Starting phenix.real_space_refine on Mon Oct 26 04:04:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rda_4811/10_2026/6rda_4811.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rda_4811/10_2026/6rda_4811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rda_4811/10_2026/6rda_4811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rda_4811/10_2026/6rda_4811.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rda_4811/10_2026/6rda_4811.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rda_4811/10_2026/6rda_4811.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rda_4811/10_2026/6rda_4811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rda_4811/10_2026/6rda_4811.cif" } resolution = 3.04 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= 0.005 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 Zn 1 6.06 5 S 33 5.16 5 C 12734 2.51 5 N 3312 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19856 Number of models: 1 Model: "" Number of chains: 18 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 646 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "T" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 330 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "6" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 4.15, per 1000 atoms: 0.21 Number of scatterers: 19856 At special positions: 0 Unit cell: (180.063, 116.883, 251.667, 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) Zn 1 29.99 S 33 16.00 O 3776 8.00 N 3312 7.00 C 12734 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: 1.92 Conformation dependent library (CDL) restraints added in 968.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4918 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 6 sheets defined 68.0% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.720A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 31 removed outlier: 3.626A pdb=" N LEU 0 21 " --> pdb=" O GLY 0 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS 0 31 " --> pdb=" O ALA 0 27 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 removed outlier: 3.551A pdb=" N ALA 0 49 " --> pdb=" O ALA 0 45 " (cutoff:3.500A) Processing helix chain '0' and resid 51 through 56 removed outlier: 3.747A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 73 removed outlier: 3.605A pdb=" N LYS 1 68 " --> pdb=" O LEU 1 64 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 100 removed outlier: 3.699A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) Processing helix chain '1' and resid 103 through 105 No H-bonds generated for 'chain '1' and resid 103 through 105' Processing helix chain '1' and resid 106 through 139 removed outlier: 3.832A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 4.112A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 204 removed outlier: 4.118A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 224 removed outlier: 3.642A pdb=" N SER 1 214 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU 1 216 " --> pdb=" O GLU 1 212 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU 1 217 " --> pdb=" O VAL 1 213 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 removed outlier: 3.534A pdb=" N LYS 1 247 " --> pdb=" O ALA 1 243 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.532A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL 1 277 " --> pdb=" O LEU 1 274 " (cutoff:3.500A) Processing helix chain '1' and resid 282 through 286 Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 removed outlier: 3.618A pdb=" N ALA 1 303 " --> pdb=" O GLU 1 299 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 316 Processing helix chain '1' and resid 323 through 327 removed outlier: 3.528A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 Processing helix chain '1' and resid 338 through 351 removed outlier: 3.524A pdb=" N GLU 1 350 " --> pdb=" O GLN 1 346 " (cutoff:3.500A) Processing helix chain '1' and resid 353 through 362 Processing helix chain '1' and resid 363 through 367 removed outlier: 3.899A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.599A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS 1 386 " --> pdb=" O VAL 1 382 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 415 removed outlier: 3.558A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 1 401 " --> pdb=" O GLU 1 397 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) Processing helix chain '1' and resid 416 through 421 removed outlier: 3.552A pdb=" N GLY 1 421 " --> pdb=" O LYS 1 417 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.935A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 444 Processing helix chain '1' and resid 446 through 460 removed outlier: 3.699A pdb=" N ALA 1 460 " --> pdb=" O LYS 1 456 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 removed outlier: 3.700A pdb=" N TYR 1 468 " --> pdb=" O PRO 1 464 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR 1 471 " --> pdb=" O ALA 1 467 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN 1 474 " --> pdb=" O VAL 1 470 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU 1 475 " --> pdb=" O THR 1 471 " (cutoff:3.500A) Processing helix chain '1' and resid 479 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 515 removed outlier: 3.525A pdb=" N GLU 1 496 " --> pdb=" O GLN 1 492 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU 1 499 " --> pdb=" O GLU 1 495 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER 1 503 " --> pdb=" O GLU 1 499 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 1 505 " --> pdb=" O GLU 1 501 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA 1 515 " --> pdb=" O ALA 1 511 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 Processing helix chain '1' and resid 541 through 549 removed outlier: 3.504A pdb=" N VAL 1 545 " --> pdb=" O PRO 1 541 " (cutoff:3.500A) Processing helix chain '1' and resid 549 through 562 removed outlier: 3.550A pdb=" N GLU 1 559 " --> pdb=" O LYS 1 555 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 586 Processing helix chain '1' and resid 588 through 591 Processing helix chain '1' and resid 592 through 597 Processing helix chain '1' and resid 597 through 606 Processing helix chain '2' and resid 8 through 17 removed outlier: 3.643A pdb=" N GLU 2 14 " --> pdb=" O ALA 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 39 Processing helix chain '2' and resid 44 through 58 removed outlier: 3.719A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 77 removed outlier: 3.788A pdb=" N THR 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 removed outlier: 3.509A pdb=" N ALA 2 91 " --> pdb=" O LEU 2 87 " (cutoff:3.500A) Processing helix