t0) REVERT: C 402 ASP cc_start: 0.7513 (p0) cc_final: 0.7145 (p0) REVERT: C 456 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8048 (tppt) REVERT: D 22 ARG cc_start: 0.8284 (mmt-90) cc_final: 0.7942 (mmt180) REVERT: D 59 MET cc_start: 0.6020 (mpp) cc_final: 0.5692 (mpp) REVERT: D 92 ILE cc_start: 0.8514 (mt) cc_final: 0.8306 (pt) REVERT: D 311 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7961 (mm-30) REVERT: D 369 ASP cc_start: 0.7247 (m-30) cc_final: 0.7013 (m-30) REVERT: D 401 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7544 (mt) REVERT: E 47 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8433 (pp) REVERT: E 184 GLU cc_start: 0.8284 (tp30) cc_final: 0.8046 (tp30) REVERT: E 333 ASP cc_start: 0.7918 (p0) cc_final: 0.7691 (p0) REVERT: E 397 ARG cc_start: 0.7908 (tpp80) cc_final: 0.7526 (tpp-160) REVERT: E 398 TYR cc_start: 0.8555 (t80) cc_final: 0.8273 (t80) REVERT: F 22 ARG cc_start: 0.8441 (mmt90) cc_final: 0.8099 (mmm-85) REVERT: F 44 TYR cc_start: 0.8509 (m-10) cc_final: 0.8083 (m-10) REVERT: F 71 ASN cc_start: 0.7411 (t0) cc_final: 0.6985 (t0) REVERT: F 214 MET cc_start: 0.8169 (mmt) cc_final: 0.7877 (mmm) REVERT: F 248 ARG cc_start: 0.7979 (mmt-90) cc_final: 0.7746 (mmt-90) REVERT: F 359 LYS cc_start: 0.8358 (ptpp) cc_final: 0.8083 (mtmm) REVERT: F 385 TYR cc_start: 0.8704 (t80) cc_final: 0.8492 (t80) REVERT: F 392 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8352 (tttm) REVERT: F 425 ARG cc_start: 0.8134 (mtp180) cc_final: 0.7925 (mtp85) REVERT: F 428 GLU cc_start: 0.7995 (tt0) cc_final: 0.7563 (tt0) REVERT: F 465 GLU cc_start: 0.7441 (pm20) cc_final: 0.7052 (mp0) REVERT: d 103 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6389 (mt) REVERT: d 112 TYR cc_start: 0.6127 (t80) cc_final: 0.5644 (t80) REVERT: d 159 LYS cc_start: 0.6931 (ttmt) cc_final: 0.6628 (ttmt) REVERT: d 176 GLU cc_start: 0.5600 (mm-30) cc_final: 0.5178 (mp0) REVERT: g 76 GLN cc_start: 0.7092 (tt0) cc_final: 0.6678 (tt0) REVERT: g 139 LYS cc_start: 0.7557 (ttmt) cc_final: 0.7090 (mtmt) REVERT: g 163 LYS cc_start: 0.8326 (mmpt) cc_final: 0.8077 (mmtm) REVERT: g 165 ASN cc_start: 0.7841 (p0) cc_final: 0.7599 (p0) REVERT: g 214 TYR cc_start: 0.8245 (p90) cc_final: 0.7546 (p90) REVERT: g 255 PHE cc_start: 0.6540 (p90) cc_final: 0.6258 (p90) REVERT: g 353 ILE cc_start: 0.8832 (mt) cc_final: 0.8381 (pt) REVERT: e 60 LEU cc_start: 0.6152 (tt) cc_final: 0.5466 (mm) REVERT: e 110 ARG cc_start: 0.5461 (ptm-80) cc_final: 0.5080 (ptm160) REVERT: e 125 ARG cc_start: 0.6970 (ttm170) cc_final: 0.6523 (ttp80) outliers start: 84 outliers final: 57 residues processed: 665 average time/residue: 0.2225 time to fit residues: 223.1355 Evaluate side-chains 652 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 590 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 231 LYS Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain g residue 287 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 308 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 324 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 326 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 chunk 147 optimal weight: 0.4980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 201 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125997 restraints weight = 35618.972| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.85 r_work: 0.3352 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27936 Z= 0.177 Angle : 0.629 11.091 37865 Z= 0.320 Chirality : 0.045 0.207 4451 Planarity : 0.004 0.055 4918 Dihedral : 6.199 116.242 3914 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 3.47 % Allowed : 17.17 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.54 (0.14), residues: 3556 helix: 0.98 (0.13), residues: 1495 sheet: -1.19 (0.20), residues: 642 loop : -1.35 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 22 TYR 0.018 0.002 TYR d 112 PHE 0.016 0.001 PHE E 441 TRP 0.002 0.001 TRP e 57 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (27936) covalent geometry : angle 0.62948 / 0.32 (37865) hydrogen bonds : bond 0.04266 / 2.95 ( 1360) hydrogen bonds : angle 4.94090 / 3.43 ( 3963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 613 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.7340 (mttp) cc_final: 0.7042 (mttp) REVERT: B 20 TYR cc_start: 0.6081 (t80) cc_final: 0.5852 (t80) REVERT: B 37 ASP cc_start: 0.5167 (OUTLIER) cc_final: 0.4436 (p0) REVERT: B 41 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7928 (mtt-85) REVERT: B 68 