Starting phenix.real_space_refine on Sat Mar 7 03:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3w_13186/03_2026/7p3w_13186.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3w_13186/03_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_13186/03_2026/7p3w_13186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3w_13186/03_2026/7p3w_13186.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p3w_13186/03_2026/7p3w_13186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3w_13186/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.53, per 1000 atoms: 0.20 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 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: 1.19 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: 7.56 Time building geometry restraints manager: 4.14 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: 21017 18.06 - 36.12: 1421 36.12 - 54.18: 243 54.18 - 72.23: 98 72.23 - 90.29: 59 Dihedral angle restraints: 22838 sinusoidal: 8906 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 22835 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: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 31.880 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 14.039 90.293 13916 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 covalent geometry : bond 0.00559 (37735) covalent geometry : angle 0.86656 (51158) hydrogen bonds : bond 0.15667 ( 2317) hydrogen bonds : angle 6.77988 ( 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 : 1.255 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: 0.2230 time to fit residues: 155.4774 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 : 1.408 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.037330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.027206 restraints weight = 364370.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.027993 restraints weight = 236232.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.028671 restraints weight = 174859.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029115 restraints weight = 138994.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.029429 restraints weight = 116577.089| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 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 = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1402 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 : 0.671 9.367 51158 Z= 0.360 Chirality : 0.044 0.257 5994 Planarity : 0.005 0.049 6634 Dihedral : 6.590 79.544 5369 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.83 % 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: 2688 sheet: -0.61 (0.21), residues: 557 loop : -1.51 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 covalent geometry : bond 0.00421 (37735) covalent geometry : angle 0.67107 (51158) hydrogen bonds : bond 0.05202 ( 2317) hydrogen bonds : angle 5.43099 ( 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 386 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 383 time to evaluate : 1.436 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: A 19 ASP cc_start: 0.8727 (m-30) cc_final: 0.8093 (t0) REVERT: A 355 PHE cc_start: 0.9330 (t80) cc_final: 0.9008 (t80) REVERT: B 49 MET cc_start: 0.8823 (tpt) cc_final: 0.8138 (tpt) REVERT: B 153 SER cc_start: 0.9589 (t) cc_final: 0.8760 (m) REVERT: B 263 ASP cc_start: 0.8680 (m-30) cc_final: 0.8448 (m-30) REVERT: B 432 MET cc_start: 0.9501 (mmm) cc_final: 0.8688 (mmt) REVERT: C 49 MET cc_start: 0.9387 (mtp) cc_final: 0.9182 (mtp) REVERT: C 157 MET cc_start: 0.9559 (mpp) cc_final: 0.9329 (mmm) REVERT: C 199 ILE cc_start: 0.9398 (mm) cc_final: 0.9124 (mm) REVERT: C 263 ASP cc_start: 0.9114 (m-30) cc_final: 0.8813 (m-30) REVERT: C 413 ASP cc_start: 0.7592 (t0) cc_final: 0.6980 (t0) REVERT: C 432 MET cc_start: 0.9535 (mmp) cc_final: 0.8502 (mmm) REVERT: D 203 MET cc_start: 0.8670 (mpp) cc_final: 0.8462 (mpp) REVERT: D 225 MET cc_start: 0.9670 (mmt) cc_final: 0.9408 (mmm) REVERT: D 245 PHE cc_start: 0.9388 (m-80) cc_final: 0.8842 (m-80) REVERT: D 280 MET cc_start: 0.9560 (tpt) cc_final: 0.8996 (tpt) REVERT: D 319 HIS cc_start: 0.9342 (m90) cc_final: 0.8498 (m90) REVERT: E 87 MET cc_start: 0.9593 (mpp) cc_final: 0.8894 (mpp) REVERT: E 203 MET cc_start: 0.9350 (mmm) cc_final: 0.9049 (mmm) REVERT: E 280 MET cc_start: 0.9356 (tpp) cc_final: 0.8974 (tpp) REVERT: E 319 HIS cc_start: 0.9023 (m90) cc_final: 0.8648 (m90) REVERT: E 450 MET cc_start: 0.9327 (mmp) cc_final: 0.8906 (mmm) REVERT: F 158 MET cc_start: 0.9687 (tpt) cc_final: 0.9340 (mmp) REVERT: F 208 MET cc_start: 