chain '2' and resid 99 through 113 removed outlier: 3.692A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 127 Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 154 through 168 removed outlier: 3.567A pdb=" N ALA 2 160 " --> pdb=" O ALA 2 156 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER 2 167 " --> pdb=" O LYS 2 163 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 198 removed outlier: 4.302A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) Processing helix chain '2' and resid 209 through 221 removed outlier: 3.637A pdb=" N LEU 2 220 " --> pdb=" O ALA 2 216 " (cutoff:3.500A) Processing helix chain '2' and resid 228 through 233 Processing helix chain '2' and resid 240 through 253 removed outlier: 3.504A pdb=" N VAL 2 245 " --> pdb=" O PRO 2 241 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.670A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 277 through 280 removed outlier: 4.242A pdb=" N LEU 2 280 " --> pdb=" O PRO 2 277 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 277 through 280' Processing helix chain '2' and resid 281 through 295 removed outlier: 3.810A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 305 through 321 removed outlier: 3.641A pdb=" N LYS 2 309 " --> pdb=" O SER 2 305 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP 2 316 " --> pdb=" O GLY 2 312 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 341 removed outlier: 3.513A pdb=" N ASP 2 332 " --> pdb=" O ALA 2 328 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA 2 335 " --> pdb=" O ALA 2 331 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 353 removed outlier: 3.535A pdb=" N SER 2 351 " --> pdb=" O PRO 2 347 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 408 removed outlier: 4.305A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 440 Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 91 through 99 removed outlier: 3.620A pdb=" N ASN 3 97 " --> pdb=" O GLU 3 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 removed outlier: 3.807A pdb=" N TRP 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 119 through 128 removed outlier: 3.752A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 3 127 " --> pdb=" O LYS 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 166 removed outlier: 3.973A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 168 through 172 removed outlier: 3.609A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) Processing helix chain '3' and resid 173 through 187 removed outlier: 4.076A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA 3 182 " --> pdb=" O LEU 3 178 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR 3 183 " --> pdb=" O GLN 3 179 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 removed outlier: 3.540A pdb=" N SER 3 201 " --> pdb=" O ASP 3 197 " (cutoff:3.500A) Processing helix chain '3' and resid 215 through 229 removed outlier: 3.546A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 Processing helix chain '3' and resid 242 through 244 No H-bonds generated for 'chain '3' and resid 242 through 244' Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 271 removed outlier: 3.882A pdb=" N SER 3 263 " --> pdb=" O ASP 3 259 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA 3 267 " --> pdb=" O SER 3 263 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR 3 270 " --> pdb=" O LYS 3 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 277 No H-bonds generated for 'chain '3' and resid 275 through 277' Processing helix chain '3' and resid 278 through 287 removed outlier: 3.827A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL 3 287 " --> pdb=" O GLY 3 283 " (cutoff:3.500A) Processing helix chain '3' and resid 288 through 292 removed outlier: 4.109A pdb=" N GLU 3 291 " --> pdb=" O SER 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 309 removed outlier: 3.552A pdb=" N LEU 3 297 " --> pdb=" O SER 3 293 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 3.563A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.606A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA 4 35 " --> pdb=" O LYS 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 3.505A pdb=" N GLN 4 52 " --> pdb=" O GLU 4 48 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.719A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 removed outlier: 3.641A pdb=" N LYS 4 107 " --> pdb=" O ILE 4 103 " (cutoff:3.500A) Processing helix chain '4' and resid 118 through 126 Processing helix chain '4' and resid 131 through 150 removed outlier: 3.866A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER 4 144 " --> pdb=" O GLU 4 140 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 164 Processing helix chain '4' and resid 164 through 177 removed outlier: 3.515A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY 4 177 " --> pdb=" O ALA 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 removed outlier: 3.567A pdb=" N GLY 4 189 " --> pdb=" O ALA 4 185 " (cutoff:3.500A) Processing helix chain '4' and resid 194 through 234 removed outlier: 3.684A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA 4 224 " --> pdb=" O LYS 4 220 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.649A pdb=" N LYS 4 243 " --> pdb=" O ALA 4 239 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.802A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 29 Processing helix chain '5' and resid 29 through 57 removed outlier: 3.946A pdb=" N THR 5 33 " --> pdb=" O GLN 5 29 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 72 through 81 Processing helix chain '5' and resid 89 through 107 removed outlier: 3.946A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN 5 107 " --> pdb=" O TYR 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 46 through 56 removed outlier: 5.402A pdb=" N LYS 6 52 " --> pdb=" O LEU 6 48 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N THR 6 53 " --> pdb=" O SER 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 94 removed outlier: 3.665A pdb=" N ILE 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 104 through 118 removed outlier: 3.513A pdb=" N LEU 6 108 " --> pdb=" O ASN 6 104 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 130 Processing helix chain '7' and resid 68 through 72 removed outlier: 4.096A pdb=" N SER 7 72 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 105 removed outlier: 3.657A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 114 removed outlier: 3.682A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 125 through 145 removed outlier: 3.503A pdb=" N PHE 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 155 removed outlier: 3.675A pdb=" N SER 