Starting phenix.real_space_refine on Mon Jul 6 17:11:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p3w_13186/07_2026/7p3w_13186.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3w_13186/07_2026/7p3w_13186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p3w_13186/07_2026/7p3w_13186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3w_13186/07_2026/7p3w_13186.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7p3w_13186/07_2026/7p3w_13186.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p3w_13186/07_2026/7p3w_13186.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p3w_13186/07_2026/7p3w_13186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3w_13186/07_2026/7p3w_13186.map" } resolution = 4.3 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 4 5.21 5 S 147 5.16 5 C 23656 2.51 5 N 6313 2.21 5 O 7018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37149 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3875 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3863 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 492} Chain: "C" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3850 Classifications: {'peptide': 509} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 440} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3533 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "G" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "H" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "L" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "O" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "P" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "Q" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "R" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "S" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "a" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2105 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 15, 'TRANS': 261} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 3, 'HIS:plan': 3, 'PHE:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "b" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 147} Chain: "d" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1347 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1010 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "g" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2243 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain: "p" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1185 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.92, per 1000 atoms: 0.21 Number of scatterers: 37149 At special positions: 0 Unit cell: (133.45, 143.65, 240.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 147 16.00 P 11 15.00 Mg 4 11.99 O 7018 8.00 N 6313 7.00 C 23656 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: 3.63 Conformation dependent library (CDL) restraints added in 1.7 seconds 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8922 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 26 sheets defined 60.4% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.728A pdb=" N THR A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.556A pdb=" N GLN A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.572A pdb=" N GLN A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.972A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 288 through 289 No H-bonds generated for 'chain 'A' and resid 288 through 289' Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.910A pdb=" N ARG A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.063A pdb=" N SER A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 404 removed outlier: 4.395A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 removed outlier: 4.292A pdb=" N ALA A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 Processing helix chain 'A' and resid 441 through 454 removed outlier: 3.551A pdb=" N GLN A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.640A pdb=" N TYR B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.732A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.615A pdb=" N ILE B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 378 through 383 removed outlier: 4.256A pdb=" N SER B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.643A pdb=" N GLN B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 480 removed outlier: 4.458A pdb=" N ASP B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 7 through 18 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix removed outlier: 3.699A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.514A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.962A pdb=" N SER C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 363 removed outlier: 3.768A pdb=" N PHE C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.927A pdb=" N SER C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 405 removed outlier: 5.118A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 415 through 432 removed outlier: 3.862A pdb=" N MET C 432 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 454 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 464 through 480 Processing helix chain 'C' and resid 480 through 491 Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.565A pdb=" N LEU D 83 " --> pdb=" O THR D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 153 through 169 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 211 through 232 removed outlier: 3.798A pdb=" N ARG D 215 " --> pdb=" O PRO D 211 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 260 removed outlier: 3.714A pdb=" N GLY D 256 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.753A pdb=" N ARG D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.712A pdb=" N ASP D 306 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 318 removed outlier: 4.178A pdb=" N THR D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.853A pdb=" N ALA D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 355 through 382 removed outlier: 3.716A pdb=" N TYR D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 406 removed outlier: 3.605A pdb=" N SER D 406 " --> pdb=" O GLN D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 438 Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'D' and resid 453 through 464 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.597A pdb=" N LEU E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 153 through 168 Processing helix chain 'E' and resid 181 through 195 Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 211 through 232 removed outlier: 3.894A pdb=" N ARG E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 263 Processing helix chain 'E' and resid 275 through 286 removed outlier: 3.563A pdb=" N GLU E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 307 removed outlier: 3.530A pdb=" N ASP E 306 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP E 307 " --> pdb=" O PRO E 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 303 through 307' Processing helix chain 'E' and resid 310 through 318 Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 355 through 382 removed outlier: 4.238A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 removed outlier: 4.176A pdb=" N SER E 406 " --> pdb=" O GLN E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 417 removed outlier: 3.752A pdb=" N PHE E 415 " --> pdb=" O VAL E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 437 Processing helix chain 'E' and resid 444 through 449 removed outlier: 3.652A pdb=" N ALA E 447 " --> pdb=" O PRO E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 464 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 211 through 217 removed outlier: 3.500A pdb=" N ARG F 217 " --> pdb=" O GLY F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.886A pdb=" N GLY F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 261 removed outlier: 3.748A pdb=" N THR F 253 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL F 259 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 285 removed outlier: 3.683A pdb=" N GLU F 279 " --> pdb=" O THR F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 304 through 307 Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.814A pdb=" N ALA F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 333 Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 355 through 382 removed outlier: 4.525A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE F 379 " --> pdb=" O LEU F 375 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 380 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 381 " --> pdb=" O ASP F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 Processing helix chain 'F' and resid 388 through 406 removed outlier: 3.782A pdb=" N SER F 406 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 415 Processing helix chain 'F' and resid 424 through 437 Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 453 through 464 Processing helix chain 'G' and resid 2 through 41 removed outlier: 3.636A pdb=" N ARG G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 Processing helix chain 'G' and resid 60 through 77 Processing helix chain 'H' and resid 2 through 41 removed outlier: 3.714A pdb=" N ARG H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 60 Processing helix chain 'H' and resid 60 through 76 Processing helix chain 'J' and resid 2 through 41 removed outlier: 3.758A pdb=" N ILE J 16 " --> pdb=" O SER J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 4.009A pdb=" N ASP J 60 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 76 Processing helix chain 'K' and resid 3 through 41 removed outlier: 3.831A pdb=" N ARG K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 60 removed outlier: 3.686A pdb=" N LEU K 58 " --> pdb=" O LEU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 76 Processing helix chain 'L' and resid 3 through 41 removed outlier: 3.715A pdb=" N ARG L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 60 removed outlier: 3.831A pdb=" N ASP L 60 " --> pdb=" O ALA L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 75 Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.671A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 60 removed outlier: 3.635A pdb=" N ASP O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 76 Processing helix chain 'P' and resid 2 through 41 removed outlier: 4.007A pdb=" N GLY P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 removed outlier: 3.773A pdb=" N ASP P 60 " --> pdb=" O ALA P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 removed outlier: 3.941A pdb=" N MET P 64 " --> pdb=" O ASP P 60 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 41 removed outlier: 4.171A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.608A pdb=" N LEU Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 76 Processing helix chain 'R' and resid 3 through 41 removed outlier: 4.052A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 Processing helix chain 'R' and resid 60 through 76 Processing helix chain 'S' and resid 2 through 41 Processing helix chain 'S' and resid 44 through 60 removed outlier: 3.696A pdb=" N LEU S 58 " --> pdb=" O LEU S 54 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 77 Processing helix chain 'a' and resid 16 through 26 Processing helix chain 'a' and resid 52 through 73 removed outlier: 3.985A pdb=" N SER a 56 " --> pdb=" O