0.9046 (ptp) cc_final: 0.8680 (ptp) REVERT: F 225 MET cc_start: 0.9612 (mmp) cc_final: 0.9309 (mmm) REVERT: F 266 MET cc_start: 0.9048 (mpp) cc_final: 0.8459 (mpp) REVERT: F 299 GLN cc_start: 0.9482 (mt0) cc_final: 0.9229 (mp10) REVERT: G 18 PHE cc_start: 0.9091 (t80) cc_final: 0.8785 (t80) REVERT: H 30 LEU cc_start: 0.9471 (mm) cc_final: 0.9195 (pp) REVERT: H 64 MET cc_start: 0.9546 (mmp) cc_final: 0.9296 (mmp) REVERT: J 18 PHE cc_start: 0.9188 (m-10) cc_final: 0.8944 (m-80) REVERT: K 73 PHE cc_start: 0.9093 (m-10) cc_final: 0.8802 (m-10) REVERT: L 18 PHE cc_start: 0.9286 (t80) cc_final: 0.8899 (t80) REVERT: L 27 PHE cc_start: 0.9584 (m-80) cc_final: 0.9333 (m-80) REVERT: L 60 ASP cc_start: 0.9216 (p0) cc_final: 0.8998 (p0) REVERT: O 55 ILE cc_start: 0.8223 (mm) cc_final: 0.7931 (mm) REVERT: O 64 MET cc_start: 0.8831 (mmp) cc_final: 0.8610 (mmm) REVERT: O 73 PHE cc_start: 0.8614 (m-80) cc_final: 0.8403 (m-80) REVERT: P 64 MET cc_start: 0.8589 (ppp) cc_final: 0.8111 (ppp) REVERT: P 65 ILE cc_start: 0.9111 (mm) cc_final: 0.8713 (mm) REVERT: Q 73 PHE cc_start: 0.9459 (m-10) cc_final: 0.9155 (m-80) REVERT: R 52 MET cc_start: 0.9707 (tmm) cc_final: 0.9402 (ptm) REVERT: R 73 PHE cc_start: 0.8967 (m-80) cc_final: 0.8651 (m-80) REVERT: a 87 GLU cc_start: 0.9658 (mt-10) cc_final: 0.9264 (mp0) REVERT: a 88 MET cc_start: 0.9479 (mmt) cc_final: 0.8864 (mmm) REVERT: a 91 GLU cc_start: 0.9273 (tt0) cc_final: 0.8968 (pt0) REVERT: a 122 MET cc_start: 0.8878 (tmm) cc_final: 0.8574 (tmm) REVERT: a 126 ASP cc_start: 0.8945 (m-30) cc_final: 0.8127 (m-30) REVERT: a 286 MET cc_start: 0.9660 (tmm) cc_final: 0.9183 (ptp) REVERT: b 17 PHE cc_start: 0.9313 (t80) cc_final: 0.8803 (m-10) REVERT: d 171 LYS cc_start: 0.9804 (ptpp) cc_final: 0.9602 (pttt) REVERT: e 51 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8604 (mmm-85) REVERT: e 77 THR cc_start: 0.9231 (t) cc_final: 0.9021 (m) REVERT: g 24 MET cc_start: 0.9529 (mmp) cc_final: 0.9116 (mmp) REVERT: g 32 MET cc_start: 0.9268 (mmm) cc_final: 0.8999 (mmm) REVERT: g 39 MET cc_start: 0.9324 (mmp) cc_final: 0.8742 (mmp) REVERT: g 229 MET cc_start: 0.9762 (mmp) cc_final: 0.9257 (mmm) REVERT: g 237 ASN cc_start: 0.9572 (OUTLIER) cc_final: 0.9308 (m-40) REVERT: p 82 ARG cc_start: 0.9276 (ttp-110) cc_final: 0.9027 (ttp-170) outliers start: 3 outliers final: 0 residues processed: 386 average time/residue: 0.2193 time to fit residues: 140.2877 Evaluate side-chains 307 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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: 0.1980 chunk 153 optimal weight: 7.9990 chunk 459 optimal weight: 8.9990 chunk 267 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 402 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 260 optimal weight: 3.9990 chunk 336 optimal weight: 4.9990 chunk 397 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.038442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.027928 restraints weight = 347086.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.028771 restraints weight = 223550.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.029454 restraints weight = 163831.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.029920 restraints weight = 130551.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030229 restraints weight = 109692.939| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37735 Z= 0.138 Angle : 0.599 8.973 51158 Z= 0.319 Chirality : 0.042 0.182 5994 Planarity : 0.004 0.052 6634 Dihedral : 6.264 81.336 5369 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % 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: 0.16 (0.12), residues: 4856 helix: 1.06 (0.10), residues: 2706 sheet: -0.45 (0.21), residues: 555 loop : -1.28 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 40 TYR 0.043 0.001 TYR a 23 PHE 0.039 0.002 PHE E 405 TRP 0.046 0.002 TRP a 261 HIS 0.007 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00285 (37735) covalent geometry : angle 0.59929 (51158) hydrogen bonds : bond 0.04682 ( 2317) hydrogen bonds : angle 5.02064 ( 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 402 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 399 time to evaluate : 1.365 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: 0.8713 (m-30) cc_final: 0.8063 (t0) REVERT: A 355 PHE cc_start: 0.9259 (t80) cc_final: 0.8925 (t80) REVERT: B 49 MET cc_start: 0.8762 (tpt) cc_final: 0.7992 (tpt) REVERT: B 153 SER cc_start: 0.9612 (t) cc_final: 0.9240 (p) REVERT: B 432 MET cc_start: 0.9564 (mmm) cc_final: 0.9077 (mmt) REVERT: C 49 MET cc_start: 0.9458 (mtp) cc_final: 0.9240 (mtp) REVERT: C 53 MET cc_start: 0.9317 (ttt) cc_final: 0.9093 (tpp) REVERT: C 157 MET cc_start: 0.9571 (mpp) cc_final: 0.9355 (mmm) REVERT: C 199 ILE cc_start: 0.9351 (mm) cc_final: 0.9097 (mp) REVERT: C 263 ASP cc_start: 0.9194 (m-30) cc_final: 0.8258 (m-30) REVERT: C 266 LYS cc_start: 0.9760 (mmtt) cc_final: 0.9555 (mtpp) REVERT: C 413 ASP cc_start: 0.7626 (t0) cc_final: 0.6985 (t0) REVERT: C 432 MET cc_start: 0.9620 (mmp) cc_final: 0.9122 (mmm) REVERT: D 159 MET cc_start: 0.9395 (mtm) cc_final: 0.9043 (ptp) REVERT: D 203 MET cc_start: 0.8796 (mpp) cc_final: 0.8482 (mpp) REVERT: D 225 MET cc_start: 0.9662 (mmt) cc_final: 0.9451 (mmm) REVERT: D 245 PHE cc_start: 0.9307 (m-80) cc_final: 0.8777 (m-80) REVERT: D 280 MET cc_start: 0.9565 (tpt) cc_final: 0.9020 (tpt) REVERT: D 319 HIS cc_start: 0.9312 (m90) cc_final: 0.8571 (m90) REVERT: E 87 MET cc_start: 0.9625 (mpp) cc_final: 0.8926 (mpp) REVERT: E 159 MET cc_start: 0.9716 (mmp) cc_final: 0.9368 (mmm) REVERT: E 203 MET cc_start: 0.9483 (mmm) cc_final: 0.9072 (mmm) REVERT: E 266 MET cc_start: 0.9129 (mtm) cc_final: 0.8448 (mpp) REVERT: E 280 MET cc_start: 0.9373 (tpp) cc_final: 0.8987 (tpp) REVERT: E 319 HIS cc_start: 0.9041 (m90) cc_final: 0.8542 (m90) REVERT: E 450 MET cc_start: 0.9379 (mmp) cc_final: 0.8989 (mmm) REVERT: F 158 MET cc_start: 0.9690 (tpt) cc_final: 0.9410 (mmp) REVERT: F 208 MET cc_start: 0.9013 (ptp) cc_final: 0.8650 (ptp) REVERT: F 225 MET cc_start: 0.9604 (mmp) cc_final: 0.9335 (mmm) REVERT: F 266 MET cc_start: 0.9012 (mpp) cc_final: 0.8753 (mpp) REVERT: F 299 GLN cc_start: 0.9551 (mt0) cc_final: 0.9252 (mp10) REVERT: F 402 GLN cc_start: 0.9551 (mt0) cc_final: 0.9336 (mt0) REVERT: H 64 MET cc_start: 0.9524 (mmp) cc_final: 0.9250 (mmp) REVERT: J 18 PHE cc_start: 0.8893 (m-10) cc_final: 0.8665 (m-80) REVERT: K 73 PHE cc_start: 0.9031 (m-10) cc_final: 0.8747 (m-80) REVERT: L 18 PHE cc_start: 0.9237 (t80) cc_final: 0.8930 (t80) REVERT: L 27 PHE cc_start: 0.9529 (m-80) cc_final: 0.8913 (m-80) REVERT: L 60 ASP cc_start: 0.9238 (p0) cc_final: 0.8787 (p0) REVERT: L 64 MET cc_start: 0.8409 (mtp) cc_final: 0.8169 (mtp) REVERT: O 55 ILE cc_start: 0.7902 (mm) cc_final: 0.7612 (mm) REVERT: O 73 PHE cc_start: 0.8566 (m-80) cc_final: 0.8277 (m-80) REVERT: P 53 PHE cc_start: 0.9058 (m-10) cc_final: 0.8818 (m-10) REVERT: P 67 VAL cc_start: 0.7698 (t) cc_final: 0.7215 (t) REVERT: Q 73 PHE cc_start: 0.9437 (m-10) cc_final: 0.9127 (m-80) REVERT: R 27 PHE cc_start: 0.7700 (m-10) cc_final: 0.7219 (m-80) REVERT: R 30 LEU cc_start: 0.9165 (mm) cc_final: 0.8526 (pp) REVERT: R 52 MET cc_start: 0.9682 (tmm) cc_final: 0.9378 (ptm) REVERT: S 36 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9136 (mm-30) REVERT: a 87 GLU cc_start: 0.9678 (mt-10) cc_final: 0.9327 (mp0) REVERT: a 88 MET cc_start: 0.9702 (mmm) cc_final: 0.9467 (mmm) REVERT: a 91 GLU cc_start: 0.9305 (tt0) cc_final: 0.8986 (pt0) REVERT: a 122 MET cc_start: 0.8819 (tmm) cc_final: 0.8392 (tmm) REVERT: a 126 ASP cc_start: 0.8834 (m-30) cc_final: 0.7868 (m-30) REVERT: a 240 GLU cc_start: 0.9225 (pt0) cc_final: 0.8748 (pt0) REVERT: a 286 MET cc_start: 0.9661 (tmm) cc_final: 0.9195 (ptp) REVERT: b 17 PHE cc_start: 0.9369 (t80) cc_final: 0.8722 (m-10) REVERT: d 171 LYS cc_start: 0.9781 (ptpp) cc_final: 0.9558 (pttt) REVERT: g 24 MET cc_start: 0.9551 (mmp) cc_final: 0.9115 (mmp) REVERT: g 32 MET cc_start: 0.9276 (mmm) cc_final: 0.9016 (mmm) REVERT: g 39 MET cc_start: 0.9260 (mmp) cc_final: 0.8722 (mmp) REVERT: g 229 MET cc_start: 0.9787 (mmp) cc_final: 0.9282 (mmm) REVERT: p 82 ARG cc_start: 0.9257 (ttp-110) cc_final: 0.8858 (ttp80) outliers start: 3 outliers final: 0 residues processed: 400 average time/residue: 0.2106 time to fit residues: 141.2024 Evaluate side-chains 304 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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: 6.9990 chunk 271 optimal weight: 10.0000 chunk 437 optimal weight: 7.9990 chunk 459 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 373 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 370 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** 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** G 47 GLN R 47 GLN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 138 GLN ** 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 = 0.2946 r_free = 0.2946 target = 0.037491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.027350 restraints weight = 367331.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.028158 restraints weight = 237913.