7 155 " --> pdb=" O SER 7 151 " (cutoff:3.500A) Processing helix chain '7' and resid 157 through 166 Processing helix chain '7' and resid 174 through 181 Processing helix chain '7' and resid 182 through 187 Processing helix chain '8' and resid 26 through 31 Processing helix chain '8' and resid 31 through 39 Processing helix chain '8' and resid 39 through 78 removed outlier: 3.729A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 16 removed outlier: 3.824A pdb=" N GLY 9 8 " --> pdb=" O THR 9 4 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS 9 13 " --> pdb=" O LYS 9 9 " (cutoff:3.500A) Processing helix chain '9' and resid 36 through 55 removed outlier: 4.021A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 97 removed outlier: 3.669A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 144 Processing helix chain 'M' and resid 147 through 164 removed outlier: 3.722A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER M 161 " --> pdb=" O CYS M 157 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 168 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 199 removed outlier: 3.519A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 265 removed outlier: 3.622A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 308 removed outlier: 4.040A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY M 276 " --> pdb=" O PRO M 272 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER M 300 " --> pdb=" O SER M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.956A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU P 170 " --> pdb=" O GLU P 166 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 226 removed outlier: 3.793A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS P 224 " --> pdb=" O ASN P 220 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 75 Proline residue: T 68 - end of helix removed outlier: 4.412A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain '2' and resid 368 through 372 removed outlier: 4.464A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 Processing sheet with id=AA4, first strand: chain '7' and resid 35 through 41 Processing sheet with id=AA5, first strand: chain '7' and resid 35 through 41 Processing sheet with id=AA6, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.270A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE P 198 " --> pdb=" O MET P 209 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3171 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: 3.76 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4741 1.33 - 1.45: 4139 1.45 - 1.57: 11305 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 20239 Sorted by residual: bond pdb=" CB THR 3 174 " pdb=" CG2 THR 3 174 " ideal model delta sigma weight residual 1.521 1.403 0.118 3.30e-02 9.18e+02 1.29e+01 bond pdb=" CB THR M 153 " pdb=" CG2 THR M 153 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.23e+01 bond pdb=" C LEU M 167 " pdb=" N MET M 168 " ideal model delta sigma weight residual 1.331 1.239 0.092 2.83e-02 1.25e+03 1.05e+01 bond pdb=" N THR M 200 " pdb=" CA THR M 200 " ideal model delta sigma weight residual 1.460 1.486 -0.026 8.20e-03 1.49e+04 9.83e+00 bond pdb=" CB ARG 6 130 " pdb=" CG ARG 6 130 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 7.97e+00 ... (remaining 20234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 26048 2.07 - 4.14: 1206 4.14 - 6.21: 144 6.21 - 8.28: 57 8.28 - 10.35: 14 Bond angle restraints: 27469 Sorted by residual: angle pdb=" N PRO 3 77 " pdb=" CA PRO 3 77 " pdb=" CB PRO 3 77 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" C THR M 200 " pdb=" CA THR M 200 " pdb=" CB THR M 200 " ideal model delta sigma weight residual 116.53 107.39 9.14 1.47e+00 4.63e-01 3.86e+01 angle pdb=" N VAL 1 204 " pdb=" CA VAL 1 204 " pdb=" C VAL 1 204 " ideal model delta sigma weight residual 111.77 105.34 6.43 1.04e+00 9.25e-01 3.82e+01 angle pdb=" N TYR 9 36 " pdb=" CA TYR 9 36 " pdb=" C TYR 9 36 " ideal model delta sigma weight residual 112.23 105.04 7.19 1.26e+00 6.30e-01 3.26e+01 angle pdb=" C VAL 7 157 " pdb=" N VAL 7 158 " pdb=" CA VAL 7 158 " ideal model delta sigma weight residual 120.33 124.86 -4.53 8.00e-01 1.56e+00 3.21e+01 ... (remaining 27464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 11094 17.51 - 35.03: 885 35.03 - 52.54: 157 52.54 - 70.05: 34 70.05 - 87.57: 12 Dihedral angle restraints: 12182 sinusoidal: 4595 harmonic: 7587 Sorted by residual: dihedral pdb=" CA VAL P 185 " pdb=" C VAL P 185 " pdb=" N MET P 186 " pdb=" CA MET P 186 " ideal model delta harmonic sigma weight residual 180.00 121.66 58.34 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA PHE 2 222 " pdb=" C PHE 2 222 " pdb=" N LYS 2 223 " pdb=" CA LYS 2 223 " ideal model delta harmonic sigma weight residual 180.00 148.42 31.58 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA LYS 5 119 " pdb=" C LYS 5 119 " pdb=" N PRO 5 120 " pdb=" CA PRO 5 120 " ideal model delta harmonic sigma weight residual -180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 12179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2567 0.077 - 0.155: 537 0.155 - 0.232: 50 0.232 - 0.309: 7 0.309 - 0.386: 2 Chirality restraints: 3163 Sorted by residual: chirality pdb=" CB ILE 3 90 " pdb=" CA ILE 3 90 " pdb=" CG1 ILE 3 90 " pdb=" CG2 ILE 3 90 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB VAL 5 113 " pdb=" CA VAL 5 113 " pdb=" CG1 VAL 5 113 " pdb=" CG2 VAL 5 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CG LEU 1 102 " pdb=" CB LEU 1 102 " pdb=" CD1 LEU 1 102 " pdb=" CD2 LEU 1 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3160 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU 5 31 " -0.056 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO 5 32 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO 5 32 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO 5 32 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO 1 93 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR 6 145 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C THR 6 145 " 0.052 2.00e-02 2.50e+03 pdb=" O THR 6 145 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE 6 146 " -0.018 2.00e-02 2.50e+03 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 278 2.64 - 3.21: 17515 3.21 - 3.77: 30847 3.77 - 4.34: 45303 4.34 - 4.90: 72434 Nonbonded interactions: 166377 Sorted by model distance: nonbonded pdb="ZN ZN M 600 " pdb=" O HOH M 709 " model vdw 2.075 2.230 nonbonded pdb="ZN ZN M 600 " pdb=" O HOH 6 205 " model vdw 2.158 2.230 nonbonded pdb=" O THR 5 83 " pdb=" OH TYR 7 119 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR M 289 " pdb=" O HOH M 701 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR 6 126 " pdb=" O HOH 6 201 " model vdw 2.268 3.040 ... (remaining 166372 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 10.