SER a 52 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL a 70 " --> pdb=" O LEU a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 101 Processing helix chain 'a' and resid 107 through 125 Processing helix chain 'a' and resid 126 through 128 No H-bonds generated for 'chain 'a' and resid 126 through 128' Processing helix chain 'a' and resid 131 through 144 removed outlier: 5.669A pdb=" N PHE a 139 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL a 140 " --> pdb=" O VAL a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 154 removed outlier: 3.553A pdb=" N PHE a 154 " --> pdb=" O HIS a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 162 through 183 Processing helix chain 'a' and resid 185 through 191 Processing helix chain 'a' and resid 201 through 247 removed outlier: 4.697A pdb=" N ILE a 210 " --> pdb=" O LYS a 206 " (cutoff:3.500A) Proline residue: a 211 - end of helix removed outlier: 3.755A pdb=" N THR a 220 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N PHE a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Proline residue: a 225 - end of helix Processing helix chain 'a' and resid 257 through 288 removed outlier: 3.881A pdb=" N TRP a 261 " --> pdb=" O LEU a 257 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU a 271 " --> pdb=" O LEU a 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 25 removed outlier: 3.658A pdb=" N VAL b 18 " --> pdb=" O PHE b 14 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA b 19 " --> pdb=" O ALA b 15 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE b 20 " --> pdb=" O PHE b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 116 removed outlier: 3.765A pdb=" N LEU b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU b 35 " --> pdb=" O ASN b 31 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN b 37 " --> pdb=" O ILE b 33 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG b 38 " --> pdb=" O SER b 34 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP b 42 " --> pdb=" O ARG b 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY b 43 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN b 60 " --> pdb=" O ASP b 56 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS b 62 " --> pdb=" O GLN b 58 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN b 63 " --> pdb=" O ALA b 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA b 84 " --> pdb=" O ASN b 80 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN b 85 " --> pdb=" O ARG b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 133 removed outlier: 3.916A pdb=" N LEU b 120 " --> pdb=" O ALA b 116 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU b 133 " --> pdb=" O VAL b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 139 removed outlier: 3.742A pdb=" N ASN b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 150 removed outlier: 3.980A pdb=" N LEU b 149 " --> pdb=" O HIS b 145 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER b 150 " --> pdb=" O ASN b 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 145 through 150' Processing helix chain 'd' and resid 4 through 23 Proline residue: d 10 - end of helix Processing helix chain 'd' and resid 24 through 41 Processing helix chain 'd' and resid 41 through 49 Processing helix chain 'd' and resid 54 through 67 removed outlier: 3.553A pdb=" N GLN d 58 " --> pdb=" O THR d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 85 Processing helix chain 'd' and resid 89 through 105 Processing helix chain 'd' and resid 119 through 133 Processing helix chain 'd' and resid 165 through 176 Processing helix chain 'e' and resid 88 through 90 No H-bonds generated for 'chain 'e' and resid 88 through 90' Processing helix chain 'e' and resid 91 through 125 removed outlier: 4.372A pdb=" N ALA e 97 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG e 98 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER e 110 " --> pdb=" O ALA e 106 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA e 115 " --> pdb=" O ASP e 111 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA e 119 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA e 125 " --> pdb=" O LEU e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 133 Processing helix chain 'g' and resid 3 through 42 removed outlier: 3.573A pdb=" N ILE g 7 " --> pdb=" O ASN g 3 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA g 40 " --> pdb=" O GLN g 36 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN g 41 " --> pdb=" O GLU g 37 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY g 42 " --> pdb=" O ARG g 38 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 60 removed outlier: 3.829A pdb=" N ALA g 46 " --> pdb=" O GLY g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 108 Processing helix chain 'g' and resid 119 through 130 removed outlier: 3.800A pdb=" N TYR g 129 " --> pdb=" O PHE g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 145 through 162 removed outlier: 3.555A pdb=" N LEU g 149 " --> pdb=" O SER g 145 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER g 152 " --> pdb=" O GLN g 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 213 through 288 Processing helix chain 'p' and resid 3 through 139 removed outlier: 3.745A pdb=" N TRP p 26 " --> pdb=" O MET p 22 " (cutoff:3.500A) Proline residue: p 27 - end of helix removed outlier: 4.146A pdb=" N ALA p 67 " --> pdb=" O GLN p 63 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG p 121 " --> pdb=" O ARG p 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN p 123 " --> pdb=" O GLU p 119 " (cutoff:3.500A) Processing helix chain 'p' and resid 141 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.404A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.017A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.497A pdb=" N VAL A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA A 228 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS A 193 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 260 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 195 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 257 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.445A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 36 removed outlier: 5.357A pdb=" N ILE B 32 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS B 43 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU B 67 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE B 61 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.271A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.585A pdb=" N ALA B 226 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ALA B 257 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU B 328 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 259 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 332 removed outlier: 6.681A pdb=" N ILE B 168 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU B 167 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 356 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 169 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 355 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 373 " --> pdb=" O PHE B 355 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 36 removed outlier: 6.428A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 4 through 10 current: chain 'C' and resid 89 through 95 Processing sheet with id=AB1, first strand: chain 'C' and resid 30 through 36 removed outlier: 6.428A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 61 through 67 current: chain 'E' and resid 29 through 32 removed outlier: 7.169A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLN E 44 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL E 49 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL E 13 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 5 " --> pdb=" O GLU E 17 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 4 through 10 current: chain 'C' and resid 89 through 95 Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.013A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.546A pdb=" N VAL C 109 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA C 226 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS C 194 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 198 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 193 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA C 257 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU C 328 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE C 259 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 330 through 332 removed outlier: 6.379A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU C 356 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE C 169 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 10 removed outlier: 6.582A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 41 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASP D 28 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA D 29 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB7, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.732A pdb=" N TYR D 205 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL D 144 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 301 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU D 146 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR D 345 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.807A pdb=" N TYR E 205 " --> pdb=" O MET E 87 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA E 202 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA E 176 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL E 204 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL E 178 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY E 206 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL E 174 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL E 242 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE E 298 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU E 244 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA E 300 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL E 246 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN E 299 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 146 " --> pdb=" O GLN E 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 10 removed outlier: 6.451A pdb=" N ILE F 6 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLU F 17 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP F 15 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL F 49 " --> pdb=" O GLN F 44 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN F 44 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 75 through 77 Processing sheet with id=AC3, first strand: chain 'F' and resid 86 through 87 removed outlier: 3.596A pdb=" N MET F 87 " --> pdb=" O MET F 203 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR F 205 " --> pdb=" O MET F 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AC5, first strand: chain 'd' and resid 137 through 144 Processing sheet with id=AC6, first strand: chain 'e' and resid 14 through 20 removed outlier: 6.365A pdb=" N VAL e 8 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER e 17 " --> pdb=" O CYS e 6 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS e 6 " --> pdb=" O SER e 17 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA e 19 " --> pdb=" O MET e 4 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N MET e 4 " --> pdb=" O ALA e 19 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN e 5 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL e 78 " --> pdb=" O GLN e 5 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP e 7 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA e 80 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL e 9 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR e 82 " --> pdb=" O VAL e 9 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL e 76 " --> pdb=" O VAL e 71 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL e 71 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL e 78 " --> pdb=" O LEU e 69 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU e 69 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA e 80 " --> pdb=" O GLY e 67 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY e 67 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 14 through 20 removed outlier: 6.365A pdb=" N VAL e 8 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER e 17 " --> pdb=" O CYS e 6 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS e 6 " --> pdb=" O SER e 17 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA e 19 " --> pdb=" O MET e 4 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N MET e 4 " --> pdb=" O ALA e 19 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN e 5 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL e 78 " --> pdb=" O GLN e 5 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP e 7 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA e 80 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL e 9 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR e 82 " --> pdb=" O VAL e 9 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL e 76 " --> pdb=" O VAL e 71 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL e 71 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL e 78 " --> pdb=" O LEU e 69 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU e 69 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA e 80 " --> pdb=" O GLY e 67 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY e 67 " --> pdb=" O ALA e 80 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 132 through 137 removed outlier: 5.511A pdb=" N VAL g 133 " --> pdb=" O VAL g 113 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE g 115 " --> pdb=" O VAL g 133 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL g 76 " --> pdb=" O GLN g 114 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA g 116 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR g 78 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE g 118 " --> pdb=" O TYR g 78 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE g 80 " --> pdb=" O ILE g 118 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG g 75 " --> pdb=" O ARG g 167 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N TYR g 169 " --> pdb=" O ARG g 75 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY g 77 " --> pdb=" O TYR g 169 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL g 171 " --> pdb=" O GLY g 77 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE g 79 " --> pdb=" O VAL g 171 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN g 173 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N VAL g 81 " --> pdb=" O ASN g 173 " (cutoff:3.500A) 2332 hydrogen bonds defined for protein. 6804 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: 8.33 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7060 1.32 - 1.45: 8530 1.45 - 1.57: 21850 1.57 - 1.69: 18 1.69 - 1.81: 277 Bond restraints: 37735 Sorted by residual: bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.92e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.80e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.36e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.31e+01 ... (remaining 37730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 50821 3.90 - 7.80: 303 7.80 - 11.70: 26 11.70 - 15.60: 3 15.60 - 19.50: 5 Bond angle restraints: 51158 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.37 19.50 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 121.74 18.13 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 119.11 17.72 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 120.06 16.77 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 123.13 16.74 1.00e+00 1.00e+00 2.80e+02 ... (remaining 51153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 20951 18.06 - 36.12: 1414 36.12 - 54.18: 235 54.18 - 72.23: 89 72.23 - 90.29: 56 Dihedral angle restraints: 22745 sinusoidal: 8813 harmonic: 13932 Sorted by residual: dihedral pdb=" N VAL D 414 " pdb=" C VAL D 414 " pdb=" CA VAL D 414 " pdb=" CB VAL D 414 " ideal model delta harmonic sigma weight residual 123.40 141.17 -17.77 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" CA TYR F 205 " pdb=" C TYR F 205 " pdb=" N GLY F 206 " pdb=" CA GLY F 206 " ideal model delta harmonic sigma weight residual 180.00 151.57 28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C VAL D 414 " pdb=" N VAL D 414 " pdb=" CA VAL D 414 " pdb=" CB VAL D 414 " ideal model delta harmonic sigma weight residual -122.00 -135.68 13.68 0 2.50e+00 1.60e-01 3.00e+01 ... (remaining 22742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 5964 0.147 - 0.293: 26 0.293 - 0.440: 3 0.440 - 0.587: 0 0.587 - 0.734: 1 Chirality restraints: 5994 Sorted by residual: chirality pdb=" CA VAL D 414 " pdb=" N VAL D 414 " pdb=" C VAL D 414 " pdb=" CB VAL D 414 " both_signs ideal model delta sigma weight residual False 2.44 1.71 0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CB ILE O 14 " pdb=" CA ILE O 14 " pdb=" CG1 ILE O 14 " pdb=" CG2 ILE O 14 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA GLU D 413 " pdb=" N GLU D 413 " pdb=" C GLU D 413 " pdb=" CB GLU D 413 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 5991 not shown) Planarity restraints: 6634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 18 " -0.047 2.00e-02 2.50e+03 3.51e-02 2.16e+01 pdb=" CG PHE Q 18 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 18 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 18 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE Q 18 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 18 " -0.041 2.00e-02 2.50e+03 3.10e-02 1.69e+01 pdb=" CG PHE R 18 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE R 18 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 18 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 18 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE R 18 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 18 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 89 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA B 89 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA B 89 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG B 90 " 0.020 2.00e-02 2.50e+03 ... (remaining 6631 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 838 2.64 - 3.20: 41262 3.20 - 3.77: 62098 3.77 - 4.33: 84233 4.33 - 4.90: 126904 Nonbonded interactions: 315335 Sorted by model distance: nonbonded pdb=" OG1 THR C 177 " pdb="MG MG C 602 " model vdw 2.074 2.170 nonbonded pdb=" OG1 THR A 177 " pdb="MG MG A 602 " model vdw 2.099 2.170 nonbonded pdb=" OG1 THR B 177 " pdb="MG MG B 602 " model vdw 2.099 2.170 nonbonded pdb=" O2G ATP B 601 " pdb="MG MG B 602 " model vdw 2.131 2.170 nonbonded pdb=" OD1 ASP D 88 " pdb=" N VAL D 89 " model vdw 2.151 3.120 ... (remaining 315330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 511 or resid 601 through 602)) selection = (chain 'B' and resid 6 through 602) selection = (chain 'C' and (resid 6 through 511 or resid 601 through 602)) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 2 through 464) selection = (chain 'F' and resid 2 through 464) } ncs_group { reference = (chain 'G' and resid 2 through 80) selection = (chain 'H' and resid 2 through 80) selection = (chain 'J' and resid 2 through 80) selection = chain 'K' selection = chain 'L' selection = (chain 'O' and resid 2 through 80) selection = (chain 'P' and resid 2 through 80) selection = chain 'Q' selection = chain 'R' selection = (chain 'S' and resid 2 through 80) } ncs_group { reference = chain 'b' selection = (chain 'p' and resid 7 through 156) } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.960 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 35.510 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 37735 Z= 0.311 Angle : 0.867 19.501 51158 Z= 0.529 Chirality : 0.047 0.734 5994 Planarity : 0.005 0.057 6634 Dihedral : 13.876 90.293 13823 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 27.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.28 % Favored : 93.70 % Rotamer: Outliers : 0.05 % Allowed : 0.70 % Favored : 99.24 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.54 % 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: -0.91 (0.12), residues: 4856 helix: 0.19 (0.10), residues: 2628 sheet: -0.86 (0.20), residues: 575 loop : -1.67 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 366 TYR 0.021 0.002 TYR E 372 PHE 0.078 0.003 PHE Q 18 TRP 0.039 0.003 TRP a 118 HIS 0.011 0.002 HIS F 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.31 (37735) covalent geometry : angle 0.86656 / 0.53 (51158) hydrogen bonds : bond 0.15667 / 10.50 ( 2317) hydrogen bonds : angle 6.77988 / 4.70 ( 6804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 423 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8709 (m-30) cc_final: 0.8159 (t0) REVERT: A 355 PHE cc_start: 0.9380 (t80) cc_final: 0.9005 (t80) REVERT: A 362 ASN cc_start: 0.9577 (m110) cc_final: 0.9319 (t0) REVERT: B 49 MET cc_start: 0.8401 (tpt) cc_final: 0.7322 (tpt) REVERT: B 53 MET cc_start: 0.9585 (mtm) cc_final: 0.9110 (mtt) REVERT: B 153 SER cc_start: 0.9641 (t) cc_final: 0.9430 (t) REVERT: B 263 ASP cc_start: 0.8911 (m-30) cc_final: 0.8638 (m-30) REVERT: B 402 ARG cc_start: 0.9078 (mtm180) cc_final: 0.8598 (mtm180) REVERT: B 432 MET cc_start: 0.9428 (mmm) cc_final: 0.9175 (tpp) REVERT: C 157 MET cc_start: 0.9446 (mpp) cc_final: 0.9142 (mpp) REVERT: C 246 MET cc_start: 0.9642 (mpp) cc_final: 0.9397 (mpp) REVERT: C 263 ASP cc_start: 0.9383 (m-30) cc_final: 0.8889 (m-30) REVERT: D 203 MET cc_start: 0.8772 (mpp) cc_final: 0.8433 (mpp) REVERT: D 225 MET cc_start: 0.9673 (mmt) cc_final: 0.9419 (mmm) REVERT: D 245 PHE cc_start: 0.9408 (m-80) cc_final: 0.9037 (m-80) REVERT: D 266 MET cc_start: 0.9040 (mmp) cc_final: 0.8752 (mmm) REVERT: D 280 MET cc_start: 0.9617 (tpt) cc_final: 0.9119 (tpp) REVERT: D 319 HIS cc_start: 0.9478 (m90) cc_final: 0.9045 (m-70) REVERT: E 159 MET cc_start: 0.9636 (mmt) cc_final: 0.9215 (mmm) REVERT: E 280 MET cc_start: 0.9355 (tpp) cc_final: 0.8936 (tpp) REVERT: E 450 MET cc_start: 0.9269 (mmp) cc_final: 0.8885 (mmm) REVERT: F 87 MET cc_start: 0.9394 (pmm) cc_final: 0.8911 (pmm) REVERT: F 208 MET cc_start: 0.9045 (ptp) cc_final: 0.8820 (ptp) REVERT: F 225 MET cc_start: 0.9615 (mmp) cc_final: 0.9294 (mmm) REVERT: F 266 MET cc_start: 0.9064 (mpp) cc_final: 0.8612 (mpp) REVERT: F 299 GLN cc_start: 0.9515 (mt0) cc_final: 0.9281 (mp10) REVERT: H 30 LEU cc_start: 0.9510 (mm) cc_final: 0.9223 (pp) REVERT: K 73 PHE cc_start: 0.9261 (m-10) cc_final: 