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.028798 restraints weight = 175371.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.029241 restraints weight = 139487.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029558 restraints weight = 117119.878| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 37735 Z= 0.214 Angle : 0.650 10.545 51158 Z= 0.345 Chirality : 0.043 0.208 5994 Planarity : 0.004 0.055 6634 Dihedral : 6.230 86.283 5369 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 0.15 (0.12), residues: 4856 helix: 1.06 (0.10), residues: 2717 sheet: -0.51 (0.21), residues: 562 loop : -1.29 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 347 TYR 0.038 0.002 TYR a 23 PHE 0.044 0.002 PHE G 18 TRP 0.046 0.002 TRP a 261 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00433 (37735) covalent geometry : angle 0.64953 (51158) hydrogen bonds : bond 0.04556 ( 2317) hydrogen bonds : angle 5.08111 ( 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 368 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.310 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: A 19 ASP cc_start: 0.8625 (m-30) cc_final: 0.7876 (t0) REVERT: A 258 LEU cc_start: 0.9607 (pp) cc_final: 0.9279 (tp) REVERT: A 355 PHE cc_start: 0.9309 (t80) cc_final: 0.9020 (t80) REVERT: B 49 MET cc_start: 0.8893 (tpt) cc_final: 0.8279 (tpt) REVERT: B 263 ASP cc_start: 0.8804 (m-30) cc_final: 0.8600 (m-30) REVERT: B 402 ARG cc_start: 0.9331 (mtm180) cc_final: 0.8920 (mtm180) REVERT: C 53 MET cc_start: 0.9403 (ttt) cc_final: 0.9200 (tpp) REVERT: C 157 MET cc_start: 0.9595 (mpp) cc_final: 0.9388 (mmm) REVERT: C 179 MET cc_start: 0.9403 (tpp) cc_final: 0.9181 (tpp) REVERT: C 199 ILE cc_start: 0.9385 (mm) cc_final: 0.9100 (mm) REVERT: C 246 MET cc_start: 0.9663 (mmp) cc_final: 0.9365 (mmm) REVERT: C 263 ASP cc_start: 0.9203 (m-30) cc_final: 0.8346 (m-30) REVERT: C 413 ASP cc_start: 0.7851 (t0) cc_final: 0.7203 (t0) REVERT: C 432 MET cc_start: 0.9633 (mmp) cc_final: 0.9098 (mmm) REVERT: D 245 PHE cc_start: 0.9495 (m-80) cc_final: 0.9000 (m-80) REVERT: D 280 MET cc_start: 0.9584 (tpt) cc_final: 0.9113 (tpt) REVERT: D 319 HIS cc_start: 0.9377 (m90) cc_final: 0.8662 (m90) REVERT: E 1 MET cc_start: 0.8557 (tmm) cc_final: 0.8330 (tmm) REVERT: E 159 MET cc_start: 0.9724 (mmp) cc_final: 0.9406 (mmm) REVERT: E 203 MET cc_start: 0.9513 (mmm) cc_final: 0.9264 (mmm) REVERT: E 280 MET cc_start: 0.9388 (tpp) cc_final: 0.8935 (tpp) REVERT: E 319 HIS cc_start: 0.9100 (m90) cc_final: 0.8650 (m-70) REVERT: E 450 MET cc_start: 0.9331 (mmp) cc_final: 0.8901 (mmm) REVERT: F 158 MET cc_start: 0.9646 (tpt) cc_final: 0.9370 (mmp) REVERT: F 208 MET cc_start: 0.9045 (ptp) cc_final: 0.8665 (ptp) REVERT: F 225 MET cc_start: 0.9599 (mmp) cc_final: 0.9317 (mmm) REVERT: F 266 MET cc_start: 0.9090 (mpp) cc_final: 0.8840 (mpp) REVERT: F 299 GLN cc_start: 0.9571 (mt0) cc_final: 0.9251 (mp-120) REVERT: F 402 GLN cc_start: 0.9522 (mt0) cc_final: 0.9300 (mt0) REVERT: H 64 MET cc_start: 0.9539 (mmp) cc_final: 0.8985 (mpp) REVERT: J 18 PHE cc_start: 0.8927 (m-10) cc_final: 0.8660 (m-80) REVERT: K 18 PHE cc_start: 0.9127 (m-80) cc_final: 0.8876 (m-80) REVERT: K 73 PHE cc_start: 0.9062 (m-10) cc_final: 0.8786 (m-80) REVERT: L 18 PHE cc_start: 0.9219 (t80) cc_final: 0.8770 (t80) REVERT: L 27 PHE cc_start: 0.9543 (m-80) cc_final: 0.9116 (m-80) REVERT: L 60 ASP cc_start: 0.9218 (p0) cc_final: 0.8750 (p0) REVERT: L 64 MET cc_start: 0.8449 (mtp) cc_final: 0.8197 (mtp) REVERT: O 55 ILE cc_start: 0.8034 (mm) cc_final: 0.7696 (mm) REVERT: O 64 MET cc_start: 0.8866 (mmp) cc_final: 0.8655 (mmm) REVERT: O 73 PHE cc_start: 0.8601 (m-80) cc_final: 0.8213 (m-80) REVERT: P 53 PHE cc_start: 0.9095 (m-10) cc_final: 0.8844 (m-80) REVERT: Q 73 PHE cc_start: 0.9468 (m-10) cc_final: 0.9168 (m-80) REVERT: R 23 THR cc_start: 0.9087 (p) cc_final: 0.8756 (p) REVERT: R 27 PHE cc_start: 0.7809 (m-10) cc_final: 0.7174 (m-80) REVERT: R 52 MET cc_start: 0.9690 (tmm) cc_final: 0.9366 (ptm) REVERT: S 36 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9146 (mm-30) REVERT: a 87 GLU cc_start: 0.9665 (mt-10) cc_final: 0.9308 (mp0) REVERT: a 88 MET cc_start: 0.9708 (mmm) cc_final: 0.9505 (mtp) REVERT: a 91 GLU cc_start: 0.9363 (tt0) cc_final: 0.9041 (pt0) REVERT: a 122 MET cc_start: 0.8824 (tmm) cc_final: 0.8421 (tmm) REVERT: a 126 ASP cc_start: 0.8948 (m-30) cc_final: 0.8382 (m-30) REVERT: a 240 GLU cc_start: 0.9283 (pt0) cc_final: 0.8766 (pt0) REVERT: a 281 ILE cc_start: 0.9795 (mt) cc_final: 0.9559 (mt) REVERT: a 286 MET cc_start: 0.9680 (tmm) cc_final: 0.9228 (ptp) REVERT: b 17 PHE cc_start: 0.9402 (t80) cc_final: 0.8872 (m-80) REVERT: b 22 MET cc_start: 0.6309 (mmm) cc_final: 0.6061 (mmm) REVERT: b 148 MET cc_start: 0.7801 (tpp) cc_final: 0.6813 (mpp) REVERT: e 127 GLN cc_start: 0.9557 (mp10) cc_final: 0.9308 (mp10) REVERT: g 24 MET cc_start: 0.9630 (mmp) cc_final: 0.9142 (mmp) REVERT: g 32 MET cc_start: 0.9283 (mmm) cc_final: 0.8997 (mmm) REVERT: g 39 MET cc_start: 0.9235 (mmp) cc_final: 0.8820 (mmm) REVERT: g 229 MET cc_start: 0.9753 (mmp) cc_final: 0.9283 (mmm) REVERT: p 82 ARG cc_start: 0.9298 (ttp-110) cc_final: 0.9054 (ttp80) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2055 time to fit residues: 126.9579 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 : 1.297 ------------------------------------------------------------------------------- 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: 0.9990 chunk 417 optimal weight: 9.9990 chunk 447 optimal weight: 0.0980 chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 289 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 321 optimal weight: 20.0000 chunk 175 optimal weight: 0.7980 chunk 442 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 273 GLN ** 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 ** b 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 138 GLN ** 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 = 0.2999 r_free = 0.2999 target = 0.039000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.028396 restraints weight = 344372.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.029227 restraints weight = 220924.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.029981 restraints weight = 160443.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.030451 restraints weight = 127090.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.030779 restraints weight = 106411.280| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37735 Z= 0.127 Angle : 0.586 8.561 51158 Z= 0.307 Chirality : 0.042 0.189 5994 Planarity : 0.004 0.055 6634 Dihedral : 5.980 89.723 5369 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.84 % 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: 0.50 (0.12), residues: 4856 helix: 1.31 (0.10), residues: 2721 sheet: -0.26 (0.21), residues: 559 loop : -1.13 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 86 TYR 0.032 0.001 TYR a 23 PHE 0.044 0.002 PHE G 18 TRP 0.046 0.002 TRP a 261 HIS 0.004 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00259 (37735) covalent geometry : angle 0.58556 (51158) hydrogen bonds : bond 0.04269 ( 2317) hydrogen bonds : angle 4.76145 ( 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 393 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 1.378 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: 0.8609 (m-30) cc_final: 0.7855 (t0) REVERT: A 258 LEU cc_start: 0.9645 (pp) cc_final: 0.9307 (tp) REVERT: A 355 PHE cc_start: 0.9218 (t80) cc_final: 0.8925 (t80) REVERT: B 49 MET cc_start: 0.8786 (tpt) cc_final: 0.7930 (tpt) REVERT: B 179 MET cc_start: 0.9417 (tpp) cc_final: 0.9208 (mmm) REVERT: B 235 MET cc_start: 0.9452 (mmp) cc_final: 0.9191 (mmm) REVERT: B 402 ARG cc_start: 0.9363 (mtm180) cc_final: 0.8940 (mtm180) REVERT: B 432 MET cc_start: 0.9529 (mmm) cc_final: 0.9321 (mmm) REVERT: C 49 MET cc_start: 0.9590 (mtm) cc_final: 0.9167 (ptp) REVERT: C 53 MET cc_start: 0.9389 (ttt) cc_final: 0.9169 (tpp) REVERT: C 157 MET cc_start: 0.9616 (mpp) cc_final: 0.9394 (mmm) REVERT: C 179 MET cc_start: 0.9391 (tpp) cc_final: 0.9139 (tpp) REVERT: C 246 MET cc_start: 0.9653 (mmp) cc_final: 0.9422 (mmm) REVERT: C 413 ASP cc_start: 0.7824 (t0) cc_final: 0.7251 (t0) REVERT: C 432 MET cc_start: 0.9642 (mmp) cc_final: 0.9033 (mmp) REVERT: D 203 MET cc_start: 0.8816 (mpp) cc_final: 0.8556 (mpp) REVERT: D 245 PHE cc_start: 0.9472 (m-80) cc_final: 0.8838 (m-80) REVERT: D 280 MET cc_start: 0.9537 (tpt) cc_final: 0.9130 (tpt) REVERT: D 319 HIS cc_start: 0.9311 (m90) cc_final: 0.8632 (m90) REVERT: E 1 MET cc_start: 0.8623 (tmm) cc_final: 0.8278 (tmm) REVERT: E 159 MET cc_start: 0.9740 (mmp) cc_final: 0.9401 (mmp) REVERT: E 203 MET cc_start: 0.9560 (mmm) cc_final: 0.9235 (mmm) REVERT: E 225 MET cc_start: 0.9510 (mmt) cc_final: 0.9211 (mmm) REVERT: E 280 MET cc_start: 0.9365 (tpp) cc_final: 0.8792 (tpp) REVERT: E 319 HIS cc_start: 0.9073 (m90) cc_final: 0.8464 (m-70) REVERT: E 450 MET cc_start: 0.9427 (mmp) cc_final: 0.9085 (mmm) REVERT: F 158 MET cc_start: 0.9714 (tpt) cc_final: 0.9421 (mmp) REVERT: F 225 MET cc_start: 0.9583 (mmp) cc_final: 0.9351 (mmm) REVERT: F 266 MET cc_start: 0.9003 (mpp) cc_final: 0.8717 (mpp) REVERT: F 299 GLN cc_start: 0.9584 (mt0) cc_final: 0.9213 (mp-120) REVERT: F 402 GLN cc_start: 0.9553 (mt0) cc_final: 0.9316 (mt0) REVERT: H 64 MET cc_start: 0.9499 (mmp) cc_final: 0.8947 (mpp) REVERT: J 18 PHE cc_start: 0.8931 (m-10) cc_final: 0.8705 (m-80) REVERT: K 18 PHE cc_start: 0.9163 (m-80) cc_final: 0.8889 (m-80) REVERT: K 73 PHE cc_start: 0.8990 (m-10) cc_final: 0.8704 (m-80) REVERT: L 18 PHE cc_start: 0.9058 (t80) cc_final: 0.8632 (t80) REVERT: L 27 PHE cc_start: 0.9451 (m-80) cc_final: 0.8856 (m-80) REVERT: L 52 MET cc_start: 0.9869 (tpt) cc_final: 0.9611 (ttp) REVERT: L 60 ASP cc_start: 0.9285 (p0) cc_final: 0.8852 (p0) REVERT: L 64 MET cc_start: 0.8447 (mtp) cc_final: 0.8233 (mtp) REVERT: O 55 ILE cc_start: 0.8004 (mm) cc_final: 0.7745 (mm) REVERT: P 33 ARG cc_start: 0.7252 (mmt180) cc_final: 0.6858 (mmt180) REVERT: P 36 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8515 (mt-10) REVERT: P 50 THR cc_start: 0.9303 (p) cc_final: 0.8974 (p) REVERT: Q 73 PHE cc_start: 0.9445 (m-10) cc_final: 0.9072 (m-80) REVERT: R 30 LEU cc_start: 0.9077 (mm) cc_final: 0.8387 (pp) REVERT: R 52 MET cc_start: 0.9641 (tmm) cc_final: 0.9342 (ptm) REVERT: S 36 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8983 (mm-30) REVERT: a 87 GLU cc_start: 0.9669 (mt-10) cc_final: 0.9293 (mp0) REVERT: a 91 GLU cc_start: 0.9348 (tt0) cc_final: 0.9034 (pt0) REVERT: a 122 MET cc_start: 0.8819 (tmm) cc_final: 0.8478 (tmm) REVERT: a 126 ASP cc_start: 0.8989 (m-30) cc_final: 0.8767 (m-30) REVERT: a 236 MET cc_start: 0.8447 (tmm) cc_final: 0.7915 (tmm) REVERT: a 281 ILE cc_start: 0.9798 (mt) cc_final: 0.9578 (mt) REVERT: a 286 MET cc_start: 0.9676 (tmm) cc_final: 0.9246 (ptp) REVERT: b 17 PHE cc_start: 0.9429 (t80) cc_final: 0.8805 (m-10) REVERT: b 22 MET cc_start: 0.6328 (mmm) cc_final: 0.6095 (mmm) REVERT: b 148 MET cc_start: 0.7643 (tpp) cc_final: 0.6652 (mpp) REVERT: e 127 GLN cc_start: 0.9533 (mp10) cc_final: 0.9273 (mp10) REVERT: g 24 MET cc_start: 0.9616 (mmp) cc_final: 0.9175 (mmp) REVERT: g 32 MET cc_start: 0.9292 (mmm) cc_final: 0.8893 (mmm) REVERT: g 39 MET cc_start: 0.9004 (mmp) cc_final: 0.8610 (mmm) REVERT: g 229 MET cc_start: 0.9754 (mmp) cc_final: 0.9204 (mmm) REVERT: p 22 MET cc_start: 0.9113 (mmp) cc_final: 0.8874 (tmm) REVERT: p 82 ARG cc_start: 0.9288 (ttp-110) cc_final: 0.8925 (ttp80) outliers start: 1 outliers final: 1 residues processed: 393 average time/residue: 0.2110 time to fit residues: 138.8155 Evaluate side-chains 301 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 420 optimal weight: 3.9990 chunk 354 optimal weight: 5.9990 chunk 375 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 378 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN G 49 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 ** 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 = 0.2974 r_free = 0.2974 target = 0.038280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.027868 restraints weight = 356560.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.028778 restraints weight = 230233.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029418 restraints weight = 168419.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.029863 restraints weight = 133717.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030188 restraints weight = 112444.069| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37735 Z= 0.165 Angle : 0.611 16.226 51158 Z= 0.320 Chirality : 0.042 0.237 5994 Planarity : 0.004 0.052 6634 Dihedral : 5.913 86.870 5369 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.94 % 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: 0.53 (0.12), residues: 4856 helix: 1.33 (0.10), residues: 2732 sheet: -0.22 (0.21), residues: 556 loop : -1.13 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 477 TYR 0.029 0.001 TYR a 23 PHE 0.067 0.002 PHE S 18 TRP 0.049 0.002 TRP a 261 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00339 (37735) covalent geometry : angle 0.61075 (51158) hydrogen bonds : bond 0.04218 ( 2317) hydrogen bonds : angle 4.80589 ( 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 366 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 363 time to evaluate : 1.591 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: A 258 LEU cc_start: 0.9666 (pp) cc_final: 0.9345 (tp) REVERT: A 355 PHE cc_start: 0.9207 (t80) cc_final: 0.8923 (t80) REVERT: B 49 MET cc_start: 0.8895 (tpt) cc_final: 0.8142 (tpt) REVERT: B 179 MET cc_start: 0.9408 (tpp) cc_final: 0.9132 (mmm) REVERT: B 235 MET cc_start: 0.9440 (mmp) cc_final: 