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.670 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.014 0.274 20241 Z= 0.578 Angle : 1.039 10.350 27469 Z= 0.573 Chirality : 0.063 0.386 3163 Planarity : 0.008 0.083 3505 Dihedral : 13.768 87.569 7264 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.06 % Favored : 94.67 % Rotamer: Outliers : 0.58 % Allowed : 5.19 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.84 (0.11), residues: 2569 helix: -4.44 (0.05), residues: 1698 sheet: -1.21 (0.70), residues: 56 loop : -2.10 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 2 46 TYR 0.038 0.003 TYR 2 61 PHE 0.032 0.003 PHE 3 121 TRP 0.016 0.003 TRP 5 44 HIS 0.014 0.003 HIS 4 233 Details of bonding type rmsd/Z covalent geometry : bond 0.01348 / 0.57 (20239) covalent geometry : angle 1.03886 / 0.57 (27469) hydrogen bonds : bond 0.29797 / 19.91 ( 1080) hydrogen bonds : angle 11.02211 / 7.71 ( 3171) metal coordination : bond 0.25427 / 12.66 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 320 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7331 (pm20) REVERT: 1 34 GLU cc_start: 0.7613 (pm20) cc_final: 0.7134 (pm20) REVERT: 1 224 LYS cc_start: 0.7751 (pttt) cc_final: 0.7547 (pttt) REVERT: 1 437 VAL cc_start: 0.8703 (m) cc_final: 0.8380 (t) REVERT: 1 456 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8237 (ttmm) REVERT: 1 572 ASP cc_start: 0.8239 (m-30) cc_final: 0.7883 (m-30) REVERT: 2 21 ARG cc_start: 0.8140 (ptt180) cc_final: 0.7874 (mtm180) REVERT: 2 31 ASP cc_start: 0.7891 (m-30) cc_final: 0.7655 (m-30) REVERT: 2 197 LEU cc_start: 0.8569 (mt) cc_final: 0.8232 (mt) REVERT: 4 134 TYR cc_start: 0.8775 (t80) cc_final: 0.8415 (t80) REVERT: 4 214 ASP cc_start: 0.8008 (m-30) cc_final: 0.7802 (m-30) REVERT: 5 111 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8166 (mmtm) REVERT: 7 135 ASP cc_start: 0.8347 (m-30) cc_final: 0.8068 (m-30) REVERT: M 199 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8137 (mmtp) REVERT: P 193 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7267 (mmtt) REVERT: P 205 ARG cc_start: 0.7711 (ptt-90) cc_final: 0.3680 (mmm160) REVERT: P 213 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8104 (tppt) REVERT: T 65 LYS cc_start: 0.8332 (mttp) cc_final: 0.8113 (mttm) outliers start: 12 outliers final: 8 residues processed: 329 average time/residue: 0.1708 time to fit residues: 81.6560 Evaluate side-chains 234 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain M residue 199 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 44 ASN 0 48 ASN 1 48 ASN 1 65 GLN 1 100 GLN 1 257 HIS 1 316 ASN 1 365 GLN 1 482 ASN 1 587 ASN 1 590 HIS 2 40 GLN 2 122 ASN 2 177 GLN 2 243 GLN 2 289 HIS 2 427 GLN 3 189 HIS 3 206 ASN 3 229 ASN 4 68 HIS 4 240 GLN 5 107 ASN 6 40 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS 7 98 ASN 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 9 35 GLN M 108 ASN M 163 ASN P 220 ASN P 223 ASN T 64 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101125 restraints weight = 26743.124| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.55 r_work: 0.2828 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20241 Z= 0.155 Angle : 0.632 11.316 27469 Z= 0.336 Chirality : 0.040 0.158 3163 Planarity : 0.006 0.062 3505 Dihedral : 5.844 43.554 2760 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.70 % Favored : 96.15 % Rotamer: Outliers : 1.55 % Allowed : 7.95 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.14), residues: 2569 helix: -2.25 (0.10), residues: 1715 sheet: -0.53 (0.73), residues: 56 loop : -1.46 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 359 TYR 0.021 0.002 TYR 4 211 PHE 0.015 0.001 PHE 1 529 TRP 0.019 0.002 TRP 4 206 HIS 0.008 0.001 HIS 8 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (20239) covalent geometry : angle 0.63231 / 0.34 (27469) hydrogen bonds : bond 0.04731 / 3.17 ( 1080) hydrogen bonds : angle 4.83043 / 3.41 ( 3171) metal coordination : bond 0.01445 / 0.75 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8885 (mt-10) cc_final: 0.7002 (pm20) REVERT: 1 34 GLU cc_start: 0.8114 (pm20) cc_final: 0.7891 (pm20) REVERT: 1 224 LYS cc_start: 0.8166 (pttt) cc_final: 0.7775 (pttt) REVERT: 1 313 GLN cc_start: 0.9092 (tt0) cc_final: 0.8773 (mt0) REVERT: 1 359 ARG cc_start: 0.8816 (mtt-85) cc_final: 0.8570 (mmt90) REVERT: 1 572 ASP cc_start: 0.8936 (m-30) cc_final: 0.8572 (m-30) REVERT: 2 21 ARG cc_start: 0.8079 (ptt180) cc_final: 0.7740 (mtm180) REVERT: 2 316 ASP cc_start: 0.8313 (m-30) cc_final: 0.7951 (m-30) REVERT: 2 353 VAL cc_start: 0.8100 (m) cc_final: 0.7849 (t) REVERT: 3 256 GLN cc_start: 0.7421 (tt0) cc_final: 0.7186 (mt0) REVERT: 3 295 GLU cc_start: 0.7671 (pm20) cc_final: 0.7369 (pm20) REVERT: 4 90 PHE cc_start: 0.8791 (m-80) cc_final: 0.8569 (m-80) REVERT: 4 111 GLN cc_start: 0.8469 (tt0) cc_final: 0.8196 (tt0) REVERT: 5 49 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8657 (mtpp) REVERT: 5 111 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8563 (mmtm) REVERT: 6 146 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8287 (t80) REVERT: 9 7 LEU cc_start: 0.7622 (mt) cc_final: 0.7375 (mp) REVERT: 9 94 LYS cc_start: 0.8255 (tptt) cc_final: 0.7919 (ttpt) REVERT: M 143 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: P 205 ARG cc_start: 0.7585 (ptt-90) cc_final: 0.3256 (mmp-170) REVERT: P 225 LEU cc_start: 0.9248 (tp) cc_final: 0.8996 (tt) outliers start: 32 outliers final: 18 residues processed: 286 average time/residue: 0.1480 time to fit residues: 64.1146 Evaluate side-chains 241 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 57 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain M residue 143 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [220, 176, 166, 20, 119, 88, 105, 169, 91, 162, 87] chunk 220 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 9 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099493 restraints weight = 26926.549| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.50 r_work: 0.2794 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20241 Z= 0.213 Angle : 0.604 11.240 27469 Z= 0.315 Chirality : 0.042 0.148 3163 Planarity : 0.005 0.057 3505 Dihedral : 5.452 46.006 2753 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.13 % Favored : 95.76 % Rotamer: Outliers : 2.18 % Allowed : 9.11 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.68 (0.16), residues: 2569 helix: -0.94 (0.12), residues: 1729 sheet: -0.17 (0.77), residues: 56 loop : -1.20 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 3 242 TYR 0.024 0.002 TYR 4 211 PHE 0.014 0.001 PHE 1 529 TRP 0.013 0.002 TRP 3 109 HIS 0.008 0.001 HIS 8 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (20239) covalent geometry : angle 0.60370 / 0.32 (27469) hydrogen bonds : bond 0.04255 / 2.86 ( 1080) hydrogen bonds : angle 4.27489 / 3.02 ( 3171) metal coordination : bond 0.00192 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 0.726 Fit side-chains REVERT: 0 41 GLU cc_start: 0.8878 (mt-10) cc_final: 0.6949 (pm20) REVERT: 1 34 GLU cc_start: 0.8200 (pm20) cc_final: 0.7983 (pm20) REVERT: 1 209 ASN cc_start: 0.7309 (p0) cc_final: 0.6971 (p0) REVERT: 1 313 GLN cc_start: 0.9058 (tt0) cc_final: 0.8781 (mt0) REVERT: 1 499 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: 1 572 ASP cc_start: 0.8948 (m-30) cc_final: 0.8581 (m-30) REVERT: 2 316 ASP cc_start: 0.8442 (m-30) cc_final: 0.8168 (m-30) REVERT: 3 256 GLN cc_start: 0.7562 (tt0) cc_final: 0.7270 (mt0) REVERT: 4 214 ASP cc_start: 0.8489 (m-30) cc_final: 0.8244 (m-30) REVERT: 5 49 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8757 (mtpp) REVERT: 5 111 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8607 (mmtm) REVERT: 6 146 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8455 (t80) REVERT: 9 94 LYS cc_start: 0.8173 (tptt) cc_final: 0.7784 (ttpt) REVERT: M 143 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8367 (m-30) REVERT: M 225 GLU cc_start: 0.7596 (tt0) cc_final: 0.7300 (tp30) REVERT: P 169 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7754 (mm-30) REVERT: P 205 ARG cc_start: 0.7582 (ptt-90) cc_final: 0.3418 (mmm160) REVERT: P 225 LEU cc_start: 0.9298 (tp) cc_final: 0.9003 (tt) outliers start: 45 outliers final: 30 residues processed: 263 average time/residue: 0.1515 time to fit residues: 60.3915 Evaluate side-chains 253 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 418 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 4 residue 124 ASN Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 57 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 30 THR Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain P residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [11, 81, 66, 204, 111, 130, 146, 26, 19, 161, 178] chunk 11 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099044 restraints weight = 27060.082| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.62 r_work: 0.2777 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20241 Z= 0.237 Angle : 0.604 10.325 27469 Z= 0.313 Chirality : 0.043 0.151 3163 Planarity : 0.005 0.054 3505 Dihedral : 5.405 53.697 2753 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 2.13 % Allowed : 11.10 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.05 (0.16), residues: 2569 helix: -0.41 (0.12), residues: 1732 sheet: -0.07 (0.76), residues: 57 loop : -1.09 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 118 TYR 0.023 0.002 TYR 4 211 PHE 0.013 0.002 PHE 1 529 TRP 0.013 0.002 TRP 3 109 HIS 0.014 0.001 HIS 8 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (20239) covalent geometry : angle 0.60406 / 0.31 (27469) hydrogen bonds : bond 0.04146 / 2.79 ( 1080) hydrogen bonds : angle 4.15207 / 2.94 ( 3171) metal coordination : bond 0.00114 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.763 Fit side-chains REVERT: 0 41 GLU cc_start: 0.8899 (mt-10) cc_final: 0.6987 (pm20) REVERT: 1 34 GLU cc_start: 0.8270 (pm20) cc_final: 0.8023 (pm20) REVERT: 1 109 LYS cc_start: 0.8491 (tptm) cc_final: 0.8256 (tppt) REVERT: 1 209 ASN cc_start: 0.7281 (p0) cc_final: 0.6884 (p0) REVERT: 1 212 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7251 (tm-30) REVERT: 1 313 GLN cc_start: 0.9072 (tt0) cc_final: 0.8788 (mt0) REVERT: 1 453 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8221 (ttp80) REVERT: 1 499 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: 1 572 ASP cc_start: 0.8977 (m-30) cc_final: 0.8634 (m-30) REVERT: 2 316 ASP cc_start: 0.8449 (m-30) cc_final: 0.8197 (m-30) REVERT: 3 256 GLN cc_start: 0.7584 (tt0) cc_final: 0.7262 (mt0) REVERT: 4 13 TYR cc_start: 0.9366 (OUTLIER) cc_final: 0.8861 (m-80) REVERT: 4 133 ASP cc_start: 0.8578 (t0) cc_final: 0.8223 (t0) REVERT: 5 111 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8630 (mmtm) REVERT: 6 69 THR cc_start: 0.5581 (OUTLIER) cc_final: 0.5138 (p) REVERT: 6 146 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8550 (t80) REVERT: 8 78 HIS cc_start: 0.8052 (t70) cc_final: 0.7851 (t-170) REVERT: M 143 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8448 (m-30) REVERT: M 225 GLU cc_start: 0.7639 (tt0) cc_final: 0.7346 (tp30) REVERT: P 169 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7892 (mm-30) REVERT: P 205 ARG cc_start: 0.7602 (ptt-90) cc_final: 0.3409 (mmm160) REVERT: P 225 LEU cc_start: 0.9300 (tp) cc_final: 0.8989 (tt) outliers start: 44 outliers final: 33 residues processed: 255 average time/residue: 0.1534 time to fit residues: 59.0286 Evaluate side-chains 261 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 418 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 30 SER Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 124 ASN Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 57 GLN Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [42, 77, 233, 137, 49, 130, 168, 150, 236, 109, 224] chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 9 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102382 restraints weight = 26637.602| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.52 r_work: 0.2849 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20241 Z= 0.140 Angle : 0.529 7.940 27469 Z= 0.276 Chirality : 0.040 0.150 3163 Planarity : 0.004 0.050 3505 Dihedral : 5.117 57.123 2753 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 2.08 % Allowed : 12.02 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.38 (0.17), residues: 2569 helix: 0.15 (0.13), residues: 1727 sheet: 0.10 (0.76), residues: 57 loop : -0.93 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 359 TYR 0.021 0.001 TYR 4 211 PHE 0.015 0.001 PHE 2 165 TRP 0.017 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (20239) covalent geometry : angle 0.52946 / 0.28 (27469) hydrogen bonds : bond 0.03568 / 2.40 ( 1080) hydrogen bonds : angle 3.87803 / 2.74 ( 3171) metal coordination : bond 0.00085 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.828 Fit side-chains REVERT: 0 41 GLU cc_start: 0.8867 (mt-10) cc_final: 0.6982 (pm20) REVERT: 1 34 GLU cc_start: 0.8260 (pm20) cc_final: 0.7732 (pm20) REVERT: 1 216 LEU cc_start: 