0.8992 (m-80) REVERT: L 27 PHE cc_start: 0.9490 (m-80) cc_final: 0.8936 (m-80) REVERT: L 60 ASP cc_start: 0.9309 (p0) cc_final: 0.9010 (p0) REVERT: O 55 ILE cc_start: 0.8281 (mm) cc_final: 0.7918 (mm) REVERT: O 64 MET cc_start: 0.8802 (mmp) cc_final: 0.8514 (mmm) REVERT: P 27 PHE cc_start: 0.7575 (m-10) cc_final: 0.7319 (m-10) REVERT: P 50 THR cc_start: 0.9290 (m) cc_final: 0.9078 (m) REVERT: Q 73 PHE cc_start: 0.9522 (m-10) cc_final: 0.9237 (m-80) REVERT: R 27 PHE cc_start: 0.7943 (m-10) cc_final: 0.7675 (m-80) REVERT: R 52 MET cc_start: 0.9720 (tmm) cc_final: 0.9442 (ptm) REVERT: a 88 MET cc_start: 0.9316 (mmt) cc_final: 0.8708 (mmm) REVERT: a 91 GLU cc_start: 0.9162 (tt0) cc_final: 0.8816 (pt0) REVERT: a 94 ASP cc_start: 0.9639 (m-30) cc_final: 0.9382 (m-30) REVERT: a 126 ASP cc_start: 0.8989 (m-30) cc_final: 0.8220 (m-30) REVERT: a 274 PHE cc_start: 0.9676 (t80) cc_final: 0.9472 (t80) REVERT: a 283 TYR cc_start: 0.9597 (m-10) cc_final: 0.8998 (m-80) REVERT: b 17 PHE cc_start: 0.9106 (t80) cc_final: 0.8698 (m-80) REVERT: b 148 MET cc_start: 0.7881 (tpp) cc_final: 0.6912 (mpp) REVERT: e 108 GLN cc_start: 0.9494 (tp-100) cc_final: 0.9260 (tp-100) REVERT: g 24 MET cc_start: 0.9508 (mmp) cc_final: 0.8993 (mmm) REVERT: g 32 MET cc_start: 0.9109 (mmm) cc_final: 0.8885 (mmm) REVERT: g 229 MET cc_start: 0.9706 (mmp) cc_final: 0.9293 (mmm) REVERT: p 82 ARG cc_start: 0.9316 (ttp-110) cc_final: 0.9078 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 425 average time/residue: 0.2358 time to fit residues: 164.4138 Evaluate side-chains 294 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 ASN B 3 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN C 173 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN C 426 GLN D 31 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN F 118 GLN F 157 ASN F 186 ASN F 190 HIS G 47 GLN P 47 GLN R 47 GLN a 17 HIS a 83 GLN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 74 GLN d 22 GLN g 48 ASN g 58 GLN g 237 ASN g 277 GLN ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.037333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.027226 restraints weight = 364275.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.028100 restraints weight = 233339.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.028725 restraints weight = 171598.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.029153 restraints weight = 136567.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029458 restraints weight = 115186.887| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37735 Z= 0.205 Angle : 0.670 9.301 51158 Z= 0.359 Chirality : 0.044 0.248 5994 Planarity : 0.005 0.049 6634 Dihedral : 5.648 76.915 5276 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.30 (0.12), residues: 4856 helix: 0.70 (0.10), residues: 2690 sheet: -0.61 (0.21), residues: 557 loop : -1.50 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 347 TYR 0.055 0.002 TYR a 23 PHE 0.043 0.002 PHE S 18 TRP 0.020 0.002 TRP a 118 HIS 0.007 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (37735) covalent geometry : angle 0.66984 / 0.36 (51158) hydrogen bonds : bond 0.05153 / 3.50 ( 2317) hydrogen bonds : angle 5.41693 / 3.76 ( 6804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 383 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8726 (m-30) cc_final: 0.8092 (t0) REVERT: A 355 PHE cc_start: 0.9326 (t80) cc_final: 0.9009 (t80) REVERT: B 49 MET cc_start: 0.8811 (tpt) cc_final: 0.8100 (tpt) REVERT: B 153 SER cc_start: 0.9588 (t) cc_final: 0.8756 (m) REVERT: B 263 ASP cc_start: 0.8677 (m-30) cc_final: 0.8444 (m-30) REVERT: B 432 MET cc_start: 0.9503 (mmm) cc_final: 0.8682 (mmt) REVERT: C 49 MET cc_start: 0.9386 (mtp) cc_final: 0.9178 (mtp) REVERT: C 157 MET cc_start: 0.9560 (mpp) cc_final: 0.9333 (mmm) REVERT: C 199 ILE cc_start: 0.9397 (mm) cc_final: 0.9121 (mm) REVERT: C 263 ASP cc_start: 0.9085 (m-30) cc_final: 0.8778 (m-30) REVERT: C 413 ASP cc_start: 0.7590 (t0) cc_final: 0.6980 (t0) REVERT: C 432 MET cc_start: 0.9536 (mmp) cc_final: 0.8504 (mmm) REVERT: D 203 MET cc_start: 0.8665 (mpp) cc_final: 0.8457 (mpp) REVERT: D 225 MET cc_start: 0.9669 (mmt) cc_final: 0.9407 (mmm) REVERT: D 245 PHE cc_start: 0.9387 (m-80) cc_final: 0.8839 (m-80) REVERT: D 280 MET cc_start: 0.9560 (tpt) cc_final: 0.8992 (tpt) REVERT: D 319 HIS cc_start: 0.9342 (m90) cc_final: 0.8495 (m90) REVERT: E 1 MET cc_start: 0.8682 (ppp) cc_final: 0.8471 (ppp) REVERT: E 87 MET cc_start: 0.9593 (mpp) cc_final: 0.8896 (mpp) REVERT: E 203 MET cc_start: 0.9357 (mmm) cc_final: 0.9049 (mmm) REVERT: E 280 MET cc_start: 0.9356 (tpp) cc_final: 0.8970 (tpp) REVERT: E 319 HIS cc_start: 0.9021 (m90) cc_final: 0.8632 (m90) REVERT: E 450 MET cc_start: 0.9327 (mmp) cc_final: 0.8903 (mmm) REVERT: F 158 MET cc_start: 0.9682 (tpt) cc_final: 0.9340 (mmp) REVERT: F 208 MET cc_start: 0.9045 (ptp) cc_final: 0.8682 (ptp) REVERT: F 225 MET cc_start: 0.9612 (mmp) cc_final: 0.9309 (mmm) REVERT: F 266 MET cc_start: 0.9050 (mpp) cc_final: 0.8472 (mpp) REVERT: F 299 GLN cc_start: 0.9484 (mt0) cc_final: 0.9230 (mp10) REVERT: G 18 PHE cc_start: 0.9084 (t80) cc_final: 0.8772 (t80) REVERT: H 30 LEU cc_start: 0.9470 (mm) cc_final: 0.9194 (pp) REVERT: H 64 MET cc_start: 0.9545 (mmp) cc_final: 0.9295 (mmp) REVERT: J 18 PHE cc_start: 0.9183 (m-10) cc_final: 0.8935 (m-80) REVERT: K 73 PHE cc_start: 0.9092 (m-10) cc_final: 0.8802 (m-10) REVERT: L 18 PHE cc_start: 0.9285 (t80) cc_final: 0.8895 (t80) REVERT: L 27 PHE cc_start: 0.9585 (m-80) cc_final: 0.9329 (m-80) REVERT: L 60 ASP cc_start: 0.9216 (p0) cc_final: 0.8996 (p0) REVERT: O 55 ILE cc_start: 0.8214 (mm) cc_final: 0.7923 (mm) REVERT: O 64 MET cc_start: 0.8829 (mmp) cc_final: 0.8609 (mmm) REVERT: O 73 PHE cc_start: 0.8610 (m-80) cc_final: 0.8398 (m-80) REVERT: P 64 MET cc_start: 0.8588 (ppp) cc_final: 0.8120 (ppp) REVERT: P 65 ILE cc_start: 0.9102 (mm) cc_final: 0.8697 (mm) REVERT: Q 73 PHE cc_start: 0.9456 (m-10) cc_final: 0.9150 (m-80) REVERT: R 52 MET cc_start: 0.9707 (tmm) cc_final: 0.9401 (ptm) REVERT: R 73 PHE cc_start: 0.8975 (m-80) cc_final: 0.8654 (m-80) REVERT: a 87 GLU cc_start: 0.9659 (mt-10) cc_final: 0.9254 (mp0) REVERT: a 88 MET cc_start: 0.9489 (mmt) cc_final: 0.8871 (mmm) REVERT: a 91 GLU cc_start: 0.9281 (tt0) cc_final: 0.8974 (pt0) REVERT: a 122 MET cc_start: 0.8878 (tmm) cc_final: 0.8571 (tmm) REVERT: a 126 ASP cc_start: 0.8945 (m-30) cc_final: 0.8121 (m-30) REVERT: a 281 ILE cc_start: 0.9811 (mt) cc_final: 0.9604 (mt) REVERT: a 286 MET cc_start: 0.9658 (tmm) cc_final: 0.9175 (ptp) REVERT: b 17 PHE cc_start: 0.9317 (t80) cc_final: 0.8812 (m-10) REVERT: d 171 LYS cc_start: 0.9803 (ptpp) cc_final: 0.9601 (pttt) REVERT: e 51 ARG cc_start: 0.8841 (mmm160) cc_final: 0.8603 (mmm-85) REVERT: e 77 THR cc_start: 0.9231 (t) cc_final: 0.9020 (m) REVERT: g 24 MET cc_start: 0.9531 (mmp) cc_final: 0.9117 (mmp) REVERT: g 32 MET cc_start: 0.9281 (mmm) cc_final: 0.9021 (mmm) REVERT: g 39 MET cc_start: 0.9312 (mmp) cc_final: 0.8727 (mmp) REVERT: g 229 MET cc_start: 0.9762 (mmp) cc_final: 0.9276 (mmm) REVERT: g 237 ASN cc_start: 0.9573 (OUTLIER) cc_final: 0.9310 (m-40) REVERT: p 82 ARG cc_start: 0.9275 (ttp-110) cc_final: 0.9027 (ttp-170) outliers start: 4 outliers final: 1 residues processed: 387 average time/residue: 0.2361 time to fit residues: 151.4272 Evaluate side-chains 307 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 305 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 111 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 459 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 227 optimal weight: 0.3980 chunk 402 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 260 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 397 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN F 366 GLN G 47 GLN R 47 GLN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.027561 restraints weight = 351978.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.028350 restraints weight = 228665.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.029085 restraints weight = 166720.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029555 restraints weight = 131248.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.029860 restraints weight = 110420.476| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37735 Z= 0.162 Angle : 0.609 9.011 51158 Z= 0.326 Chirality : 0.042 0.179 5994 Planarity : 0.004 0.052 6634 Dihedral : 5.355 69.468 5276 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.09 (0.12), residues: 4856 helix: 1.01 (0.10), residues: 2706 sheet: -0.53 (0.21), residues: 557 loop : -1.31 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 231 TYR 0.044 0.002 TYR a 23 PHE 0.039 0.002 PHE E 405 TRP 0.041 0.002 TRP a 261 HIS 0.007 0.001 HIS F 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (37735) covalent geometry : angle 0.60938 / 0.33 (51158) hydrogen bonds : bond 0.04692 / 3.20 ( 2317) hydrogen bonds : angle 5.07928 / 3.54 ( 6804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 383 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8759 (m-30) cc_final: 0.8107 (t0) REVERT: A 355 PHE cc_start: 0.9312 (t80) cc_final: 0.8990 (t80) REVERT: B 49 MET cc_start: 0.8827 (tpt) cc_final: 0.8130 (tpt) REVERT: B 153 SER cc_start: 0.9634 (t) cc_final: 0.9282 (p) REVERT: B 157 MET cc_start: 0.9641 (mtm) cc_final: 0.9434 (mtm) REVERT: B 432 MET cc_start: 0.9562 (mmm) cc_final: 0.9119 (mmm) REVERT: C 49 MET cc_start: 0.9451 (mtp) cc_final: 0.9241 (mtp) REVERT: C 53 MET cc_start: 0.9328 (ttt) cc_final: 0.9100 (tpp) REVERT: C 157 MET cc_start: 0.9583 (mpp) cc_final: 0.9374 (mmm) REVERT: C 199 ILE cc_start: 0.9361 (mm) cc_final: 0.9068 (mm) REVERT: C 263 ASP cc_start: 0.9224 (m-30) cc_final: 0.8339 (m-30) REVERT: C 266 LYS cc_start: 0.9763 (mmtt) cc_final: 0.9557 (mtpp) REVERT: C 413 ASP cc_start: 0.7700 (t0) cc_final: 0.7060 (t0) REVERT: C 432 MET cc_start: 0.9616 (mmp) cc_final: 0.9097 (mmm) REVERT: D 203 MET cc_start: 0.8801 (mpp) cc_final: 0.8513 (mpp) REVERT: D 225 MET cc_start: 0.9661 (mmt) cc_final: 0.9451 (mmm) REVERT: D 245 PHE cc_start: 0.9348 (m-80) cc_final: 0.8810 (m-80) REVERT: D 280 MET cc_start: 0.9565 (tpt) cc_final: 0.9049 (tpt) REVERT: D 319 HIS cc_start: 0.9304 (m90) cc_final: 0.8550 (m90) REVERT: E 1 MET cc_start: 0.8709 (ppp) cc_final: 0.8387 (tmm) REVERT: E 87 MET cc_start: 0.9635 (mpp) cc_final: 0.8935 (mpp) REVERT: E 159 MET cc_start: 0.9735 (mmp) cc_final: 0.9364 (mmm) REVERT: E 203 MET cc_start: 0.9471 (mmm) cc_final: 0.9089 (mmm) REVERT: E 280 MET cc_start: 0.9386 (tpp) cc_final: 0.8986 (tpp) REVERT: E 319 HIS cc_start: 0.9116 (m90) cc_final: 0.8691 (m-70) REVERT: E 450 MET cc_start: 0.9367 (mmp) cc_final: 0.8980 (mmm) REVERT: F 87 MET cc_start: 0.9362 (pmm) cc_final: 0.8562 (pmm) REVERT: F 158 MET cc_start: 0.9708 (tpt) cc_final: 0.9416 (mmp) REVERT: F 208 MET cc_start: 0.9061 (ptp) cc_final: 0.8676 (ptp) REVERT: F 225 MET cc_start: 0.9630 (mmp) cc_final: 0.9362 (mmm) REVERT: F 266 MET cc_start: 0.9002 (mpp) cc_final: 0.8756 (mpp) REVERT: F 299 GLN cc_start: 0.9580 (mt0) cc_final: 0.9250 (mp10) REVERT: H 64 MET cc_start: 0.9530 (mmp) cc_final: 0.9261 (mmp) REVERT: J 18 PHE cc_start: 0.8894 (m-10) cc_final: 0.8669 (m-80) REVERT: K 73 PHE cc_start: 0.9087 (m-10) cc_final: 0.8799 (m-80) REVERT: L 18 PHE cc_start: 0.9232 (t80) cc_final: 0.8905 (t80) REVERT: L 27 PHE cc_start: 