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7980 (mt-10) REVERT: B 77 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7759 (mmp) REVERT: B 260 ILE cc_start: 0.9033 (mt) cc_final: 0.8765 (mp) REVERT: B 378 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7549 (mtmt) REVERT: B 387 LEU cc_start: 0.8086 (mt) cc_final: 0.7663 (mt) REVERT: B 450 GLU cc_start: 0.6544 (mp0) cc_final: 0.6331 (tp30) REVERT: B 489 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5639 (pp) REVERT: B 498 MET cc_start: 0.6841 (tpt) cc_final: 0.4841 (tmm) REVERT: C 85 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 366 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7877 (mtm-85) REVERT: C 402 ASP cc_start: 0.7535 (p0) cc_final: 0.7166 (p0) REVERT: C 456 LYS cc_start: 0.8291 (ttpt) cc_final: 0.8015 (tppt) REVERT: D 59 MET cc_start: 0.6002 (mpp) cc_final: 0.5659 (mpp) REVERT: D 92 ILE cc_start: 0.8486 (mt) cc_final: 0.8260 (pt) REVERT: D 134 ARG cc_start: 0.8086 (ptm-80) cc_final: 0.7312 (ptp-110) REVERT: D 311 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7962 (mm-30) REVERT: D 401 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7526 (mt) REVERT: D 481 ASP cc_start: 0.7787 (p0) cc_final: 0.7577 (p0) REVERT: E 45 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8587 (t0) REVERT: E 47 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8422 (pp) REVERT: E 145 LYS cc_start: 0.7909 (tptt) cc_final: 0.7623 (tptt) REVERT: E 397 ARG cc_start: 0.7929 (tpp80) cc_final: 0.7544 (tpp-160) REVERT: E 398 TYR cc_start: 0.8538 (t80) cc_final: 0.8239 (t80) REVERT: F 22 ARG cc_start: 0.8419 (mmt90) cc_final: 0.8075 (mmm-85) REVERT: F 44 TYR cc_start: 0.8490 (m-10) cc_final: 0.8062 (m-10) REVERT: F 71 ASN cc_start: 0.7444 (t0) cc_final: 0.7012 (t0) REVERT: F 214 MET cc_start: 0.8132 (mmt) cc_final: 0.7846 (mmm) REVERT: F 248 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7757 (mmt-90) REVERT: F 359 LYS cc_start: 0.8355 (ptpp) cc_final: 0.8100 (mtmm) REVERT: F 428 GLU cc_start: 0.8007 (tt0) cc_final: 0.7580 (tt0) REVERT: F 465 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: d 103 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6413 (mt) REVERT: d 176 GLU cc_start: 0.5722 (mm-30) cc_final: 0.5289 (mp0) REVERT: g 76 GLN cc_start: 0.7056 (tt0) cc_final: 0.6637 (tt0) REVERT: g 139 LYS cc_start: 0.7547 (ttmt) cc_final: 0.7087 (mtmt) REVERT: g 163 LYS cc_start: 0.8334 (mmpt) cc_final: 0.8095 (mmtm) REVERT: g 165 ASN cc_start: 0.7862 (p0) cc_final: 0.7615 (p0) REVERT: g 173 GLU cc_start: 0.6305 (mp0) cc_final: 0.5937 (pm20) REVERT: g 205 GLU cc_start: 0.7171 (tp30) cc_final: 0.6786 (tp30) REVERT: g 214 TYR cc_start: 0.8246 (p90) cc_final: 0.7430 (p90) REVERT: g 353 ILE cc_start: 0.8834 (mt) cc_final: 0.8368 (pt) REVERT: e 60 LEU cc_start: 0.5765 (tt) cc_final: 0.5141 (mm) REVERT: e 104 ARG cc_start: 0.6659 (mpt180) cc_final: 0.5426 (tpp-160) REVERT: e 125 ARG cc_start: 0.7063 (ttm170) cc_final: 0.6568 (ttp80) outliers start: 102 outliers final: 70 residues processed: 667 average time/residue: 0.2181 time to fit residues: 220.3470 Evaluate side-chains 663 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 585 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 186 optimal weight: 0.0570 chunk 334 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 232 optimal weight: 0.0470 chunk 114 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN C 28 ASN D 389 GLN g 286 GLN e 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126848 restraints weight = 35670.368| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.79 r_work: 0.3366 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27936 Z= 0.134 Angle : 0.602 11.585 37865 Z= 0.305 Chirality : 0.044 0.220 4451 Planarity : 0.004 0.052 4918 Dihedral : 5.997 113.156 3914 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 3.20 % Allowed : 17.98 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.30 (0.14), residues: 3556 helix: 1.19 (0.14), residues: 1498 sheet: -1.08 (0.20), residues: 651 loop : -1.23 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 141 TYR 0.019 0.001 TYR d 225 PHE 0.016 0.001 PHE E 441 TRP 0.003 0.001 TRP e 15 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (27936) covalent geometry : angle 0.60216 / 0.31 (37865) hydrogen bonds : bond 0.03884 / 2.68 ( 1360) hydrogen bonds : angle 4.79477 / 3.33 ( 3963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 617 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8546 (p) cc_final: 0.8143 (m) REVERT: A 216 