0.9188 (mmm) REVERT: B 432 MET cc_start: 0.9568 (mmm) cc_final: 0.9134 (mmm) REVERT: C 49 MET cc_start: 0.9558 (mtm) cc_final: 0.9055 (ptp) REVERT: C 157 MET cc_start: 0.9640 (mpp) cc_final: 0.9414 (mmm) REVERT: C 179 MET cc_start: 0.9350 (tpp) cc_final: 0.9119 (tpp) REVERT: C 246 MET cc_start: 0.9645 (mmp) cc_final: 0.9418 (mmm) REVERT: C 263 ASP cc_start: 0.9107 (m-30) cc_final: 0.8571 (m-30) REVERT: C 432 MET cc_start: 0.9664 (mmp) cc_final: 0.9148 (mmm) REVERT: D 203 MET cc_start: 0.8649 (mpp) cc_final: 0.8448 (mpp) REVERT: D 245 PHE cc_start: 0.9472 (m-80) cc_final: 0.8963 (m-80) REVERT: D 280 MET cc_start: 0.9554 (tpt) cc_final: 0.9163 (tpt) REVERT: D 319 HIS cc_start: 0.9372 (m90) cc_final: 0.8734 (m90) REVERT: E 1 MET cc_start: 0.8729 (tmm) cc_final: 0.8325 (tmm) REVERT: E 87 MET cc_start: 0.9297 (mpp) cc_final: 0.8471 (mpp) REVERT: E 159 MET cc_start: 0.9743 (mmp) cc_final: 0.9415 (mmp) REVERT: E 203 MET cc_start: 0.9522 (mmm) cc_final: 0.8984 (mmm) REVERT: E 280 MET cc_start: 0.9415 (tpp) cc_final: 0.8972 (tpp) REVERT: E 319 HIS cc_start: 0.9109 (m90) cc_final: 0.8524 (m-70) REVERT: E 450 MET cc_start: 0.9424 (mmp) cc_final: 0.9042 (mmm) REVERT: F 158 MET cc_start: 0.9721 (tpt) cc_final: 0.9400 (mmp) REVERT: F 192 MET cc_start: 0.9715 (mmp) cc_final: 0.9513 (mmm) REVERT: F 208 MET cc_start: 0.9041 (ptp) cc_final: 0.8839 (pmm) REVERT: F 225 MET cc_start: 0.9611 (mmp) cc_final: 0.9357 (mmm) REVERT: F 266 MET cc_start: 0.9046 (mpp) cc_final: 0.8750 (mpp) REVERT: F 299 GLN cc_start: 0.9600 (mt0) cc_final: 0.9213 (mp-120) REVERT: F 402 GLN cc_start: 0.9533 (mt0) cc_final: 0.9296 (mt0) REVERT: H 64 MET cc_start: 0.9493 (mmp) cc_final: 0.9276 (mmp) REVERT: J 18 PHE cc_start: 0.8754 (m-10) cc_final: 0.8520 (m-10) REVERT: K 18 PHE cc_start: 0.9212 (m-80) cc_final: 0.8947 (m-80) REVERT: K 73 PHE cc_start: 0.9042 (m-10) cc_final: 0.8753 (m-80) REVERT: L 18 PHE cc_start: 0.9042 (t80) cc_final: 0.8490 (t80) REVERT: L 27 PHE cc_start: 0.9531 (m-80) cc_final: 0.8969 (t80) REVERT: L 64 MET cc_start: 0.8415 (mtp) cc_final: 0.8190 (mtt) REVERT: O 18 PHE cc_start: 0.9589 (m-10) cc_final: 0.9372 (m-80) REVERT: O 55 ILE cc_start: 0.7973 (mm) cc_final: 0.7703 (mm) REVERT: P 67 VAL cc_start: 0.8528 (p) cc_final: 0.8188 (m) REVERT: Q 73 PHE cc_start: 0.9458 (m-10) cc_final: 0.9129 (m-80) REVERT: R 23 THR cc_start: 0.9070 (p) cc_final: 0.8778 (p) REVERT: R 27 PHE cc_start: 0.7623 (m-10) cc_final: 0.6937 (m-80) REVERT: R 30 LEU cc_start: 0.9064 (mm) cc_final: 0.8430 (pp) REVERT: R 52 MET cc_start: 0.9642 (tmm) cc_final: 0.9327 (ptm) REVERT: S 36 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9044 (mm-30) REVERT: a 87 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9169 (mp0) REVERT: a 88 MET cc_start: 0.9332 (mtt) cc_final: 0.9077 (mtt) REVERT: a 91 GLU cc_start: 0.9301 (tt0) cc_final: 0.9034 (pt0) REVERT: a 122 MET cc_start: 0.8873 (tmm) cc_final: 0.8452 (tmm) REVERT: a 126 ASP cc_start: 0.8852 (m-30) cc_final: 0.8462 (m-30) REVERT: a 281 ILE cc_start: 0.9769 (mt) cc_final: 0.9542 (mt) REVERT: a 286 MET cc_start: 0.9693 (tmm) cc_final: 0.9234 (ptp) REVERT: b 17 PHE cc_start: 0.9486 (t80) cc_final: 0.8825 (m-10) REVERT: b 148 MET cc_start: 0.7613 (tpp) cc_final: 0.6616 (mpp) REVERT: e 123 GLU cc_start: 0.9620 (OUTLIER) cc_final: 0.9342 (pp20) REVERT: e 127 GLN cc_start: 0.9546 (mp10) cc_final: 0.9280 (mp10) REVERT: g 24 MET cc_start: 0.9667 (mmp) cc_final: 0.9238 (mmp) REVERT: g 32 MET cc_start: 0.9274 (mmm) cc_final: 0.8985 (mmm) REVERT: g 39 MET cc_start: 0.9010 (mmp) cc_final: 0.8642 (mmm) REVERT: g 229 MET cc_start: 0.9744 (mmp) cc_final: 0.9206 (mmm) REVERT: p 82 ARG cc_start: 0.9268 (ttp-110) cc_final: 0.8905 (ttp80) outliers start: 3 outliers final: 0 residues processed: 366 average time/residue: 0.2068 time to fit residues: 127.4282 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 : 1.231 ------------------------------------------------------------------------------- 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: 6.9990 chunk 225 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 330 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 348 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 270 optimal weight: 3.9990 chunk 411 optimal weight: 2.9990 chunk 273 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN F 207 GLN G 47 GLN 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** p 151 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.038754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.028211 restraints weight = 361351.