0.9533 (m-80) cc_final: 0.8896 (m-80) REVERT: L 60 ASP cc_start: 0.9227 (p0) cc_final: 0.8766 (p0) REVERT: L 64 MET cc_start: 0.8404 (mtp) cc_final: 0.8159 (mtp) REVERT: O 55 ILE cc_start: 0.7954 (mm) cc_final: 0.7660 (mm) REVERT: O 73 PHE cc_start: 0.8586 (m-80) cc_final: 0.8254 (m-80) REVERT: P 53 PHE cc_start: 0.9064 (m-10) cc_final: 0.8802 (m-10) REVERT: P 67 VAL cc_start: 0.7757 (t) cc_final: 0.7295 (t) REVERT: Q 18 PHE cc_start: 0.9434 (t80) cc_final: 0.9232 (t80) REVERT: Q 73 PHE cc_start: 0.9444 (m-10) cc_final: 0.9140 (m-80) REVERT: R 27 PHE cc_start: 0.7717 (m-10) cc_final: 0.7430 (m-80) REVERT: R 52 MET cc_start: 0.9692 (tmm) cc_final: 0.9362 (ptm) REVERT: S 36 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9115 (mm-30) REVERT: a 87 GLU cc_start: 0.9674 (mt-10) cc_final: 0.9324 (mp0) REVERT: a 88 MET cc_start: 0.9716 (mmm) cc_final: 0.9490 (mmm) REVERT: a 91 GLU cc_start: 0.9328 (tt0) cc_final: 0.9030 (pt0) REVERT: a 122 MET cc_start: 0.8839 (tmm) cc_final: 0.8436 (tmm) REVERT: a 126 ASP cc_start: 0.8858 (m-30) cc_final: 0.7938 (m-30) REVERT: a 240 GLU cc_start: 0.9224 (pt0) cc_final: 0.8737 (pt0) REVERT: a 286 MET cc_start: 0.9660 (tmm) cc_final: 0.9187 (ptp) REVERT: b 17 PHE cc_start: 0.9376 (t80) cc_final: 0.8727 (m-10) REVERT: e 127 GLN cc_start: 0.9501 (mp10) cc_final: 0.9300 (mp10) REVERT: g 24 MET cc_start: 0.9573 (mmp) cc_final: 0.9137 (mmp) REVERT: g 32 MET cc_start: 0.9275 (mmm) cc_final: 0.8959 (mmm) REVERT: g 39 MET cc_start: 0.9252 (mmp) cc_final: 0.8747 (mmp) REVERT: g 229 MET cc_start: 0.9778 (mmp) cc_final: 0.9271 (mmm) REVERT: p 82 ARG cc_start: 0.9273 (ttp-110) cc_final: 0.8903 (ttp80) outliers start: 4 outliers final: 1 residues processed: 385 average time/residue: 0.2323 time to fit residues: 149.7143 Evaluate side-chains 298 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 151 optimal weight: 4.9990 chunk 185 optimal weight: 0.0070 chunk 271 optimal weight: 0.7980 chunk 437 optimal weight: 2.9990 chunk 459 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 266 optimal weight: 0.9980 chunk 373 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 370 optimal weight: 20.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN H 47 GLN R 47 GLN b 45 ASN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.038902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.028255 restraints weight = 344621.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.029200 restraints weight = 221459.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029843 restraints weight = 160350.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030314 restraints weight = 127032.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.030635 restraints weight = 106506.360| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37735 Z= 0.125 Angle : 0.587 9.211 51158 Z= 0.310 Chirality : 0.042 0.193 5994 Planarity : 0.004 0.055 6634 Dihedral : 5.143 61.148 5276 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.36 (0.12), residues: 4856 helix: 1.21 (0.10), residues: 2719 sheet: -0.38 (0.21), residues: 563 loop : -1.18 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 51 TYR 0.037 0.001 TYR a 23 PHE 0.041 0.002 PHE S 18 TRP 0.044 0.002 TRP a 261 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (37735) covalent geometry : angle 0.58723 / 0.31 (51158) hydrogen bonds : bond 0.04410 / 3.01 ( 2317) hydrogen bonds : angle 4.84361 / 3.37 ( 6804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8628 (m-30) cc_final: 0.7913 (t0) REVERT: A 258 LEU cc_start: 0.9586 (pp) cc_final: 0.9185 (tp) REVERT: A 355 PHE cc_start: 0.9226 (t80) cc_final: 0.8922 (t80) REVERT: B 49 MET cc_start: 0.8704 (tpt) cc_final: 0.7801 (tpt) REVERT: B 53 MET cc_start: 0.9402 (mtm) cc_final: 0.9015 (mtt) REVERT: B 263 ASP cc_start: 0.8799 (m-30) cc_final: 0.8598 (m-30) REVERT: B 402 ARG cc_start: 0.9331 (mtm180) cc_final: 0.8880 (mtm180) REVERT: B 432 MET cc_start: 0.9532 (mmm) cc_final: 0.9144 (mmm) REVERT: C 49 MET cc_start: 0.9447 (mtp) cc_final: 0.9235 (mtp) REVERT: C 53 MET cc_start: 0.9368 (ttt) cc_final: 0.9109 (tpp) REVERT: C 157 MET cc_start: 0.9586 (mpp) cc_final: 0.9358 (mmm) REVERT: C 179 MET cc_start: 0.9404 (tpp) cc_final: 0.9156 (tpp) REVERT: C 246 MET cc_start: 0.9644 (mmp) cc_final: 0.9356 (mmm) REVERT: C 266 LYS cc_start: 0.9762 (mmtt) cc_final: 0.9510 (mtpp) REVERT: C 413 ASP cc_start: 0.7744 (t0) cc_final: 0.7085 (t0) REVERT: C 432 MET cc_start: 0.9636 (mmp) cc_final: 0.9160 (mmm) REVERT: D 203 MET cc_start: 0.8558 (mpp) cc_final: 0.8354 (mpp) REVERT: D 245 PHE cc_start: 0.9281 (m-80) cc_final: 0.8794 (m-80) REVERT: D 280 MET cc_start: 0.9548 (tpt) cc_final: 0.9044 (tpt) REVERT: D 319 HIS cc_start: 0.9325 (m90) cc_final: 0.8559 (m90) REVERT: E 1 MET cc_start: 0.8705 (ppp) cc_final: 0.8127 (ppp) REVERT: E 159 MET cc_start: 0.9721 (mmp) cc_final: 0.9425 (mmp) REVERT: E 203 MET cc_start: 0.9534 (mmm) cc_final: 0.9220 (mmm) REVERT: E 225 MET cc_start: 0.9482 (mmt) cc_final: 0.9186 (mmm) REVERT: E 280 MET cc_start: 0.9357 (tpp) cc_final: 0.8898 (tpp) REVERT: E 319 HIS cc_start: 0.9045 (m90) cc_final: 0.8599 (m-70) REVERT: E 450 MET cc_start: 0.9355 (mmp) cc_final: 0.8942 (mmm) REVERT: F 158 MET cc_start: 0.9630 (tpt) cc_final: 0.9372 (mmp) REVERT: F 225 MET cc_start: 0.9562 (mmp) cc_final: 0.9302 (mmm) REVERT: F 266 MET cc_start: 0.9071 (mpp) cc_final: 0.8810 (mpp) REVERT: F 299 GLN cc_start: 0.9536 (mt0) cc_final: 0.9229 (mp-120) REVERT: F 402 GLN cc_start: 0.9545 (mt0) cc_final: 0.9277 (mt0) REVERT: H 64 MET cc_start: 0.9505 (mmp) cc_final: 0.8935 (mpp) REVERT: J 18 PHE cc_start: 0.8895 (m-10) cc_final: 0.8630 (m-80) REVERT: K 18 PHE cc_start: 0.9105 (m-80) cc_final: 0.8855 (m-80) REVERT: K 73 PHE cc_start: 0.8984 (m-10) cc_final: 0.8703 (m-80) REVERT: L 18 PHE cc_start: 0.9253 (t80) cc_final: 0.8807 (t80) REVERT: L 27 PHE cc_start: 0.9472 (m-80) cc_final: 0.9065 (m-80) REVERT: L 60 ASP cc_start: 0.9257 (p0) cc_final: 0.8793 (p0) REVERT: L 64 MET cc_start: 0.8434 (mtp) cc_final: 0.8160 (mtp) REVERT: O 55 ILE cc_start: 0.7883 (mm) cc_final: 0.7556 (mm) REVERT: P 33 ARG cc_start: 0.7403 (mmt180) cc_final: 0.6936 (mmt180) REVERT: P 36 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8523 (mt-10) REVERT: P 53 PHE cc_start: 0.9070 (m-10) cc_final: 0.8865 (m-80) REVERT: R 23 THR cc_start: 0.9079 (p) cc_final: 0.8701 (p) REVERT: R 27 PHE cc_start: 0.7670 (m-10) cc_final: 0.7070 (m-80) REVERT: R 52 MET cc_start: 0.9650 (tmm) cc_final: 0.9339 (ptm) REVERT: a 87 GLU cc_start: 0.9673 (mt-10) cc_final: 0.9320 (mp0) REVERT: a 91 GLU cc_start: 0.9343 (tt0) cc_final: 0.8975 (pt0) REVERT: a 122 MET cc_start: 0.8812 (tmm) cc_final: 0.8391 (tmm) REVERT: a 126 ASP cc_start: 0.8835 (m-30) cc_final: 0.8232 (m-30) REVERT: a 240 GLU cc_start: 0.9284 (pt0) cc_final: 0.8755 (pt0) REVERT: a 286 MET cc_start: 0.9667 (tmm) cc_final: 0.9218 (ptp) REVERT: b 17 PHE cc_start: 0.9324 (t80) cc_final: 0.8802 (m-10) REVERT: b 22 MET cc_start: 0.6334 (mmm) cc_final: 0.6095 (mmm) REVERT: b 148 MET cc_start: 0.7750 (tpp) cc_final: 0.6787 (mpp) REVERT: e 127 GLN cc_start: 0.9467 (mp10) cc_final: 0.9243 (mp10) REVERT: g 24 MET cc_start: 0.9595 (mmp) cc_final: 0.9108 (mmp) REVERT: g 32 MET cc_start: 0.9287 (mmm) cc_final: 0.8927 (mmm) REVERT: g 39 MET cc_start: 0.9235 (mmp) cc_final: 0.8780 (mmm) REVERT: g 229 MET cc_start: 0.9751 (mmp) cc_final: 0.9227 (mmm) REVERT: p 82 ARG cc_start: 0.9252 (ttp-110) cc_final: 0.8834 (ttp80) outliers start: 2 outliers final: 2 residues processed: 395 average time/residue: 0.2316 time to fit residues: 152.7988 Evaluate side-chains 305 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 303 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 122 optimal weight: 4.9990 chunk 417 optimal weight: 10.0000 chunk 447 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 289 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 442 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS G 47 GLN R 47 GLN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 138 GLN e 136 ASN g 58 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.037336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.027208 restraints weight = 367791.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.028099 restraints weight = 238616.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.028692 restraints weight = 173369.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.029115 restraints weight = 137887.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.029416 restraints weight = 116423.291| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37735 Z= 0.233 Angle : 0.669 13.791 51158 Z= 0.353 Chirality : 0.043 0.271 5994 Planarity : 0.004 0.051 6634 Dihedral : 5.199 62.225 5276 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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 (0.12), residues: 4856 helix: 1.16 (0.10), residues: 2710 sheet: -0.42 (0.21), residues: 558 loop : -1.23 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 165 TYR 0.034 0.002 TYR a 23 PHE 0.045 0.002 PHE G 18 TRP 0.047 0.002 TRP a 261 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 (37735) covalent geometry : angle 0.66861 / 0.35 (51158) hydrogen bonds : bond 0.04431 / 3.03 ( 2317) hydrogen bonds : angle 5.01160 / 3.50 ( 6804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.9620 (pp) cc_final: 0.9289 (tp) REVERT: A 355 PHE cc_start: 0.9253 (t80) cc_final: 0.8990 (t80) REVERT: B 49 MET cc_start: 0.8926 (tpt) cc_final: 0.8153 (tpt) REVERT: B 53 MET cc_start: 0.9417 (mtm) cc_final: 0.8830 (mtt) REVERT: B 153 SER cc_start: 0.9500 (t) cc_final: 0.9023 (p) REVERT: B 157 MET cc_start: 0.9429 (mtm) cc_final: 0.9073 (mpp) REVERT: B 402 ARG cc_start: 0.9349 (mtm180) cc_final: 0.8931 (mtm180) REVERT: C 53 MET cc_start: 0.9422 (ttt) cc_final: 0.9200 (tpp) REVERT: C 157 MET cc_start: 0.9633 (mpp) cc_final: 0.9424 (mmm) REVERT: C 179 MET cc_start: 0.9375 (tpp) cc_final: 0.9140 (tpp) REVERT: C 246 MET cc_start: 0.9645 (mmp) cc_final: 0.9421 (mmm) REVERT: C 263 ASP cc_start: 0.9227 (m-30) cc_final: 0.8411 (m-30) REVERT: C 413 ASP cc_start: 0.7904 (t0) cc_final: 0.7249 (t0) REVERT: C 432 MET cc_start: 0.9637 (mmp) cc_final: 0.9078 (mmm) REVERT: D 159 MET cc_start: 0.9716 (tpp) cc_final: 0.9332 (tpp) REVERT: D 245 PHE cc_start: 0.9379 (m-80) cc_final: 0.8894 (m-80) REVERT: D 280 MET cc_start: 0.9588 (tpt) cc_final: 0.9125 (tpt) REVERT: D 319 HIS cc_start: 0.9395 (m90) cc_final: 0.8662 (m90) REVERT: E 1 MET cc_start: 0.8762 (ppp) cc_final: 0.8540 (ppp) REVERT: E 87 MET cc_start: 0.9317 (mpp) cc_final: 0.8501 (mpp) REVERT: E 159 MET cc_start: 0.9733 (mmp) cc_final: 0.9396 (mmp) REVERT: E 203 MET cc_start: 0.9510 (mmm) cc_final: 0.8964 (mmm) REVERT: E 450 MET cc_start: 0.9383 (mmp) cc_final: 0.9026 (mmm) REVERT: F 158 MET cc_start: 0.9664 (tpt) cc_final: 0.9350 (mmp) REVERT: F 208 MET cc_start: 0.9091 (ptp) cc_final: 0.8866 (pmm) REVERT: F 225 MET cc_start: 0.9593 (mmp) cc_final: 0.9325 (mmm) REVERT: F 266 MET cc_start: 0.9115 (mpp) cc_final: 0.8859 (mpp) REVERT: F 299 GLN cc_start: 0.9580 (mt0) cc_final: 0.9247 (mp-120) REVERT: F 402 GLN cc_start: 0.9536 (mt0) cc_final: 0.9282 (mt0) REVERT: H 64 MET cc_start: 0.9506 (mmp) cc_final: 0.9040 (mtp) REVERT: J 18 PHE cc_start: 0.8991 (m-10) cc_final: 0.8765 (m-80) REVERT: K 18 PHE cc_start: 0.9169 (m-80) cc_final: 0.8905 (m-80) REVERT: K 73 PHE cc_start: 0.9057 (m-10) cc_final: 0.8789 (m-80) REVERT: L 18 PHE cc_start: 0.9038 (t80) cc_final: 0.8500 (t80) REVERT: L 27 PHE cc_start: 0.9514 (m-80) cc_final: 0.8999 (m-80) REVERT: L 60 ASP cc_start: 0.9288 (p0) cc_final: 0.8820 (p0) REVERT: L 64 MET cc_start: 0.8458 (mtp) cc_final: 0.8192 (mtp) REVERT: O 55 ILE cc_start: 0.8109 (mm) cc_final: 0.7785 (mm) REVERT: O 64 MET cc_start: 0.8913 (mmp) cc_final: 0.8710 (mmm) REVERT: O 73 PHE cc_start: 0.8860 (m-80) cc_final: 0.8490 (m-80) REVERT: P 53 PHE cc_start: 0.9082 (m-10) cc_final: 0.8829 (m-80) REVERT: P 67 VAL cc_start: 0.8659 (p) cc_final: 0.8257 (m) REVERT: Q 73 PHE cc_start: 0.9455 (m-10) cc_final: 0.9113 (m-80) REVERT: R 23 THR cc_start: 0.9114 (p) cc_final: 0.8790 (p) REVERT: R 27 PHE cc_start: 0.7733 (m-10) cc_final: 0.7120 (m-80) REVERT: R 52 MET cc_start: 0.9683 (tmm) cc_final: 0.9357 (ptm) REVERT: a 87 GLU cc_start: 0.9639 (mt-10) cc_final: 0.9284 (mp0) REVERT: a 88 MET cc_start: 0.9215 (mtt) cc_final: 0.8904 (mtp) REVERT: a 91 GLU cc_start: 0.9347 (tt0) cc_final: 0.9029 (pt0) REVERT: a 236 MET cc_start: 0.8560 (tmm) cc_final: 0.7259 (tmm) REVERT: a 240 GLU cc_start: 0.9358 (pt0) cc_final: 0.8799 (pt0) REVERT: a 281 ILE cc_start: 0.9797 (mt) cc_final: 0.9570 (mt) REVERT: a 286 MET cc_start: 0.9695 (tmm) cc_final: 0.9243 (ptp) REVERT: b 17 PHE cc_start: 0.9423 (t80) cc_final: 0.8803 (m-10) REVERT: b 148 MET cc_start: 0.7766 (tpp) cc_final: 0.6759 (mpp) REVERT: e 127 GLN cc_start: 0.9490 (mp10) cc_final: 0.9267 (mp10) REVERT: g 24 MET cc_start: 0.9671 (mmp) cc_final: 0.9205 (mmp) REVERT: g 32 MET cc_start: 0.9277 (mmm) cc_final: 0.8817 (tpt) REVERT: g 39 MET cc_start: 0.9232 (mmp) cc_final: 0.8814 (mmm) REVERT: g 229 MET cc_start: 0.9715 (mmp) cc_final: 0.9195 (mmm) REVERT: p 82 ARG cc_start: 0.9311 (ttp-110) cc_final: 0.9037 (ttp80) outliers start: 1 outliers final: 1 residues processed: 368 average time/residue: 0.2270 time to fit residues: 140.4436 Evaluate side-chains 290 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 214 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 420 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 chunk 375 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN R 47 GLN ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.027430 restraints weight = 360344.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.028334 restraints weight = 234474.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.028968 restraints weight = 169806.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.029409 restraints weight = 134151.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.029719 restraints weight = 112856.180| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37735 Z= 0.175 Angle : 0.614 10.202 51158 Z= 0.326 Chirality : 0.042 0.224 5994 Planarity : 0.004 0.052 6634 Dihedral : 5.123 61.694 5276 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.38 (0.12), residues: 4856 helix: 1.22 (0.10), residues: 2730 sheet: -0.40 (0.21), residues: 568 loop : -1.17 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 132 TYR 0.031 0.001 TYR a 23 PHE 0.048 0.002 PHE S 18 TRP 0.051 0.002 TRP a 261 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (37735) covalent geometry : angle 0.61361 / 0.33 (51158) hydrogen bonds : bond 0.04303 / 2.94 ( 2317) hydrogen bonds : angle 4.87935 / 3.41 ( 6804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 365 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.9643 (pp) cc_final: 0.9287 (tp) REVERT: A 355 PHE cc_start: 0.9207 (t80) cc_final: 0.8952 (t80) REVERT: B 49 MET cc_start: 0.8883 (tpt) cc_final: 0.7976 (tpt) REVERT: B 53 MET cc_start: 0.9420 (mtm) cc_final: 0.8831 (mtt) REVERT: B 153 SER cc_start: 0.9634 (t) cc_final: 0.9426 (p) REVERT: B 157 MET cc_start: 0.9676 (mtm) cc_final: 0.9406 (mtm) REVERT: B 402 ARG cc_start: 0.9335 (mtm180) cc_final: 0.8920 (mtm180) REVERT: B 432 MET cc_start: 0.9573 (mmm) cc_final: 0.9123 (tpp) REVERT: C 49 MET cc_start: 0.9512 (mtm) cc_final: 0.9178 (mpp) REVERT: C 53 MET cc_start: 0.9426 (ttt) cc_final: 0.9201 (tpp) REVERT: C 157 MET cc_start: 0.9649 (mpp) cc_final: 0.9425 (mmm) REVERT: C 179 MET cc_start: 0.9357 (tpp) cc_final: 0.9127 (tpp) REVERT: C 235 MET cc_start: 0.9461 (tpt) cc_final: 0.9154 (tpt) REVERT: C 246 MET cc_start: 0.9628 (mmp) cc_final: 0.9415 (mmm) REVERT: C 263 ASP cc_start: 0.9125 (m-30) cc_final: 0.8587 (m-30) REVERT: C 413 ASP cc_start: 0.8067 (t0) cc_final: 0.7506 (t0) REVERT: C 432 MET cc_start: 0.9636 (mmp) cc_final: 0.8944 (mmp) REVERT: D 159 MET cc_start: 0.9716 (tpp) cc_final: 0.9328 (tpp) REVERT: D 245 PHE cc_start: 0.9377 (m-80) cc_final: 0.8868 (m-80) REVERT: D 280 MET cc_start: 0.9543 (tpt) cc_final: 0.9150 (tpt) REVERT: D 319 HIS cc_start: 0.9367 (m90) cc_final: 0.8735 (m90) REVERT: E 1 MET cc_start: 0.8804 (ppp) cc_final: 0.8556 (ppp) REVERT: E 87 MET cc_start: 0.9301 (mpp) cc_final: 0.8498 (mpp) REVERT: E 159 MET cc_start: 0.9731 (mmp) cc_final: 0.9406 (mmp) REVERT: E 203 MET cc_start: 0.9513 (mmm) cc_final: 0.8989 (mmm) REVERT: E 280 MET cc_start: 0.9414 (ttm) cc_final: 0.9054 (ttm) REVERT: E 319 HIS cc_start: 0.9124 (m-70) cc_final: 0.8743 (m170) REVERT: E 450 MET cc_start: 0.9410 (mmp) cc_final: 0.8996 (mmm) REVERT: F 158 MET cc_start: 0.9678 (tpt) cc_final: 0.9352 (mmp) REVERT: F 192 MET cc_start: 0.9703 (mmp) cc_final: 0.9493 (mmm) REVERT: F 225 MET cc_start: 0.9594 (mmp) cc_final: 0.9328 (mmm) REVERT: F 266 MET cc_start: 0.9111 (mpp) cc_final: 0.8829 (mpp) REVERT: F 299 GLN cc_start: 0.9578 (mt0) cc_final: 0.9254 (mp-120) REVERT: F 402 GLN cc_start: 0.9523 (mt0) cc_final: 0.9292 (mt0) REVERT: G 18 PHE cc_start: 0.8914 (t80) cc_final: 0.8677 (t80) REVERT: H 30 LEU cc_start: 0.9463 (mm) cc_final: 0.9186 (pp) REVERT: H 64 MET cc_start: 0.9501 (mmp) cc_final: 0.9003 (mtp) REVERT: J 18 PHE cc_start: 0.8762 (m-10) cc_final: 0.8519 (m-10) REVERT: K 18 PHE cc_start: 0.9211 (m-80) cc_final: 0.8944 (m-80) REVERT: K 73 PHE cc_start: 0.9045 (m-10) cc_final: 0.8773 (m-80) REVERT: L 18 PHE cc_start: 0.9017 (t80) cc_final: 0.8457 (t80) REVERT: L 27 PHE cc_start: 0.9544 (m-80) cc_final: 0.8978 (t80) REVERT: L 52 MET cc_start: 0.9870 (tpt) cc_final: 0.9667 (tpt) REVERT: L 64 MET cc_start: 0.8428 (mtp) cc_final: 0.8189 (mtt) REVERT: O 18 PHE cc_start: 0.9565 (m-10) cc_final: 0.9357 (m-80) REVERT: O 55 ILE cc_start: 0.8126 (mm) cc_final: 0.7800 (mm) REVERT: O 73 PHE cc_start: 0.8792 (m-80) cc_final: 0.8397 (m-80) REVERT: P 53 PHE cc_start: 0.9057 (m-10) cc_final: 0.8807 (m-80) REVERT: P 65 ILE cc_start: 0.8705 (mp) cc_final: 0.7392 (mp) REVERT: P 67 VAL cc_start: 0.8576 (p) cc_final: 0.8275 (m) REVERT: R 23 THR cc_start: 0.9075 (p) cc_final: 0.8759 (p) REVERT: R 27 PHE cc_start: 0.7687 (m-10) cc_final: 0.6980 (m-80) REVERT: R 30 LEU cc_start: 0.9112 (mm) cc_final: 0.8497 (pp) REVERT: R 52 MET cc_start: 0.9651 (tmm) cc_final: 0.9339 (ptm) REVERT: a 87 GLU cc_start: 0.9630 (mt-10) cc_final: 0.9217 (mp0) REVERT: a 88 MET cc_start: 0.9282 (mtt) cc_final: 0.8747 (mmm) REVERT: a 91 GLU cc_start: 0.9301 (tt0) cc_final: 0.8989 (pt0) REVERT: a 122 MET cc_start: 0.8898 (tmm) cc_final: 0.8691 (tmm) REVERT: a 126 ASP cc_start: 0.8709 (m-30) cc_final: 0.8151 (m-30) REVERT: a 281 ILE cc_start: 0.9805 (mt) cc_final: 0.9602 (mt) REVERT: a 286 MET cc_start: 0.9703 (tmm) cc_final: 0.9241 (ptp) REVERT: b 17 PHE cc_start: 0.9491 (t80) cc_final: 0.8787 (m-10) REVERT: b 148 MET cc_start: 0.7663 (tpp) cc_final: 0.6660 (mpp) REVERT: e 123 GLU cc_start: 0.9611 (OUTLIER) cc_final: 0.9345 (pp20) REVERT: e 127 GLN cc_start: 0.9476 (mp10) cc_final: 0.9235 (mp10) REVERT: g 24 MET cc_start: 0.9690 (mmp) cc_final: 0.9230 (mmp) REVERT: g 32 MET cc_start: 0.9286 (mmm) cc_final: 0.9006 (mmm) REVERT: g 39 MET cc_start: 0.9065 (mmp) cc_final: 0.8674 (mmm) REVERT: g 229 MET cc_start: 0.9721 (mmp) cc_final: 0.9186 (mmm) REVERT: p 82 ARG cc_start: 0.9285 (ttp-110) cc_final: 0.8921 (ttp80) outliers start: 3 outliers final: 1 residues processed: 368 average time/residue: 0.2273 time to fit residues: 140.9331 Evaluate side-chains 293 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 71 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 348 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 270 optimal weight: 2.9990 chunk 411 optimal weight: 7.9990 chunk 273 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 208 ASN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN G 47 GLN G 49 GLN R 47 GLN ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.038165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.027750 restraints weight = 356149.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.028696 restraints weight = 230706.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029331 restraints weight = 167207.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.029784 restraints weight = 132533.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030096 restraints weight = 111180.722| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37735 Z= 0.143 Angle : 0.601 10.111 51158 Z= 0.316 Chirality : 0.042 0.299 5994 Planarity : 0.004 0.052 6634 Dihedral : 5.006 59.346 5276 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.55 (0.12), residues: 4856 helix: 1.35 (0.10), residues: 2728 sheet: -0.28 (0.21), residues: 550 loop : -1.09 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 90 TYR 0.026 0.001 TYR a 23 PHE 0.046 0.001 PHE S 18 TRP 0.053 0.002 TRP a 261 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (37735) covalent geometry : angle 0.60091 / 0.32 (51158) hydrogen bonds : bond 0.04203 / 2.88 ( 2317) hydrogen bonds : angle 4.77990 / 3.35 ( 6804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.9691 (pp) cc_final: 0.9358 (tp) REVERT: A 355 PHE cc_start: 0.9183 (t80) cc_final: 0.8914 (t80) REVERT: B 49 MET cc_start: 0.8898 (tpt) cc_final: 0.8067 (tpt) REVERT: B 53 MET cc_start: 0.9432 (mtm) cc_final: 0.8771 (mtt) REVERT: B 153 SER cc_start: 0.9657 (t) cc_final: 0.9304 (p) REVERT: B 157 MET cc_start: 0.9688 (mtm) cc_final: 0.9272 (ptp) REVERT: B 235 MET cc_start: 0.9464 (mmp) cc_final: 0.9182 (mmm) REVERT: B 402 ARG cc_start: 0.9370 (mtm180) cc_final: 0.9095 (mtm180) REVERT: B 432 MET cc_start: 0.9578 (mmm) cc_final: 0.8985 (mmt) REVERT: C 49 MET cc_start: 0.9551 (mtm) cc_final: 0.9157 (mtm) REVERT: C 157 MET cc_start: 0.9664 (mpp) cc_final: 0.9451 (mmm) REVERT: C 179 MET cc_start: 0.9344 (tpp) cc_final: 0.9117 (tpp) REVERT: C 246 MET cc_start: 0.9632 (mmp) cc_final: 0.9417 (mmm) REVERT: C 263 ASP cc_start: 0.9089 (m-30) cc_final: 0.8533 (m-30) REVERT: C 413 ASP cc_start: 0.8080 (t0) cc_final: 0.7504 (t0) REVERT: C 432 MET cc_start: 0.9650 (mmp) cc_final: 0.8986 (mmp) REVERT: D 159 MET cc_start: 0.9744 (tpp) cc_final: 0.9379 (tpp) REVERT: D 203 MET cc_start: 0.8768 (mpp) cc_final: 0.8543 (mpp) REVERT: D 245 PHE cc_start: 0.9364 (m-80) cc_final: 0.8890 (m-80) REVERT: D 280 MET cc_start: 0.9531 (tpt) cc_final: 0.9162 (tpt) REVERT: D 319 HIS cc_start: 0.9329 (m90) cc_final: 0.8717 (m90) REVERT: E 1 MET cc_start: 0.8841 (ppp) cc_final: 0.8387 (ppp) REVERT: E 87 MET cc_start: 0.9299 (mpp) cc_final: 0.8522 (mpp) REVERT: E 159 MET cc_start: 0.9745 (mmp) cc_final: 0.9427 (mmp) REVERT: E 203 MET cc_start: 0.9505 (mmm) cc_final: 0.9008 (mmm) REVERT: E 280 MET cc_start: 0.9361 (ttm) cc_final: 0.9037 (ttm) REVERT: E 319 HIS cc_start: 