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7756 (mtt-85) REVERT: A 266 LYS cc_start: 0.7217 (mttp) cc_final: 0.6931 (mttp) REVERT: A 348 ASP cc_start: 0.7880 (m-30) cc_final: 0.7496 (m-30) REVERT: A 386 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 37 ASP cc_start: 0.5133 (OUTLIER) cc_final: 0.4350 (p0) REVERT: B 48 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8509 (p) REVERT: B 68 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7985 (mt-10) REVERT: B 77 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7872 (mmp) REVERT: B 94 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7839 (mtm110) REVERT: B 260 ILE cc_start: 0.9005 (mt) cc_final: 0.8723 (mp) REVERT: B 266 LYS cc_start: 0.7480 (tppt) cc_final: 0.7025 (tppt) REVERT: B 378 LYS cc_start: 0.7778 (mtpt) cc_final: 0.7501 (mtmt) REVERT: B 387 LEU cc_start: 0.7894 (mt) cc_final: 0.7644 (mt) REVERT: B 489 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5588 (pp) REVERT: B 498 MET cc_start: 0.6754 (tpt) cc_final: 0.4678 (tmm) REVERT: C 155 ASP cc_start: 0.8235 (m-30) cc_final: 0.7900 (m-30) REVERT: C 402 ASP cc_start: 0.7503 (p0) cc_final: 0.7143 (p0) REVERT: C 456 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7994 (tppt) REVERT: D 59 MET cc_start: 0.5924 (mpp) cc_final: 0.5633 (mpp) REVERT: D 311 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7934 (mm-30) REVERT: D 401 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7576 (mt) REVERT: D 481 ASP cc_start: 0.7712 (p0) cc_final: 0.7509 (p0) REVERT: E 47 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8403 (pp) REVERT: E 52 ARG cc_start: 0.6804 (ttm-80) cc_final: 0.6300 (mmm160) REVERT: E 397 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7485 (tpp-160) REVERT: E 398 TYR cc_start: 0.8522 (t80) cc_final: 0.8235 (t80) REVERT: E 453 GLU cc_start: 0.6827 (mp0) cc_final: 0.6562 (mp0) REVERT: F 22 ARG cc_start: 0.8396 (mmt90) cc_final: 0.8070 (mmm-85) REVERT: F 44 TYR cc_start: 0.8478 (m-10) cc_final: 0.8010 (m-10) REVERT: F 66 GLN cc_start: 0.8425 (mm110) cc_final: 0.8123 (mm110) REVERT: F 71 ASN cc_start: 0.7400 (t0) cc_final: 0.6990 (t0) REVERT: F 214 MET cc_start: 0.8175 (mmt) cc_final: 0.7878 (mmm) REVERT: F 359 LYS cc_start: 0.8257 (ptpp) cc_final: 0.8038 (mtmm) REVERT: F 385 TYR cc_start: 0.8661 (t80) cc_final: 0.8334 (t80) REVERT: F 392 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8341 (tttm) REVERT: F 428 GLU cc_start: 0.7963 (tt0) cc_final: 0.7540 (tt0) REVERT: d 95 THR cc_start: 0.7396 (t) cc_final: 0.7143 (p) REVERT: d 103 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6508 (mt) REVERT: d 176 GLU cc_start: 0.5699 (mm-30) cc_final: 0.5178 (mp0) REVERT: g 50 ARG cc_start: 0.7346 (tpt-90) cc_final: 0.7123 (tpt-90) REVERT: g 76 GLN cc_start: 0.7079 (tt0) cc_final: 0.6649 (tt0) REVERT: g 130 CYS cc_start: 0.5946 (m) cc_final: 0.5577 (m) REVERT: g 139 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7042 (mtmt) REVERT: g 163 LYS cc_start: 0.8296 (mmpt) cc_final: 0.8088 (mmtm) REVERT: g 165 ASN cc_start: 0.7869 (p0) cc_final: 0.7616 (p0) REVERT: g 214 TYR cc_start: 0.8203 (p90) cc_final: 0.7448 (p90) REVERT: g 353 ILE cc_start: 0.8821 (mt) cc_final: 0.8347 (pt) REVERT: e 58 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.4971 (mm) REVERT: e 60 LEU cc_start: 0.5909 (tt) cc_final: 0.5401 (mm) REVERT: e 104 ARG cc_start: 0.6668 (mpt180) cc_final: 0.5505 (tpp-160) REVERT: e 110 ARG cc_start: 0.5488 (ptm-80) cc_final: 0.4936 (ptm160) REVERT: e 125 ARG cc_start: 0.7044 (ttm170) cc_final: 0.6550 (ttp80) outliers start: 94 outliers final: 64 residues processed: 673 average time/residue: 0.2172 time to fit residues: 221.9807 Evaluate side-chains 664 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 592 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain g residue 286 GLN Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 244 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 334 optimal weight: 0.4980 chunk 345 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN B 28 ASN B 71 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN g 290 GLN e 27 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128134 restraints weight = 35428.393| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.86 r_work: 0.3337 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27936 Z= 0.166 Angle : 0.628 12.349 37865 Z= 0.318 Chirality : 0.045 0.254 4451 Planarity : 0.004 0.052 4918 Dihedral : 6.036 113.174 3914 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 3.37 % Allowed : 18.52 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.27 (0.14), residues: 3556 helix: 1.21 (0.14), residues: 1498 sheet: -1.05 (0.20), residues: 637 loop : -1.22 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 41 TYR 0.018 0.002 TYR C 464 PHE 0.017 0.001 PHE E 441 TRP 0.002 0.001 TRP e 57 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (27936) covalent geometry : angle 0.62819 / 0.32 (37865) hydrogen bonds : bond 0.04093 / 2.83 ( 1360) hydrogen bonds : angle 4.80844 / 3.34 ( 3963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 602 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8579 (p) cc_final: 0.8167 (m) REVERT: A 266 LYS cc_start: 0.7324 (mttp) cc_final: 0.7013 (mttp) REVERT: A 348 ASP cc_start: 0.7863 (m-30) cc_final: 0.7514 (m-30) REVERT: B 37 ASP cc_start: 0.5129 (OUTLIER) cc_final: 0.4330 (p0) REVERT: B 48 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8539 (p) REVERT: B 68 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7995 (mt-10) REVERT: B 77 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7905 (mmp) REVERT: B 260 ILE cc_start: 0.9035 (mt) cc_final: 0.8740 (mp) REVERT: B 266 LYS cc_start: 0.7496 (tppt) cc_final: 0.7043 (tppt) REVERT: B 378 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7537 (mtmt) REVERT: B 387 LEU cc_start: 0.7919 (mt) cc_final: 0.7635 (mt) REVERT: B 432 GLU cc_start: 0.6995 (pm20) cc_final: 0.6772 (pm20) REVERT: B 489 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5679 (pp) REVERT: B 498 MET cc_start: 0.6739 (tpt) cc_final: 0.4700 (tmm) REVERT: C 155 ASP cc_start: 0.8242 (m-30) cc_final: 0.7906 (m-30) REVERT: C 402 ASP cc_start: 0.7509 (p0) cc_final: 0.7154 (p0) REVERT: C 456 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8037 (tppt) REVERT: D 59 MET cc_start: 0.5942 (mpp) cc_final: 0.5652 (mpp) REVERT: D 311 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7970 (mm-30) REVERT: D 401 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7629 (mt) REVERT: D 481 ASP cc_start: 0.7713 (p0) cc_final: 0.7506 (p0) REVERT: E 47 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8416 (pp) REVERT: E 52 ARG cc_start: 0.6661 (ttm-80) cc_final: 0.6211 (mmm160) REVERT: E 145 LYS cc_start: 0.8006 (tptt) cc_final: 0.7715 (tptt) REVERT: E 397 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7513 (tpp-160) REVERT: E 398 TYR cc_start: 0.8554 (t80) cc_final: 0.8263 (t80) REVERT: E 453 GLU cc_start: 0.6861 (mp0) cc_final: 0.6556 (mp0) REVERT: F 22 ARG cc_start: 0.8429 (mmt90) cc_final: 0.8089 (mmm-85) REVERT: F 44 TYR cc_start: 0.8474 (m-10) cc_final: 0.7993 (m-10) REVERT: F 71 ASN cc_start: 0.7440 (t0) cc_final: 0.6995 (t0) REVERT: F 214 MET cc_start: 0.8182 (mmt) cc_final: 0.7884 (mmm) REVERT: F 359 LYS cc_start: 0.8313 (ptpp) cc_final: 0.8087 (mtmm) REVERT: F 428 GLU cc_start: 0.7973 (tt0) cc_final: 0.7569 (tt0) REVERT: F 465 GLU cc_start: 0.7355 (pm20) cc_final: 0.7105 (mp0) REVERT: d 103 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6541 (mt) REVERT: d 176 GLU cc_start: 0.5744 (mm-30) cc_final: 0.5189 (mp0) REVERT: d 250 MET cc_start: 0.0605 (ttt) cc_final: 0.0387 (ttt) REVERT: g 50 ARG cc_start: 0.7350 (tpt-90) cc_final: 0.7131 (tpt-90) REVERT: g 76 GLN cc_start: 0.7042 (tt0) cc_final: 0.6645 (tt0) REVERT: g 139 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7070 (mtmt) REVERT: g 163 LYS cc_start: 0.8319 (mmpt) cc_final: 0.8112 (mmtm) REVERT: g 165 ASN cc_start: 0.7844 (p0) cc_final: 0.7594 (p0) REVERT: g 173 GLU cc_start: 0.6445 (mp0) cc_final: 0.5883 (mp0) REVERT: g 214 TYR cc_start: 0.8197 (p90) cc_final: 0.7232 (p90) REVERT: g 286 GLN cc_start: 0.5558 (OUTLIER) cc_final: 0.3752 (tm-30) REVERT: g 290 GLN cc_start: 0.5489 (OUTLIER) cc_final: 0.4786 (tm-30) REVERT: g 353 ILE cc_start: 0.8826 (mt) cc_final: 0.8350 (pt) REVERT: e 60 LEU cc_start: 0.5803 (tt) cc_final: 0.5346 (mm) REVERT: e 104 ARG cc_start: 0.6717 (mpt180) cc_final: 0.5929 (mmm160) REVERT: e 110 ARG cc_start: 0.5482 (ptm-80) cc_final: 0.5261 (ptm-80) REVERT: e 125 ARG cc_start: 0.7089 (ttm170) cc_final: 0.6558 (ttp80) outliers start: 99 outliers final: 79 residues processed: 660 average time/residue: 0.2140 time to fit residues: 214.6079 Evaluate side-chains 675 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 587 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain g residue 286 GLN Chi-restraints excluded: chain g residue 290 GLN Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 100 GLU Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 319 optimal weight: 2.9990 chunk 256 optimal weight: 0.0000 chunk 163 optimal weight: 0.9980 chunk 343 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.0270 chunk 122 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 153 optimal weight: 0.0370 chunk 179 optimal weight: 2.9990 chunk 285 optimal weight: 0.5980 overall best weight: 0.