0.8584 (mm) cc_final: 0.8343 (tt) REVERT: 1 219 LYS cc_start: 0.7831 (mttp) cc_final: 0.7585 (mttt) REVERT: 1 313 GLN cc_start: 0.9090 (tt0) cc_final: 0.8815 (mt0) REVERT: 1 352 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7785 (mm-30) REVERT: 1 453 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8264 (ttp80) REVERT: 1 499 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: 1 572 ASP cc_start: 0.8926 (m-30) cc_final: 0.8572 (m-30) REVERT: 2 316 ASP cc_start: 0.8410 (m-30) cc_final: 0.8130 (m-30) REVERT: 2 394 LYS cc_start: 0.8381 (pttt) cc_final: 0.7914 (ttpp) REVERT: 3 256 GLN cc_start: 0.7648 (tt0) cc_final: 0.7369 (mt0) REVERT: 4 133 ASP cc_start: 0.8553 (t0) cc_final: 0.8211 (t0) REVERT: 4 198 LYS cc_start: 0.8190 (pptt) cc_final: 0.7792 (mptt) REVERT: 5 111 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8535 (mmtm) REVERT: 6 146 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8542 (t80) REVERT: 9 13 LYS cc_start: 0.7607 (pttt) cc_final: 0.6966 (tttm) REVERT: 9 94 LYS cc_start: 0.8149 (tptt) cc_final: 0.7844 (ttpt) REVERT: M 199 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8368 (mmtp) REVERT: M 225 GLU cc_start: 0.7635 (tt0) cc_final: 0.7388 (tp30) REVERT: P 169 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7879 (mm-30) REVERT: P 186 MET cc_start: 0.5987 (tpp) cc_final: 0.4117 (mmm) REVERT: P 205 ARG cc_start: 0.7478 (ptt-90) cc_final: 0.3427 (mmm160) REVERT: P 225 LEU cc_start: 0.9287 (tp) cc_final: 0.8984 (tt) outliers start: 43 outliers final: 28 residues processed: 280 average time/residue: 0.1489 time to fit residues: 63.1937 Evaluate side-chains 250 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 418 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 30 SER Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 57 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [84, 60, 50, 58, 170, 243, 223, 247, 17, 110, 44] chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 170 optimal weight: 0.4980 chunk 243 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 562 ASN 8 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102607 restraints weight = 26537.685| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.43 r_work: 0.2852 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20241 Z= 0.145 Angle : 0.536 10.036 27469 Z= 0.277 Chirality : 0.040 0.154 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.997 59.613 2753 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 2.28 % Allowed : 12.22 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.17), residues: 2569 helix: 0.47 (0.13), residues: 1728 sheet: 0.14 (0.74), residues: 57 loop : -0.89 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 213 TYR 0.021 0.001 TYR 4 211 PHE 0.021 0.001 PHE 2 165 TRP 0.013 0.001 TRP 9 73 HIS 0.012 0.001 HIS 8 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (20239) covalent geometry : angle 0.53614 / 0.28 (27469) hydrogen bonds : bond 0.03525 / 2.38 ( 1080) hydrogen bonds : angle 3.78840 / 2.67 ( 3171) metal coordination : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 0.532 Fit side-chains REVERT: 0 41 GLU cc_start: 0.8837 (mt-10) cc_final: 0.7017 (pm20) REVERT: 1 34 GLU cc_start: 0.8262 (pm20) cc_final: 0.7743 (pm20) REVERT: 1 216 LEU cc_start: 0.8506 (mm) cc_final: 0.8265 (tt) REVERT: 1 219 LYS cc_start: 0.7861 (mttp) cc_final: 0.7548 (mtpt) REVERT: 1 313 GLN cc_start: 0.9064 (tt0) cc_final: 0.8849 (mt0) REVERT: 1 352 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7700 (mm-30) REVERT: 1 453 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8295 (ttp80) REVERT: 1 499 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: 1 572 ASP cc_start: 0.8911 (m-30) cc_final: 0.8564 (m-30) REVERT: 2 316 ASP cc_start: 0.8378 (m-30) cc_final: 0.8108 (m-30) REVERT: 2 394 LYS cc_start: 0.8412 (pttt) cc_final: 0.8117 (ttpt) REVERT: 3 256 GLN cc_start: 0.7674 (tt0) cc_final: 0.7380 (mt0) REVERT: 4 13 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.8723 (m-80) REVERT: 4 133 ASP cc_start: 0.8588 (t0) cc_final: 0.8225 (t0) REVERT: 4 198 LYS cc_start: 0.8224 (pptt) cc_final: 0.7750 (mmmt) REVERT: 5 111 LYS cc_start: 0.8863 (mtpp) cc_final: 0.8468 (mmtm) REVERT: 6 69 THR cc_start: 0.5308 (OUTLIER) cc_final: 0.4839 (p) REVERT: 6 146 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8525 (t80) REVERT: M 199 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8351 (mmtp) REVERT: M 225 GLU cc_start: 0.7643 (tt0) cc_final: 0.7441 (tp30) REVERT: M 270 MET cc_start: 0.6761 (tmm) cc_final: 0.6196 (mtp) REVERT: P 169 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7798 (mm-30) REVERT: P 186 MET cc_start: 0.5779 (tpp) cc_final: 0.4820 (mmm) REVERT: P 205 ARG cc_start: 0.7501 (ptt-90) cc_final: 0.3372 (mmm160) REVERT: P 225 LEU cc_start: 0.9288 (tp) cc_final: 0.8966 (tt) outliers start: 47 outliers final: 36 residues processed: 272 average time/residue: 0.1492 time to fit residues: 61.4881 Evaluate side-chains 270 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 181 LYS Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 30 SER Chi-restraints excluded: chain 2 residue 154 ASP Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [106, 143, 3, 110, 44, 79, 163, 167, 239, 178, 46] chunk 106 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 167 optimal weight: 0.3980 chunk 239 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 319 GLN 8 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.101983 restraints weight = 26526.761| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.41 r_work: 0.2858 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20241 Z= 0.140 Angle : 0.529 10.820 27469 Z= 0.273 Chirality : 0.040 0.148 3163 Planarity : 0.004 0.048 3505 Dihedral : 4.880 56.193 2753 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 2.23 % Allowed : 12.75 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2569 helix: 0.70 (0.13), residues: 1725 sheet: 0.19 (0.74), residues: 57 loop : -0.80 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 213 TYR 0.022 0.001 TYR 4 211 PHE 0.025 0.001 PHE 2 165 TRP 0.015 0.001 TRP 9 73 HIS 0.015 0.001 HIS 8 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (20239) covalent geometry : angle 0.52933 / 0.27 (27469) hydrogen bonds : bond 0.03436 / 2.32 ( 1080) hydrogen bonds : angle 3.70812 / 2.62 ( 3171) metal coordination : bond 0.00058 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 0.777 Fit side-chains REVERT: 0 41 GLU cc_start: 0.8839 (mt-10) cc_final: 0.6977 (pm20) REVERT: 1 34 GLU cc_start: 0.8264 (pm20) cc_final: 0.7741 (pm20) REVERT: 1 216 LEU cc_start: 0.8468 (mm) cc_final: 