0.9163 (m-70) cc_final: 0.8718 (m170) REVERT: E 450 MET cc_start: 0.9434 (mmp) cc_final: 0.9049 (mmm) REVERT: F 158 MET cc_start: 0.9732 (tpt) cc_final: 0.9367 (mmp) REVERT: F 192 MET cc_start: 0.9730 (mmp) cc_final: 0.9522 (mmm) REVERT: F 225 MET cc_start: 0.9601 (mmp) cc_final: 0.9340 (mmm) REVERT: F 266 MET cc_start: 0.9082 (mpp) cc_final: 0.8791 (mpp) REVERT: F 299 GLN cc_start: 0.9595 (mt0) cc_final: 0.9230 (mp-120) REVERT: F 402 GLN cc_start: 0.9538 (mt0) cc_final: 0.9274 (mt0) REVERT: G 18 PHE cc_start: 0.9023 (t80) cc_final: 0.8741 (t80) REVERT: H 30 LEU cc_start: 0.9465 (mm) cc_final: 0.9148 (pp) REVERT: H 64 MET cc_start: 0.9468 (mmp) cc_final: 0.8963 (mtp) REVERT: J 14 ILE cc_start: 0.9420 (mm) cc_final: 0.8640 (pt) REVERT: K 18 PHE cc_start: 0.9224 (m-80) cc_final: 0.8848 (m-80) REVERT: K 73 PHE cc_start: 0.9036 (m-10) cc_final: 0.8765 (m-80) REVERT: L 27 PHE cc_start: 0.9512 (m-80) cc_final: 0.8980 (m-80) REVERT: O 18 PHE cc_start: 0.9562 (m-10) cc_final: 0.9348 (m-80) REVERT: O 55 ILE cc_start: 0.8020 (mm) cc_final: 0.7686 (mm) REVERT: O 73 PHE cc_start: 0.8820 (m-80) cc_final: 0.8411 (m-80) REVERT: P 53 PHE cc_start: 0.9027 (m-10) cc_final: 0.8763 (m-10) REVERT: P 67 VAL cc_start: 0.8652 (p) cc_final: 0.8383 (m) REVERT: R 23 THR cc_start: 0.9052 (p) cc_final: 0.8708 (p) REVERT: R 27 PHE cc_start: 0.7643 (m-10) cc_final: 0.6973 (m-80) REVERT: R 30 LEU cc_start: 0.9054 (mm) cc_final: 0.8437 (pp) REVERT: R 52 MET cc_start: 0.9620 (tmm) cc_final: 0.9313 (ptm) REVERT: a 87 GLU cc_start: 0.9631 (mt-10) cc_final: 0.9215 (mp0) REVERT: a 88 MET cc_start: 0.9376 (mtt) cc_final: 0.8993 (mtt) REVERT: a 91 GLU cc_start: 0.9290 (tt0) cc_final: 0.8983 (pt0) REVERT: a 126 ASP cc_start: 0.8500 (m-30) cc_final: 0.8112 (m-30) REVERT: a 236 MET cc_start: 0.8471 (tmm) cc_final: 0.7370 (ppp) REVERT: a 240 GLU cc_start: 0.9246 (pt0) cc_final: 0.8780 (pt0) REVERT: a 286 MET cc_start: 0.9704 (tmm) cc_final: 0.9256 (ptp) REVERT: b 17 PHE cc_start: 0.9521 (t80) cc_final: 0.8854 (m-10) REVERT: b 22 MET cc_start: 0.6012 (mmm) cc_final: 0.5740 (mmm) REVERT: e 113 ASP cc_start: 0.9664 (t70) cc_final: 0.9389 (t0) REVERT: e 127 GLN cc_start: 0.9489 (mp10) cc_final: 0.9240 (mp10) REVERT: g 24 MET cc_start: 0.9661 (mmp) cc_final: 0.9199 (mmp) REVERT: g 26 MET cc_start: 0.9354 (ptp) cc_final: 0.8981 (ptp) REVERT: g 39 MET cc_start: 0.9035 (mmp) cc_final: 0.8661 (mmm) REVERT: g 229 MET cc_start: 0.9737 (mmp) cc_final: 0.9190 (mmm) REVERT: p 82 ARG cc_start: 0.9301 (ttp-110) cc_final: 0.8947 (ttp80) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.2297 time to fit residues: 142.5172 Evaluate side-chains 298 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 414 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 417 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 415 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 233 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 270 optimal weight: 0.0570 chunk 366 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 273 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS G 47 GLN ** O 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.028650 restraints weight = 345152.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029612 restraints weight = 219376.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030257 restraints weight = 158675.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030718 restraints weight = 124956.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.031044 restraints weight = 104729.663| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37735 Z= 0.123 Angle : 0.603 12.493 51158 Z= 0.313 Chirality : 0.043 0.236 5994 Planarity : 0.004 0.062 6634 Dihedral : 4.864 55.626 5276 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.70 (0.12), residues: 4856 helix: 1.43 (0.10), residues: 2728 sheet: -0.13 (0.21), residues: 546 loop : -0.98 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 40 TYR 0.023 0.001 TYR a 23 PHE 0.040 0.001 PHE E 405 TRP 0.057 0.002 TRP a 261 HIS 0.006 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (37735) covalent geometry : angle 0.60268 / 0.31 (51158) hydrogen bonds : bond 0.04112 / 2.83 ( 2317) hydrogen bonds : angle 4.64049 / 3.25 ( 6804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.9665 (pp) cc_final: 0.9299 (tp) REVERT: A 355 PHE cc_start: 0.9107 (t80) cc_final: 0.8863 (t80) REVERT: A 484 MET cc_start: 0.9493 (ptp) cc_final: 0.9277 (mpp) REVERT: B 49 MET cc_start: 0.8801 (tpt) cc_final: 0.7802 (tpt) REVERT: B 53 MET cc_start: 0.9456 (mtm) cc_final: 0.9167 (mtt) REVERT: B 157 MET cc_start: 0.9653 (mtm) cc_final: 0.9337 (ptp) REVERT: B 402 ARG cc_start: 0.9379 (mtm180) cc_final: 0.8985 (mtm180) REVERT: B 432 MET cc_start: 0.9523 (mmm) cc_final: 0.9313 (tpp) REVERT: C 49 MET cc_start: 0.9578 (mtm) cc_final: 0.9213 (mpp) REVERT: C 157 MET cc_start: 0.9665 (mpp) cc_final: 0.9440 (mmm) REVERT: C 246 MET cc_start: 0.9626 (mmp) cc_final: 0.9416 (mmm) REVERT: C 263 ASP cc_start: 0.9028 (m-30) cc_final: 0.8438 (m-30) REVERT: C 432 MET cc_start: 0.9641 (mmp) cc_final: 0.9006 (mmp) REVERT: D 203 MET cc_start: 0.8710 (mpp) cc_final: 0.8476 (mpp) REVERT: D 245 PHE cc_start: 0.9298 (m-80) cc_final: 0.8882 (m-80) REVERT: D 280 MET cc_start: 0.9489 (tpt) cc_final: 0.9127 (tpt) REVERT: D 319 HIS cc_start: 0.9372 (m90) cc_final: 0.8803 (m90) REVERT: E 1 MET cc_start: 0.8850 (ppp) cc_final: 0.8195 (ppp) REVERT: E 87 MET cc_start: 0.9272 (mpp) cc_final: 0.8510 (mpp) REVERT: E 159 MET cc_start: 0.9717 (mmp) cc_final: 0.9307 (mmp) REVERT: E 203 MET cc_start: 0.9434 (mmm) cc_final: 0.8963 (mmm) REVERT: E 225 MET cc_start: 0.9449 (mmt) cc_final: 0.9164 (mmm) REVERT: E 280 MET cc_start: 0.9356 (ttm) cc_final: 0.9105 (ttm) REVERT: E 319 HIS cc_start: 0.9111 (m-70) cc_final: 0.8747 (m170) REVERT: E 450 MET cc_start: 0.9436 (mmp) cc_final: 0.9063 (mmm) REVERT: F 55 MET cc_start: 0.9545 (mmm) cc_final: 0.8869 (mmm) REVERT: F 158 MET cc_start: 0.9699 (tpt) cc_final: 0.9349 (mmp) REVERT: F 225 MET cc_start: 0.9566 (mmp) cc_final: 0.9325 (mmm) REVERT: F 266 MET cc_start: 0.9052 (mpp) cc_final: 0.8765 (mpp) REVERT: F 299 GLN cc_start: 0.9554 (mt0) cc_final: 0.9197 (mp-120) REVERT: F 402 GLN cc_start: 0.9527 (mt0) cc_final: 0.9271 (mt0) REVERT: H 30 LEU cc_start: 0.9487 (mm) cc_final: 0.9054 (pp) REVERT: H 64 MET cc_start: 0.9442 (mmp) cc_final: 0.8925 (mtp) REVERT: J 14 ILE cc_start: 0.9354 (mm) cc_final: 0.8587 (pt) REVERT: J 18 PHE cc_start: 0.8669 (m-10) cc_final: 0.8466 (m-80) REVERT: K 18 PHE cc_start: 0.9211 (m-80) cc_final: 0.8901 (m-80) REVERT: K 73 PHE cc_start: 0.8949 (m-10) cc_final: 0.8671 (m-80) REVERT: L 27 PHE cc_start: 0.9500 (m-80) cc_final: 0.9014 (m-80) REVERT: L 30 LEU cc_start: 0.9194 (pp) cc_final: 0.8887 (pp) REVERT: L 52 MET cc_start: 0.9860 (tpt) cc_final: 0.9582 (ttp) REVERT: L 60 ASP cc_start: 0.8529 (m-30) cc_final: 0.8328 (m-30) REVERT: O 55 ILE cc_start: 0.7879 (mm) cc_final: 0.7657 (mm) REVERT: O 73 PHE cc_start: 0.8800 (m-80) cc_final: 0.8506 (m-80) REVERT: P 36 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8426 (mt-10) REVERT: P 50 THR cc_start: 0.9288 (p) cc_final: 0.8974 (p) REVERT: P 53 PHE cc_start: 0.9042 (m-10) cc_final: 0.8826 (m-10) REVERT: P 67 VAL cc_start: 0.8499 (p) cc_final: 0.8177 (m) REVERT: Q 73 PHE cc_start: 0.9455 (m-10) cc_final: 0.9122 (m-80) REVERT: R 27 PHE cc_start: 0.7726 (m-10) cc_final: 0.7150 (m-80) REVERT: R 52 MET cc_start: 0.9600 (tmm) cc_final: 0.9321 (ptm) REVERT: a 87 GLU cc_start: 0.9639 (mt-10) cc_final: 0.9231 (mp0) REVERT: a 88 MET cc_start: 0.9410 (mtt) cc_final: 0.9005 (mtt) REVERT: a 91 GLU cc_start: 0.9286 (tt0) cc_final: 0.9016 (pt0) REVERT: a 236 MET cc_start: 0.8360 (tmm) cc_final: 0.7730 (ppp) REVERT: a 281 ILE cc_start: 0.9805 (mt) cc_final: 0.9569 (mt) REVERT: a 286 MET cc_start: 0.9695 (tmm) cc_final: 0.9266 (ptp) REVERT: b 17 PHE cc_start: 0.9512 (t80) cc_final: 0.9018 (m-10) REVERT: b 22 MET cc_start: 0.6013 (mmm) cc_final: 0.5717 (mmm) REVERT: e 22 MET cc_start: 0.9598 (mpp) cc_final: 0.9390 (mpp) REVERT: e 113 ASP cc_start: 0.9666 (t70) cc_final: 0.9407 (t0) REVERT: e 127 GLN cc_start: 0.9451 (mp10) cc_final: 0.9198 (mp10) REVERT: g 24 MET cc_start: 0.9665 (mmp) cc_final: 0.9193 (mmp) REVERT: g 26 MET cc_start: 0.9333 (ptp) cc_final: 0.8974 (ptp) REVERT: g 39 MET cc_start: 0.9012 (mmp) cc_final: 0.8632 (mmm) REVERT: g 49 MET cc_start: 0.9430 (ttt) cc_final: 0.9047 (tmm) REVERT: g 229 MET cc_start: 0.9759 (mmp) cc_final: 0.9197 (mmm) REVERT: p 22 MET cc_start: 0.9106 (mmp) cc_final: 0.8887 (tmm) REVERT: p 82 ARG cc_start: 0.9294 (ttp-110) cc_final: 0.8968 (ttp80) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2267 time to fit residues: 142.1391 Evaluate side-chains 296 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 355 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 381 optimal weight: 7.9990 chunk 393 optimal weight: 2.9990 chunk 337 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 447 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN R 47 GLN ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 151 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.038541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.027987 restraints weight = 350911.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.028914 restraints weight = 228186.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029559 restraints weight = 165930.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030011 restraints weight = 131293.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.030339 restraints weight = 110384.491| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37735 Z= 0.147 Angle : 0.606 11.121 51158 Z= 0.317 Chirality : 0.042 0.308 5994 Planarity : 0.004 0.052 6634 Dihedral : 4.822 56.386 5276 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.73 (0.12), residues: 4856 helix: 1.46 (0.10), residues: 2723 sheet: -0.12 (0.21), residues: 550 loop : -0.96 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 231 TYR 0.051 0.001 TYR a 23 PHE 0.063 0.002 PHE G 18 TRP 0.061 0.002 TRP a 261 HIS 0.004 0.001 HIS p 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (37735) covalent geometry : angle 0.60643 / 0.32 (51158) hydrogen bonds : bond 0.04070 / 2.80 ( 2317) hydrogen bonds : angle 4.68556 / 3.28 ( 6804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.9685 (pp) cc_final: 0.9352 (tp) REVERT: A 457 MET cc_start: 0.9360 (mmm) cc_final: 0.8569 (tpp) REVERT: B 49 MET cc_start: 0.8864 (tpt) cc_final: 0.8103 (tpt) REVERT: B 53 MET cc_start: 0.9456 (mtm) cc_final: 0.8808 (mtt) REVERT: B 157 MET cc_start: 0.9700 (mtm) cc_final: 0.9193 (ptp) REVERT: B 179 MET cc_start: 0.9230 (mmp) cc_final: 0.8937 (mmm) REVERT: B 402 ARG cc_start: 0.9382 (mtm180) cc_final: 0.8997 (mtm180) REVERT: B 432 MET cc_start: 0.9532 (mmm) cc_final: 0.9298 (tpp) REVERT: C 49 MET cc_start: 0.9559 (mtm) cc_final: 0.9167 (mtm) REVERT: C 246 MET cc_start: 0.9623 (mmp) cc_final: 0.9412 (mmm) REVERT: C 432 MET cc_start: 0.9669 (mmp) cc_final: 0.8999 (mmp) REVERT: D 159 MET cc_start: 0.9632 (tpp) cc_final: 0.9364 (tpp) REVERT: D 245 PHE cc_start: 0.9365 (m-80) cc_final: 0.8893 (m-80) REVERT: D 280 MET cc_start: 0.9509 (tpt) cc_final: 0.9163 (tpt) REVERT: D 319 HIS cc_start: 0.9410 (m90) cc_final: 0.8876 (m90) REVERT: D 410 HIS cc_start: 0.8591 (t70) cc_final: 0.8229 (m90) REVERT: E 1 MET cc_start: 0.8842 (ppp) cc_final: 0.8187 (ppp) REVERT: E 87 MET cc_start: 0.9228 (mpp) cc_final: 0.8552 (mpp) REVERT: E 159 MET cc_start: 0.9716 (mmp) cc_final: 0.9418 (mmp) REVERT: E 203 MET cc_start: 0.9395 (mmm) cc_final: 0.8519 (mmm) REVERT: E 225 MET cc_start: 0.9471 (mmt) cc_final: 0.9190 (mmm) REVERT: E 319 HIS cc_start: 0.9143 (m-70) cc_final: 0.8834 (m-70) REVERT: E 450 MET cc_start: 0.9421 (mmp) cc_final: 0.9007 (mmm) REVERT: F 158 MET cc_start: 0.9706 (tpt) cc_final: 0.9348 (mmp) REVERT: F 225 MET cc_start: 0.9591 (mmp) cc_final: 0.9343 (mmm) REVERT: F 266 MET cc_start: 0.9086 (mpp) cc_final: 0.8787 (mpp) REVERT: F 280 MET cc_start: 0.9418 (mmp) cc_final: 0.8494 (mmm) REVERT: F 299 GLN cc_start: 0.9558 (mt0) cc_final: 0.9193 (mp-120) REVERT: F 402 GLN cc_start: 0.9516 (mt0) cc_final: 0.9275 (mt0) REVERT: H 30 LEU cc_start: 0.9499 (mm) cc_final: 0.9157 (pp) REVERT: H 64 MET cc_start: 0.9446 (mmp) cc_final: 0.8935 (mtp) REVERT: J 14 ILE cc_start: 0.9376 (mm) cc_final: 0.8605 (pt) REVERT: J 18 PHE cc_start: 0.8705 (m-10) cc_final: 0.8478 (m-80) REVERT: K 18 PHE cc_start: 0.9164 (m-80) cc_final: 0.8860 (m-80) REVERT: K 73 PHE cc_start: 0.8995 (m-10) cc_final: 0.8688 (m-10) REVERT: L 27 PHE cc_start: 0.9540 (m-80) cc_final: 0.8979 (m-80) REVERT: L 30 LEU cc_start: 0.9224 (pp) cc_final: 0.8978 (pp) REVERT: L 60 ASP cc_start: 0.8682 (m-30) cc_final: 0.8346 (m-30) REVERT: O 55 ILE cc_start: 0.7882 (mm) cc_final: 0.7668 (mm) REVERT: O 64 MET cc_start: 0.8929 (mmp) cc_final: 0.8702 (mmm) REVERT: O 73 PHE cc_start: 0.8802 (m-80) cc_final: 0.8394 (m-80) REVERT: P 36 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8367 (mt-10) REVERT: P 53 PHE cc_start: 0.9087 (m-10) cc_final: 0.8846 (m-80) REVERT: P 67 VAL cc_start: 0.8561 (p) cc_final: 0.8273 (m) REVERT: Q 73 PHE cc_start: 0.9480 (m-10) cc_final: 0.9150 (m-80) REVERT: R 23 THR cc_start: 0.9074 (p) cc_final: 0.8743 (p) REVERT: R 27 PHE cc_start: 0.7757 (m-10) cc_final: 0.7211 (m-80) REVERT: R 52 MET cc_start: 0.9598 (tmm) cc_final: 0.9316 (ptm) REVERT: a 87 GLU cc_start: 0.9643 (mt-10) cc_final: 0.9222 (mp0) REVERT: a 88 MET cc_start: 0.9422 (mtt) cc_final: 0.8955 (mtt) REVERT: a 91 GLU cc_start: 0.9306 (tt0) cc_final: 0.8984 (pt0) REVERT: a 118 TRP cc_start: 0.8045 (t60) cc_final: 0.7448 (t60) REVERT: a 126 ASP cc_start: 0.8586 (m-30) cc_final: 0.7990 (m-30) REVERT: a 286 MET cc_start: 0.9705 (tmm) cc_final: 0.9260 (ptp) REVERT: b 17 PHE cc_start: 0.9536 (t80) cc_final: 0.8962 (m-80) REVERT: e 113 ASP cc_start: 0.9671 (t70) cc_final: 0.9420 (t0) REVERT: g 24 MET cc_start: 0.9693 (mmp) cc_final: 0.9222 (mmp) REVERT: g 26 MET cc_start: 0.9345 (ptp) cc_final: 0.8966 (ptp) REVERT: g 39 MET cc_start: 0.9042 (mmp) cc_final: 0.8663 (mmm) REVERT: g 49 MET cc_start: 0.9432 (ttt) cc_final: 0.9054 (tmm) REVERT: g 229 MET cc_start: 0.9742 (mmp) cc_final: 0.9174 (mmm) REVERT: p 82 ARG cc_start: 0.9297 (ttp-110) cc_final: 0.8924 (ttp80) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.2325 time to fit residues: 137.6356 Evaluate side-chains 288 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 128 optimal weight: 1.9990 chunk 236 optimal weight: 0.0060 chunk 144 optimal weight: 5.9990 chunk 458 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 193 optimal weight: 40.0000 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN R 47 GLN ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 138 GLN b 139 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.038206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.027966 restraints weight = 356592.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.028864 restraints weight = 230717.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.029469 restraints weight = 168454.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.029896 restraints weight = 134106.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030197 restraints weight = 113198.617| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37735 Z= 0.169 Angle : 0.628 10.947 51158 Z= 0.329 Chirality : 0.042 0.212 5994 Planarity : 0.004 0.052 6634 Dihedral : 4.864 58.670 5276 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.68 (0.12), residues: 4856 helix: 1.40 (0.10), residues: 2731 sheet: -0.17 (0.21), residues: 550 loop : -0.94 (0.17), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 33 TYR 0.046 0.001 TYR a 23 PHE 0.051 0.002 PHE G 18 TRP 0.062 0.002 TRP a 261 HIS 0.005 0.001 HIS b 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (37735) covalent geometry : angle 0.62816 / 0.33 (51158) hydrogen bonds : bond 0.04066 / 2.79 ( 2317) hydrogen bonds : angle 4.72528 / 3.32 ( 6804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9712 Ramachandran restraints generated. 4856 Oldfield, 0 Emsley, 4856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9052 (tpp) cc_final: 0.8674 (tpp) REVERT: A 258 LEU cc_start: 0.9718 (pp) cc_final: 0.9378 (tp) REVERT: A 457 MET cc_start: 0.9371 (mmm) cc_final: 0.8573 (tpp) REVERT: B 49 MET cc_start: 0.8926 (tpt) cc_final: 0.8252 (tpt) REVERT: B 53 MET cc_start: 0.9467 (mtm) cc_final: 0.9176 (mtt) REVERT: B 157 MET cc_start: 0.9722 (mtm) cc_final: 0.9214 (ptp) REVERT: B 179 MET cc_start: 0.9247 (mmp) cc_final: 0.8968 (mmm) REVERT: B 402 ARG cc_start: 0.9399 (mtm180) cc_final: 0.9055 (ptm160) REVERT: B 432 MET cc_start: 0.9541 (mmm) cc_final: 0.9336 (tpp) REVERT: C 49 MET cc_start: 0.9558 (mtm) cc_final: 0.9197 (mpp) REVERT: C 157 MET cc_start: 0.9550 (mmp) cc_final: 0.9340 (mmm) REVERT: C 246 MET cc_start: 0.9624 (mmp) cc_final: 0.9412 (mmm) REVERT: C 432 MET cc_start: 0.9678 (mmp) cc_final: 0.8990 (mmp) REVERT: D 245 PHE cc_start: 0.9429 (m-80) cc_final: 0.8900 (m-80) REVERT: D 280 MET cc_start: 0.9509 (tpt) cc_final: 0.9163 (tpt) REVERT: D 319 HIS cc_start: 0.9418 (m90) cc_final: 0.8886 (m90) REVERT: D 410 HIS cc_start: 0.8627 (t70) cc_final: 0.8267 (m90) REVERT: E 1 MET cc_start: 0.8868 (ppp) cc_final: 0.8210 (ppp) REVERT: E 87 MET cc_start: 0.9243 (mpp) cc_final: 0.8560 (mpp) REVERT: E 159 MET cc_start: 0.9744 (mmp) cc_final: 0.9401 (mmm) REVERT: E 203 MET cc_start: 0.9431 (mmm) cc_final: 0.8542 (mmm) REVERT: E 225 MET cc_start: 0.9497 (mmt) cc_final: 0.9235 (mmm) REVERT: E 280 MET cc_start: 0.9448 (ttm) cc_final: 0.9163 (ttm) REVERT: E 319 HIS cc_start: 0.9172 (m-70) cc_final: 0.8795 (m-70) REVERT: E 450 MET cc_start: 0.9431 (mmp) cc_final: 0.9045 (mmm) REVERT: F 158 MET cc_start: 0.9735 (tpt) cc_final: 0.9363 (mmp) REVERT: F 225 MET cc_start: 0.9606 (mmp) cc_final: 0.9366 (mmm) REVERT: F 266 MET cc_start: 0.9089 (mpp) cc_final: 0.8786 (mpp) REVERT: F 280 MET cc_start: 0.9467 (mmp) cc_final: 0.8552 (mmm) REVERT: F 299 GLN cc_start: 0.9582 (mt0) cc_final: 0.9197 (mp-120) REVERT: F 402 GLN cc_start: 0.9503 (mt0) cc_final: 0.9256 (mt0) REVERT: G 18 PHE cc_start: 0.8963 (t80) cc_final: 0.8731 (t80) REVERT: G 30 LEU cc_start: 0.9647 (tt) cc_final: 0.9393 (pp) REVERT: G 52 MET cc_start: 0.9512 (tmm) cc_final: 0.9221 (tmm) REVERT: H 1 MET cc_start: 0.8703 (mmp) cc_final: 0.8075 (tpp) REVERT: H 30 LEU cc_start: 0.9510 (mm) cc_final: 0.9200 (pp) REVERT: H 64 MET cc_start: 0.9441 (mmp) cc_final: 0.8949 (mtp) REVERT: J 14 ILE cc_start: 0.9394 (mm) cc_final: 0.8617 (pt) REVERT: J 18 PHE cc_start: 0.8732 (m-10) cc_final: 0.8501 (m-80) REVERT: K 18 PHE cc_start: 0.9219 (m-80) cc_final: 0.8754 (m-80) REVERT: K 73 PHE cc_start: 0.9031 (m-10) cc_final: 0.8745 (m-80) REVERT: L 18 PHE cc_start: 0.9412 (m-10) cc_final: 0.9128 (m-10) REVERT: L 27 PHE cc_start: 0.9560 (m-80) cc_final: 0.8915 (m-80) REVERT: L 30 LEU cc_start: 0.9220 (pp) cc_final: 0.8864 (pp) REVERT: L 52 MET cc_start: 0.9865 (tpt) cc_final: 0.9472 (mmm) REVERT: L 60 ASP cc_start: 0.8898 (m-30) cc_final: 0.8561 (m-30) REVERT: O 18 PHE cc_start: 0.9611 (m-80) cc_final: 0.9287 (m-10) REVERT: O 55 ILE cc_start: 0.7885 (mm) cc_final: 0.7648 (mm) REVERT: O 64 MET cc_start: 0.8928 (mmp) cc_final: 0.8675 (mmm) REVERT: O 73 PHE cc_start: 0.8779 (m-80) cc_final: 0.8392 (m-80) REVERT: P 36 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8332 (mt-10) REVERT: P 53 PHE cc_start: 0.9072 (m-10) cc_final: 0.8826 (m-80) REVERT: P 67 VAL cc_start: 0.8586 (p) cc_final: 0.8306 (m) REVERT: Q 73 PHE cc_start: 0.9483 (m-10) cc_final: 0.9159 (m-80) REVERT: R 23 THR cc_start: 0.9090 (p) cc_final: 0.8750 (p) REVERT: R 27 PHE cc_start: 0.7712 (m-10) cc_final: 0.7182 (m-80) REVERT: R 52 MET cc_start: 0.9600 (tmm) cc_final: 0.9322 (ptm) REVERT: a 87 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9237 (mp0) REVERT: a 88 MET cc_start: 0.9447 (mtt) cc_final: 0.8908 (mtt) REVERT: a 91 GLU cc_start: 0.9322 (tt0) cc_final: 0.9006 (pt0) REVERT: a 126 ASP cc_start: 0.8659 (m-30) cc_final: 0.7980 (m-30) REVERT: a 236 MET cc_start: 0.7770 (tmm) cc_final: 0.7015 (tmm) REVERT: a 240 GLU cc_start: 0.9268 (pt0) cc_final: 0.8816 (pt0) REVERT: a 286 MET cc_start: 0.9708 (tmm) cc_final: 0.9257 (ptp) REVERT: b 17 PHE cc_start: 0.9310 (t80) cc_final: 0.9050 (m-80) REVERT: b 22 MET cc_start: 0.5994 (mmm) cc_final: 0.5700 (mmm) REVERT: e 113 ASP cc_start: 0.9668 (t70) cc_final: 0.9426 (t0) REVERT: e 127 GLN cc_start: 0.9448 (mp10) cc_final: 0.9232 (mp10) REVERT: g 24 MET cc_start: 0.9703 (mmp) cc_final: 0.9240 (mmp) REVERT: g 26 MET cc_start: 0.9346 (ptp) cc_final: 0.8950 (ptp) REVERT: g 39 MET cc_start: 0.9072 (mmp) cc_final: 0.8703 (mmm) REVERT: g 229 MET cc_start: 0.9734 (mmp) cc_final: 0.9192 (mmm) REVERT: p 82 ARG cc_start: 0.9307 (ttp-110) cc_final: 0.8938 (ttp80) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2280 time to fit residues: 134.7470 Evaluate side-chains 285 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 212 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 461 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 419 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 310 optimal weight: 8.9990 chunk 466 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN R 47 GLN ** a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 138 GLN b 139 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.038319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.027878 restraints weight = 347733.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.028706 restraints weight = 226219.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029412 restraints weight = 166302.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.029850 restraints weight = 131262.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030155 restraints weight = 110707.344| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37735 Z= 0.150 Angle : 0.612 10.973 51158 Z= 0.319 Chirality : 0.042 0.208 5994 Planarity : 0.004 0.055 6634 Dihedral : 4.825 57.343 5276 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.73 (0.12), residues: 4856 helix: 1.41 (0.10), residues: 2731 sheet: -0.09 (0.22), residues: 548 loop : -0.90 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 231 TYR 0.046 0.001 TYR a 23 PHE 0.043 0.002 PHE G 18 TRP 0.056 0.002 TRP a 261 HIS 0.004 0.001 HIS p 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (37735) covalent geometry : angle 0.61185 / 0.32 (51158) hydrogen bonds : bond 0.04015 / 2.77 ( 2317) hydrogen bonds : angle 4.68657 / 3.29 ( 6804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7095.52 seconds wall clock time: 124 minutes 6.73 seconds (7446.73 seconds total)