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN B 273 GLN B 497 GLN C 389 GLN F 133 HIS F 389 GLN d 144 ASN g 286 GLN e 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131560 restraints weight = 35292.412| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.82 r_work: 0.3400 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27936 Z= 0.116 Angle : 0.595 12.436 37865 Z= 0.301 Chirality : 0.044 0.258 4451 Planarity : 0.004 0.045 4918 Dihedral : 5.816 110.633 3914 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.69 % Rotamer: Outliers : 2.62 % Allowed : 19.51 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.06 (0.14), residues: 3556 helix: 1.43 (0.14), residues: 1490 sheet: -1.03 (0.20), residues: 649 loop : -1.09 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 41 TYR 0.027 0.001 TYR B 237 PHE 0.016 0.001 PHE E 441 TRP 0.005 0.001 TRP e 15 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (27936) covalent geometry : angle 0.59493 / 0.30 (37865) hydrogen bonds : bond 0.03612 / 2.49 ( 1360) hydrogen bonds : angle 4.66509 / 3.24 ( 3963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 632 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8575 (p) cc_final: 0.8174 (m) REVERT: A 266 LYS cc_start: 0.7132 (mttp) cc_final: 0.6883 (mttp) REVERT: A 348 ASP cc_start: 0.7909 (m-30) cc_final: 0.7545 (m-30) REVERT: B 37 ASP cc_start: 0.5019 (OUTLIER) cc_final: 0.4245 (p0) REVERT: B 48 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8458 (p) REVERT: B 77 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7820 (mmp) REVERT: B 266 LYS cc_start: 0.7466 (tppt) cc_final: 0.7013 (tppt) REVERT: B 376 MET cc_start: 0.8925 (tpp) cc_final: 0.8497 (tpt) REVERT: B 378 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7516 (mtmt) REVERT: B 387 LEU cc_start: 0.7950 (mt) cc_final: 0.7675 (mt) REVERT: B 392 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6364 (pm20) REVERT: B 489 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5596 (pp) REVERT: B 495 GLN cc_start: 0.6930 (mt0) cc_final: 0.6632 (tm-30) REVERT: B 498 MET cc_start: 0.6678 (tpt) cc_final: 0.4710 (tmm) REVERT: C 90 LYS cc_start: 0.8176 (pttm) cc_final: 0.7948 (pptt) REVERT: C 155 ASP cc_start: 0.8215 (m-30) cc_final: 0.7890 (m-30) REVERT: C 402 ASP cc_start: 0.7420 (p0) cc_final: 0.7076 (p0) REVERT: C 456 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7994 (tppt) REVERT: D 225 GLN cc_start: 0.7358 (pm20) cc_final: 0.7038 (mp10) REVERT: D 311 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7840 (mm-30) REVERT: D 401 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7565 (mt) REVERT: D 481 ASP cc_start: 0.7730 (p0) cc_final: 0.7525 (p0) REVERT: E 47 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8310 (pp) REVERT: E 52 ARG cc_start: 0.6563 (ttm-80) cc_final: 0.6247 (mmm160) REVERT: E 145 LYS cc_start: 0.7982 (tptt) cc_final: 0.7711 (tptt) REVERT: E 328 TYR cc_start: 0.8513 (t80) cc_final: 0.8223 (t80) REVERT: E 397 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7446 (tpp-160) REVERT: E 398 TYR cc_start: 0.8522 (t80) cc_final: 0.8247 (t80) REVERT: E 453 GLU cc_start: 0.6858 (mp0) cc_final: 0.6513 (mp0) REVERT: F 22 ARG cc_start: 0.8406 (mmt90) cc_final: 0.8071 (mmm-85) REVERT: F 71 ASN cc_start: 0.7358 (t0) cc_final: 0.6971 (t0) REVERT: F 214 MET cc_start: 0.8204 (mmt) cc_final: 0.7897 (mmm) REVERT: F 385 TYR cc_start: 0.8606 (t80) cc_final: 0.8243 (t80) REVERT: F 389 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8328 (mm110) REVERT: F 392 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8235 (tttm) REVERT: F 428 GLU cc_start: 0.7891 (tt0) cc_final: 0.7510 (tt0) REVERT: F 465 GLU cc_start: 0.7307 (pm20) cc_final: 0.7055 (mp0) REVERT: d 176 GLU cc_start: 0.5753 (mm-30) cc_final: 0.5351 (mp0) REVERT: g 50 ARG cc_start: 0.7258 (tpt-90) cc_final: 0.7042 (tpt-90) REVERT: g 94 TYR cc_start: 0.6346 (t80) cc_final: 0.5652 (t80) REVERT: g 130 CYS cc_start: 0.5425 (m) cc_final: 0.4676 (p) REVERT: g 139 LYS cc_start: 0.7444 (ttmt) cc_final: 0.7011 (mtmt) REVERT: g 165 ASN cc_start: 0.7817 (p0) cc_final: 0.7596 (p0) REVERT: g 171 ARG cc_start: 0.5480 (mtp-110) cc_final: 0.5171 (ttm-80) REVERT: g 173 GLU cc_start: 