0.8215 (tt) REVERT: 1 219 LYS cc_start: 0.7726 (mttp) cc_final: 0.7442 (mtpt) REVERT: 1 313 GLN cc_start: 0.9038 (tt0) cc_final: 0.8822 (mt0) REVERT: 1 352 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7647 (mm-30) REVERT: 1 453 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8295 (ttp80) REVERT: 1 499 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: 1 549 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8675 (t0) REVERT: 1 572 ASP cc_start: 0.8918 (m-30) cc_final: 0.8563 (m-30) REVERT: 2 108 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: 2 165 PHE cc_start: 0.8074 (m-10) cc_final: 0.7826 (m-80) REVERT: 2 394 LYS cc_start: 0.8387 (pttt) cc_final: 0.8119 (ttpt) REVERT: 4 13 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: 4 133 ASP cc_start: 0.8553 (t0) cc_final: 0.8189 (t0) REVERT: 4 198 LYS cc_start: 0.8186 (pptt) cc_final: 0.7728 (mmmt) REVERT: 5 111 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8387 (mmtm) REVERT: 6 146 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8536 (t80) REVERT: 9 13 LYS cc_start: 0.7707 (pttt) cc_final: 0.7067 (tttm) REVERT: M 199 LYS cc_start: 0.8550 (mmtp) cc_final: 0.8292 (mmtp) REVERT: M 270 MET cc_start: 0.6847 (tmm) cc_final: 0.6323 (mtp) REVERT: P 169 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7830 (mm-30) REVERT: P 186 MET cc_start: 0.5201 (tpp) cc_final: 0.4423 (mmm) REVERT: P 205 ARG cc_start: 0.7399 (ptt-90) cc_final: 0.3350 (mmm160) REVERT: P 225 LEU cc_start: 0.9265 (tp) cc_final: 0.8947 (tt) outliers start: 46 outliers final: 39 residues processed: 268 average time/residue: 0.1574 time to fit residues: 63.7163 Evaluate side-chains 262 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 181 LYS Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 30 SER Chi-restraints excluded: chain 2 residue 108 GLU Chi-restraints excluded: chain 2 residue 154 ASP Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 124 ASN Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [50, 125, 235, 226, 33, 94, 206, 224, 103, 166, 239] chunk 50 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 94 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 239 optimal weight: 0.7980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 319 GLN 8 78 HIS 9 41 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102325 restraints weight = 26661.540| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.38 r_work: 0.2868 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20241 Z= 0.130 Angle : 0.526 13.559 27469 Z= 0.270 Chirality : 0.039 0.149 3163 Planarity : 0.004 0.048 3505 Dihedral : 4.774 52.590 2753 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 2.38 % Allowed : 12.80 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.17), residues: 2569 helix: 0.90 (0.13), residues: 1720 sheet: 0.17 (0.73), residues: 57 loop : -0.76 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 213 TYR 0.020 0.001 TYR 4 211 PHE 0.023 0.001 PHE 2 165 TRP 0.013 0.001 TRP 9 73 HIS 0.012 0.001 HIS 8 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (20239) covalent geometry : angle 0.52588 / 0.27 (27469) hydrogen bonds : bond 0.03369 / 2.27 ( 1080) hydrogen bonds : angle 3.65300 / 2.57 ( 3171) metal coordination : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8841 (mt-10) cc_final: 0.6971 (pm20) REVERT: 1 34 GLU cc_start: 0.8247 (pm20) cc_final: 0.7749 (pm20) REVERT: 1 216 LEU cc_start: 0.8443 (mm) cc_final: 0.8201 (tt) REVERT: 1 219 LYS cc_start: 0.7704 (mttp) cc_final: 0.7408 (mtpt) REVERT: 1 313 GLN cc_start: 0.9020 (tt0) cc_final: 0.8815 (mt0) REVERT: 1 352 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7597 (mm-30) REVERT: 1 453 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8290 (ttp80) REVERT: 1 499 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: 1 549 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8658 (t0) REVERT: 1 572 ASP cc_start: 0.8866 (m-30) cc_final: 0.8505 (m-30) REVERT: 2 41 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7771 (t) REVERT: 2 394 LYS cc_start: 0.8374 (pttt) cc_final: 0.8140 (ttpt) REVERT: 4 13 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: 4 133 ASP cc_start: 0.8498 (t0) cc_final: 0.8138 (t0) REVERT: 4 198 LYS cc_start: 0.8190 (pptt) cc_final: 0.7735 (mmmt) REVERT: 5 111 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8407 (mmtm) REVERT: 6 146 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8526 (t80) REVERT: 9 89 MET cc_start: 0.8424 (mtp) cc_final: 0.8164 (mtp) REVERT: M 199 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8239 (mmtt) REVERT: M 270 MET cc_start: 0.6761 (tmm) cc_final: 0.6248 (mtp) REVERT: P 169 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7839 (mm-30) REVERT: P 186 MET cc_start: 0.5149 (tpp) cc_final: 0.4501 (mmm) REVERT: P 205 ARG cc_start: 0.7402 (ptt-90) cc_final: 0.3321 (mmm160) REVERT: P 225 LEU cc_start: 0.9266 (tp) cc_final: 0.8964 (tt) outliers start: 49 outliers final: 39 residues processed: 271 average time/residue: 0.1562 time to fit residues: 63.8855 Evaluate side-chains 274 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 181 LYS Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 30 SER Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 154 ASP Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 269 GLN Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [7, 42, 159, 63, 126, 99, 142, 240, 251, 48, 100] chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 100 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101076 restraints weight = 26500.544| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.43 r_work: 0.2847 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20241 Z= 0.173 Angle : 0.552 13.315 27469 Z= 0.282 Chirality : 0.041 0.148 3163 Planarity : 0.004 0.049 3505 Dihedral : 4.839 51.579 2753 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Rotamer: Outliers : 2.13 % Allowed : 12.94 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2569 helix: 0.85 (0.13), residues: 1723 sheet: 0.13 (0.73), residues: 57 loop : -0.78 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 213 TYR 0.020 0.001 TYR 4 211 PHE 0.021 0.001 PHE 2 165 TRP 0.012 0.001 TRP 3 109 HIS 0.007 0.001 HIS 4 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (20239) covalent geometry : angle 0.55182 / 0.28 (27469) hydrogen bonds : bond 0.03590 / 2.42 ( 1080) hydrogen bonds : angle 3.73120 / 2.62 ( 3171) metal coordination : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.747 Fit side-chains REVERT: 0 41 GLU cc_start: 0.8841 (mt-10) cc_final: 0.6986 (pm20) REVERT: 1 34 GLU cc_start: 0.8261 (pm20) cc_final: 