0.6520 (mp0) cc_final: 0.5922 (mp0) REVERT: g 214 TYR cc_start: 0.8086 (p90) cc_final: 0.7243 (p90) REVERT: g 303 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7877 (mm-40) REVERT: g 353 ILE cc_start: 0.8797 (mt) cc_final: 0.8272 (pt) REVERT: e 58 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.4711 (mm) REVERT: e 60 LEU cc_start: 0.5936 (tt) cc_final: 0.5422 (mm) REVERT: e 104 ARG cc_start: 0.6644 (mpt180) cc_final: 0.5856 (mmm160) REVERT: e 110 ARG cc_start: 0.5407 (ptm-80) cc_final: 0.5184 (ptm-80) REVERT: e 117 LEU cc_start: 0.7201 (tp) cc_final: 0.6732 (tt) REVERT: e 125 ARG cc_start: 0.7077 (ttm170) cc_final: 0.6545 (ttp80) outliers start: 77 outliers final: 52 residues processed: 677 average time/residue: 0.2118 time to fit residues: 217.5578 Evaluate side-chains 647 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 587 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain g residue 286 GLN Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 100 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 284 optimal weight: 0.0570 chunk 201 optimal weight: 0.9990 chunk 341 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 297 optimal weight: 0.7980 chunk 354 optimal weight: 2.9990 chunk 80 optimal weight: 0.0170 chunk 222 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN C 97 GLN D 133 HIS D 472 GLN E 472 GLN g 76 GLN g 286 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.158773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131066 restraints weight = 35443.750| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.89 r_work: 0.3382 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27936 Z= 0.127 Angle : 0.607 12.808 37865 Z= 0.305 Chirality : 0.044 0.258 4451 Planarity : 0.004 0.084 4918 Dihedral : 5.785 110.945 3914 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 2.41 % Allowed : 19.95 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.03 (0.14), residues: 3556 helix: 1.46 (0.14), residues: 1497 sheet: -0.97 (0.20), residues: 628 loop : -1.03 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 41 TYR 0.023 0.001 TYR D 259 PHE 0.020 0.001 PHE E 199 TRP 0.002 0.001 TRP e 15 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (27936) covalent geometry : angle 0.60736 / 0.31 (37865) hydrogen bonds : bond 0.03668 / 2.53 ( 1360) hydrogen bonds : angle 4.64660 / 3.23 ( 3963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 601 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8559 (p) cc_final: 0.8173 (m) REVERT: A 266 LYS cc_start: 0.7140 (mttp) cc_final: 0.6887 (mttp) REVERT: A 348 ASP cc_start: 0.7896 (m-30) cc_final: 0.7528 (m-30) REVERT: B 37 ASP cc_start: 0.4972 (OUTLIER) cc_final: 0.4202 (p0) REVERT: B 48 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 68 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7821 (mt-10) REVERT: B 77 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7821 (mmp) REVERT: B 266 LYS cc_start: 0.7478 (tppt) cc_final: 0.7050 (tppt) REVERT: B 376 MET cc_start: 0.8921 (tpp) cc_final: 0.8491 (tpt) REVERT: B 378 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7431 (mtmt) REVERT: B 384 LYS cc_start: 0.6696 (tptt) cc_final: 0.6495 (tmtt) REVERT: B 387 LEU cc_start: 0.7932 (mt) cc_final: 0.7624 (mt) REVERT: B 392 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: B 489 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5600 (pp) REVERT: B 495 GLN cc_start: 0.6838 (mt0) cc_final: 0.6511 (tm-30) REVERT: B 498 MET cc_start: 0.6767 (tpt) cc_final: 0.4700 (tmm) REVERT: C 90 LYS cc_start: 0.8090 (pttm) cc_final: 0.7863 (pptt) REVERT: C 155 ASP cc_start: 0.8206 (m-30) cc_final: 0.7892 (m-30) REVERT: C 366 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7856 (mtt-85) REVERT: C 402 ASP cc_start: 0.7478 (p0) cc_final: 0.7140 (p0) REVERT: C 456 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7990 (tppt) REVERT: D 225 GLN cc_start: 0.7378 (pm20) cc_final: 0.7057 (mp10) REVERT: D 239 MET cc_start: 0.8274 (mtp) cc_final: 0.8073 (mtp) REVERT: D 311 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7863 (mm-30) REVERT: D 401 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7583 (mt) REVERT: D 481 ASP cc_start: 0.7742 (p0) cc_final: 0.7540 (p0) REVERT: E 47 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8310 (pp) REVERT: E 52 ARG cc_start: 0.6706 (ttm-80) cc_final: 0.6311 (mmm160) REVERT: E 127 ARG cc_start: 0.6622 (ptt-90) cc_final: 0.6415 (ptt90) REVERT: E 145 LYS cc_start: 0.7989 (tptt) cc_final: 0.7713 (tptt) REVERT: E 328 TYR