0.7777 (pm20) REVERT: 1 216 LEU cc_start: 0.8478 (mm) cc_final: 0.8209 (tt) REVERT: 1 219 LYS cc_start: 0.7723 (mttp) cc_final: 0.7425 (mtpt) REVERT: 1 313 GLN cc_start: 0.9065 (tt0) cc_final: 0.8841 (mt0) REVERT: 1 352 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7647 (mm-30) REVERT: 1 453 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8265 (ttp80) REVERT: 1 499 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: 1 549 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8666 (t0) REVERT: 1 572 ASP cc_start: 0.8898 (m-30) cc_final: 0.8560 (m-30) REVERT: 2 108 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: 2 394 LYS cc_start: 0.8397 (pttt) cc_final: 0.8169 (ttpt) REVERT: 4 13 TYR cc_start: 0.9339 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: 4 133 ASP cc_start: 0.8508 (t0) cc_final: 0.8143 (t0) REVERT: 4 198 LYS cc_start: 0.8207 (pptt) cc_final: 0.7741 (mmmt) REVERT: 5 111 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8499 (mmtm) REVERT: 6 146 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8550 (t80) REVERT: 9 13 LYS cc_start: 0.7703 (pttt) cc_final: 0.7046 (tttm) REVERT: 9 89 MET cc_start: 0.8445 (mtp) cc_final: 0.8169 (mtp) REVERT: M 199 LYS cc_start: 0.8571 (mmtp) cc_final: 0.8302 (mmtp) REVERT: M 270 MET cc_start: 0.6707 (tmm) cc_final: 0.6326 (mtp) REVERT: P 169 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7915 (mm-30) REVERT: P 205 ARG cc_start: 0.7398 (ptt-90) cc_final: 0.3273 (mmm160) REVERT: P 225 LEU cc_start: 0.9296 (tp) cc_final: 0.8999 (tt) outliers start: 44 outliers final: 37 residues processed: 270 average time/residue: 0.1557 time to fit residues: 63.9149 Evaluate side-chains 275 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 181 LYS Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 30 SER Chi-restraints excluded: chain 2 residue 108 GLU Chi-restraints excluded: chain 2 residue 154 ASP Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 124 ASN Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [216, 174, 86, 4, 3, 9, 189, 67, 232, 162, 7] chunk 216 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 chunk 86 optimal weight: 0.0060 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 319 GLN 8 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102003 restraints weight = 26605.288| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.42 r_work: 0.2857 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20241 Z= 0.136 Angle : 0.533 14.547 27469 Z= 0.274 Chirality : 0.040 0.147 3163 Planarity : 0.004 0.048 3505 Dihedral : 4.760 48.354 2753 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 2.04 % Allowed : 12.99 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2569 helix: 1.00 (0.13), residues: 1721 sheet: 0.20 (0.73), residues: 57 loop : -0.69 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 67 TYR 0.019 0.001 TYR 4 211 PHE 0.018 0.001 PHE 2 165 TRP 0.015 0.001 TRP 9 73 HIS 0.006 0.001 HIS 4 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (20239) covalent geometry : angle 0.53348 / 0.27 (27469) hydrogen bonds : bond 0.03401 / 2.30 ( 1080) hydrogen bonds : angle 3.65568 / 2.57 ( 3171) metal coordination : bond 0.00045 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.705 Fit side-chains REVERT: 0 41 GLU cc_start: 0.8851 (mt-10) cc_final: 0.7025 (pm20) REVERT: 1 34 GLU cc_start: 0.8205 (pm20) cc_final: 0.7707 (pm20) REVERT: 1 216 LEU cc_start: 0.8474 (mm) cc_final: 0.8208 (tt) REVERT: 1 219 LYS cc_start: 0.7693 (mttp) cc_final: 0.7390 (mtpt) REVERT: 1 313 GLN cc_start: 0.9043 (tt0) cc_final: 0.8830 (mt0) REVERT: 1 352 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7638 (mm-30) REVERT: 1 453 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8296 (ttp80) REVERT: 1 499 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: 1 549 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8678 (t0) REVERT: 1 572 ASP cc_start: 0.8911 (m-30) cc_final: 0.8563 (m-30) REVERT: 2 108 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: 2 223 LYS cc_start: 0.6313 (tptt) cc_final: 0.6019 (mptt) REVERT: 2 394 LYS cc_start: 0.8379 (pttt) cc_final: 0.8167 (ttpt) REVERT: 4 13 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8675 (m-80) REVERT: 4 133 ASP cc_start: 0.8508 (t0) cc_final: 0.8154 (t0) REVERT: 4 198 LYS cc_start: 0.8197 (pptt) cc_final: 0.7731 (mmmt) REVERT: 5 111 LYS cc_start: 0.8871 (mtpp) cc_final: 0.8463 (mmtm) REVERT: 6 146 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8588 (t80) REVERT: 9 89 MET cc_start: 0.8444 (mtp) cc_final: 0.8128 (mtp) REVERT: M 199 LYS cc_start: 0.8545 (mmtp) cc_final: 0.8224 (mmtp) REVERT: M 270 MET cc_start: 0.6696 (tmm) cc_final: 0.6255 (mtp) REVERT: P 169 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7934 (mm-30) REVERT: P 205 ARG cc_start: 0.7418 (ptt-90) cc_final: 0.3318 (mmm160) REVERT: P 225 LEU cc_start: 0.9251 (tp) cc_final: 0.8953 (tt) outliers start: 42 outliers final: 37 residues processed: 267 average time/residue: 0.1492 time to fit residues: 60.6288 Evaluate side-chains 274 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 181 LYS Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 30 SER Chi-restraints excluded: chain 2 residue 108 GLU Chi-restraints excluded: chain 2 residue 154 ASP Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: [166, 244, 30, 111, 87, 138, 207, 73, 12, 222, 58] chunk 166 optimal weight: 0.5980 chunk 244 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 138 optimal weight: 0.0970 chunk 207 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 319 GLN 8 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102627 restraints weight = 26586.432| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.34 r_work: 0.2880 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20241 Z= 0.121 Angle : 0.522 14.779 27469 Z= 0.269 Chirality : 0.039 0.146 3163 Planarity : 0.004 0.047 3505 Dihedral : 4.620 43.091 2752 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 2.04 % Allowed : 12.99 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2569 helix: 1.15 (0.13), residues: 1719 sheet: 0.32 (0.73), residues: 57 loop : -0.67 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 149 TYR 0.021 0.001 TYR 4 211 PHE 0.022 0.001 PHE 3 121 TRP 0.016 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (20239) covalent geometry : angle 0.52227 / 0.27 (27469) hydrogen bonds : bond 0.03272 / 2.20 ( 1080) hydrogen bonds : angle 3.58419 / 2.52 ( 3171) metal coordination : bond 0.00052 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7272.55 seconds wall clock time: 124 minutes 37.28 seconds (7477.28 seconds total)