cc_start: 0.8519 (t80) cc_final: 0.8252 (t80) REVERT: E 397 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7462 (tpp-160) REVERT: E 398 TYR cc_start: 0.8501 (t80) cc_final: 0.8239 (t80) REVERT: E 453 GLU cc_start: 0.6914 (mp0) cc_final: 0.6554 (mp0) REVERT: F 22 ARG cc_start: 0.8410 (mmt90) cc_final: 0.8067 (mmm-85) REVERT: F 71 ASN cc_start: 0.7361 (t0) cc_final: 0.6982 (t0) REVERT: F 214 MET cc_start: 0.8205 (mmt) cc_final: 0.7903 (mmm) REVERT: F 385 TYR cc_start: 0.8612 (t80) cc_final: 0.8228 (t80) REVERT: F 389 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8299 (mm110) REVERT: F 392 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8262 (tttm) REVERT: F 428 GLU cc_start: 0.7896 (tt0) cc_final: 0.7485 (tt0) REVERT: F 465 GLU cc_start: 0.7390 (pm20) cc_final: 0.7124 (mp0) REVERT: d 176 GLU cc_start: 0.5799 (mm-30) cc_final: 0.5235 (mp0) REVERT: d 250 MET cc_start: 0.0594 (ttt) cc_final: 0.0306 (ttt) REVERT: g 89 LEU cc_start: 0.6815 (tt) cc_final: 0.6535 (tp) REVERT: g 94 TYR cc_start: 0.6400 (t80) cc_final: 0.5702 (t80) REVERT: g 130 CYS cc_start: 0.5352 (m) cc_final: 0.4576 (p) REVERT: g 139 LYS cc_start: 0.7396 (ttmt) cc_final: 0.6983 (mtmt) REVERT: g 165 ASN cc_start: 0.7784 (p0) cc_final: 0.7567 (p0) REVERT: g 173 GLU cc_start: 0.6490 (mp0) cc_final: 0.5934 (mp0) REVERT: g 211 GLU cc_start: 0.7439 (pm20) cc_final: 0.7239 (pm20) REVERT: g 214 TYR cc_start: 0.8070 (p90) cc_final: 0.7184 (p90) REVERT: g 303 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7861 (mm-40) REVERT: g 353 ILE cc_start: 0.8802 (mt) cc_final: 0.8262 (pt) REVERT: e 58 LEU cc_start: 0.5306 (OUTLIER) cc_final: 0.4687 (mm) REVERT: e 60 LEU cc_start: 0.5939 (tt) cc_final: 0.5461 (mt) REVERT: e 110 ARG cc_start: 0.5373 (ptm-80) cc_final: 0.5155 (ptm-80) REVERT: e 117 LEU cc_start: 0.7212 (tp) cc_final: 0.6904 (tt) REVERT: e 125 ARG cc_start: 0.7161 (ttm170) cc_final: 0.6748 (ttp80) outliers start: 71 outliers final: 57 residues processed: 647 average time/residue: 0.2119 time to fit residues: 207.6658 Evaluate side-chains 651 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 586 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain g residue 286 GLN Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 100 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 152 optimal weight: 0.3980 chunk 156 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 230 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN C 97 GLN C 389 GLN D 112 ASN E 25 GLN E 472 GLN g 286 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123850 restraints weight = 35874.485| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.99 r_work: 0.3275 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27936 Z= 0.169 Angle : 0.638 13.201 37865 Z= 0.322 Chirality : 0.045 0.283 4451 Planarity : 0.004 0.080 4918 Dihedral : 5.900 111.813 3914 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 2.38 % Allowed : 20.09 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.03 (0.14), residues: 3556 helix: 1.39 (0.14), residues: 1497 sheet: -0.98 (0.21), residues: 608 loop : -1.05 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG g 171 TYR 0.024 0.002 TYR D 259 PHE 0.018 0.001 PHE E 441 TRP 0.002 0.001 TRP e 15 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (27936) covalent geometry : angle 0.63814 / 0.32 (37865) hydrogen bonds : bond 0.03968 / 2.74 ( 1360) hydrogen bonds : angle 4.72766 / 3.29 ( 3963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 596 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.8590 (p) cc_final: 0.8194 (m) REVERT: A 266 LYS cc_start: 0.7397 (mttp) cc_final: 0.7032 (mttp) REVERT: A 348 ASP cc_start: 0.7945 (m-30) cc_final: 0.7549 (m-30) REVERT: B 37 ASP cc_start: 0.4886 (OUTLIER) cc_final: 0.4088 (p0) REVERT: B 48 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8521 (p) REVERT: B 68 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7813 (mt-10) REVERT: B 77 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8052 (mmp) REVERT: B 266 LYS cc_start: 0.7541 (tppt) cc_final: 0.7064 (tppt) REVERT: B 344 PHE cc_start: 0.8250 (m-80) cc_final: 0.7935 (m-80) REVERT: B 378 LYS cc_start: 0.7668 (mtpt) cc_final: 0.7311 (mtmt) REVERT: B 384 LYS cc_start: 0.6580 (tptt) cc_final: 0.6325 (tmtt) REVERT: B 387 LEU cc_start: 0.7898 (mt) cc_final: 0.7620 (mt) REVERT: B 392 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6372 (pm20) REVERT: B 489 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5650 (pp) REVERT: B 495 GLN cc_start: 0.6800 (mt0) cc_final: 0.6431 (tm-30) REVERT: B 498 MET cc_start: 0.6809 (tpt) cc_final: 0.4673 (tmm) REVERT: C 90 LYS cc_start: 0.8231 (pttm) cc_final: 0.7940 (pptt) REVERT: C 155 ASP cc_start: 0.8264 (m-30) cc_final: 0.7950 (m-30) REVERT: C 402 ASP cc_start: 0.7611 (p0) cc_final: 0.7245 (p0) REVERT: C 456 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7941 (tppt) REVERT: D 311 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7948 (mm-30) REVERT: D 401 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7615 (mt) REVERT: D 481 ASP cc_start: 0.7713 (p0) cc_final: 0.7507 (p0) REVERT: E 47 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8368 (pp) REVERT: E 52 ARG cc_start: 0.6838 (ttm-80) cc_final: 0.6393 (mmm160) REVERT: E 145 LYS cc_start: 0.8096 (tptt) cc_final: 0.7733 (tptt) REVERT: E 328 TYR cc_start: 0.8517 (t80) cc_final: 0.7982 (t80) REVERT: E 397 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7509 (tpp-160) REVERT: E 398 TYR cc_start: 0.8529 (t80) cc_final: 0.8223 (t80) REVERT: E 453 GLU cc_start: 0.6930 (mp0) cc_final: 0.6581 (mp0) REVERT: F 22 ARG cc_start: 0.8386 (mmt90) cc_final: 0.7999 (mmm-85) REVERT: F 71 ASN cc_start: 0.7547 (t0) cc_final: 0.7112 (t0) REVERT: F 214 MET cc_start: 0.8116 (mmt) cc_final: 0.7825 (mmm) REVERT: F 236 TYR cc_start: 0.8598 (m-80) cc_final: 0.8256 (m-80) REVERT: F 392 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8324 (tttm) REVERT: F 428 GLU cc_start: 0.8026 (tt0) cc_final: 0.7583 (tt0) REVERT: d 103 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6501 (mt) REVERT: d 176 GLU cc_start: 0.5872 (mm-30) cc_final: 0.5199 (mp0) REVERT: d 250 MET cc_start: 0.0604 (ttt) cc_final: 0.0334 (ttt) REVERT: g 50 ARG cc_start: 0.7444 (tpt-90) cc_final: 0.7198 (tpt-90) REVERT: g 89 LEU cc_start: 0.6758 (tt) cc_final: 0.6488 (tp) REVERT: g 94 TYR cc_start: 0.6427 (t80) cc_final: 0.5756 (t80) REVERT: g 130 CYS cc_start: 0.5317 (m) cc_final: 0.4610 (p) REVERT: g 139 LYS cc_start: 0.7293 (ttmt) cc_final: 0.6860 (mtmt) REVERT: g 173 GLU cc_start: 0.6579 (mp0) cc_final: 0.6037 (mp0) REVERT: g 211 GLU cc_start: 0.7444 (pm20) cc_final: 0.7237 (pm20) REVERT: g 303 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7844 (mm-40) REVERT: g 353 ILE cc_start: 0.8831 (mt) cc_final: 0.8265 (pt) REVERT: e 58 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.4862 (mm) REVERT: e 60 LEU cc_start: 0.5725 (tt) cc_final: 0.5227 (mm) REVERT: e 110 ARG cc_start: 0.5392 (ptm-80) cc_final: 0.5084 (ptm-80) REVERT: e 117 LEU cc_start: 0.7057 (tp) cc_final: 0.6522 (tt) REVERT: e 121 ARG cc_start: 0.6396 (ttm-80) cc_final: 0.5819 (mtm-85) REVERT: e 125 ARG cc_start: 0.7128 (ttm170) cc_final: 0.6695 (ttp80) outliers start: 70 outliers final: 56 residues processed: 639 average time/residue: 0.2125 time to fit residues: 206.2485 Evaluate side-chains 655 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 590 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain g residue 286 GLN Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 100 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 12 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 287 optimal weight: 0.0070 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 343 optimal weight: 0.9980 chunk 177 optimal weight: 0.0050 chunk 14 optimal weight: 0.9980 chunk 272 optimal weight: 0.0970 chunk 327 optimal weight: 0.8980 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN C 389 GLN E 472 GLN F 389 GLN g 286 GLN e 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131548 restraints weight = 35251.252| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.67 r_work: 0.3400 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27936 Z= 0.124 Angle : 0.614 12.918 37865 Z= 0.308 Chirality : 0.044 0.272 4451 Planarity : 0.004 0.066 4918 Dihedral : 5.786 109.881 3914 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 2.18 % Allowed : 20.33 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.08 (0.14), residues: 3556 helix: 1.53 (0.14), residues: 1492 sheet: -0.97 (0.21), residues: 607 loop : -1.01 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG g 171 TYR 0.021 0.001 TYR g 214 PHE 0.017 0.001 PHE E 441 TRP 0.003 0.001 TRP e 15 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (27936) covalent geometry : angle 0.61392 / 0.31 (37865) hydrogen bonds : bond 0.03634 / 2.51 ( 1360) hydrogen bonds : angle 4.65563 / 3.24 ( 3963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8947.56 seconds wall clock time: 153 minutes 33.80 seconds (9213.80 seconds total)