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.029157 restraints weight = 228432.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.029829 restraints weight = 163976.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.030305 restraints weight = 128607.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.030637 restraints weight = 106883.925| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2871 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= 0.133 Angle : 0.593 11.057 51158 Z= 0.310 Chirality : 0.042 0.273 5994 Planarity : 0.004 0.056 6634 Dihedral : 5.824 87.078 5369 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 0.63 (0.12), residues: 4856 helix: 1.39 (0.10), residues: 2727 sheet: -0.15 (0.21), residues: 554 loop : -1.05 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 33 TYR 0.026 0.001 TYR a 23 PHE 0.049 0.001 PHE S 18 TRP 0.052 0.002 TRP a 261 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00281 (37735) covalent geometry : angle 0.59346 (51158) hydrogen bonds : bond 0.04135 ( 2317) hydrogen bonds : angle 4.69062 ( 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 360 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 1.480 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: 0.9686 (pp) cc_final: 0.9356 (tp) REVERT: A 355 PHE cc_start: 0.9172 (t80) cc_final: 0.8922 (t80) REVERT: B 49 MET cc_start: 0.8897 (tpt) cc_final: 0.8075 (tpt) REVERT: B 235 MET cc_start: 0.9420 (mmp) cc_final: 0.9187 (mmm) REVERT: B 432 MET cc_start: 0.9531 (mmm) cc_final: 0.9075 (mmt) REVERT: C 49 MET cc_start: 0.9574 (mtm) cc_final: 0.9198 (mpp) REVERT: C 157 MET cc_start: 0.9646 (mpp) cc_final: 0.9414 (mmm) REVERT: C 235 MET cc_start: 0.9424 (tpt) cc_final: 0.9210 (tpt) REVERT: C 246 MET cc_start: 0.9636 (mmp) cc_final: 0.9417 (mmm) REVERT: C 263 ASP cc_start: 0.9042 (m-30) cc_final: 0.8477 (m-30) REVERT: C 432 MET cc_start: 0.9651 (mmp) cc_final: 0.8998 (mmp) REVERT: D 203 MET cc_start: 0.8635 (mpp) cc_final: 0.8402 (mpp) REVERT: D 245 PHE cc_start: 0.9465 (m-80) cc_final: 0.8967 (m-80) REVERT: D 280 MET cc_start: 0.9529 (tpt) cc_final: 0.9162 (tpt) REVERT: D 319 HIS cc_start: 0.9383 (m90) cc_final: 0.8766 (m90) REVERT: E 1 MET cc_start: 0.8793 (tmm) cc_final: 0.8329 (tmm) REVERT: E 87 MET cc_start: 0.9287 (mpp) cc_final: 0.8501 (mpp) REVERT: E 159 MET cc_start: 0.9747 (mmp) cc_final: 0.9412 (mmp) REVERT: E 203 MET cc_start: 0.9507 (mmm) cc_final: 0.9004 (mmm) REVERT: E 225 MET cc_start: 0.9505 (mmt) cc_final: 0.9233 (mmm) REVERT: E 280 MET cc_start: 0.9399 (tpp) cc_final: 0.8962 (tpp) REVERT: E 319 HIS cc_start: 0.9099 (m90) cc_final: 0.8484 (m-70) REVERT: E 450 MET cc_start: 0.9430 (mmp) cc_final: 0.9050 (mmm) REVERT: F 158 MET cc_start: 0.9718 (tpt) cc_final: 0.9400 (mmp) REVERT: F 225 MET cc_start: 0.9601 (mmp) cc_final: 0.9356 (mmm) REVERT: F 266 MET cc_start: 0.9090 (mpp) cc_final: 0.8793 (mpp) REVERT: F 299 GLN cc_start: 0.9577 (mt0) cc_final: 0.9208 (mp-120) REVERT: F 402 GLN cc_start: 0.9543 (mt0) cc_final: 0.9277 (mt0) REVERT: G 18 PHE cc_start: 0.8696 (t80) cc_final: 0.8333 (t80) REVERT: H 64 MET cc_start: 0.9456 (mmp) cc_final: 0.9200 (mmp) REVERT: J 18 PHE cc_start: 0.8764 (m-10) cc_final: 0.8559 (m-10) REVERT: K 18 PHE cc_start: 0.9235 (m-80) cc_final: 0.8971 (m-80) REVERT: K 73 PHE cc_start: 0.9055 (m-10) cc_final: 0.8750 (m-10) REVERT: L 18 PHE cc_start: 0.9053 (t80) cc_final: 0.8475 (t80) REVERT: L 27 PHE cc_start: 0.9535 (m-80) cc_final: 0.9016 (m-80) REVERT: L 30 LEU cc_start: 0.9248 (pp) cc_final: 0.9042 (pp) REVERT: O 18 PHE cc_start: 0.9577 (m-10) cc_final: 0.9354 (m-80) REVERT: O 55 ILE cc_start: 0.7960 (mm) cc_final: 0.7724 (mm) REVERT: P 33 ARG cc_start: 0.7288 (mmt180) cc_final: 0.6818 (mmt180) REVERT: P 36 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8478 (mt-10) REVERT: P 67 VAL cc_start: 0.8738 (p) cc_final: 0.8415 (m) REVERT: Q 73 PHE cc_start: 0.9448 (m-10) cc_final: 0.9121 (m-80) REVERT: R 23 THR cc_start: 0.9091 (p) cc_final: 0.8778 (p) REVERT: R 27 PHE cc_start: 0.7688 (m-10) cc_final: 0.7077 (m-80) REVERT: R 52 MET cc_start: 0.9611 (tmm) cc_final: 0.9325 (ptm) REVERT: a 87 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9363 (mp0) REVERT: a 126 ASP cc_start: 0.8657 (m-30) cc_final: 0.8137 (m-30) REVERT: a 236 MET cc_start: 0.8386 (tmm) cc_final: 0.7560 (tmm) REVERT: a 240 GLU cc_start: 0.9262 (pt0) cc_final: 0.8829 (pt0) REVERT: a 275 ILE cc_start: 0.9747 (pt) cc_final: 0.9543 (pt) REVERT: a 278 MET cc_start: 0.9702 (mmp) cc_final: 0.9410 (mmm) REVERT: a 286 MET cc_start: 0.9705 (tmm) cc_final: 0.9264 (ptp) REVERT: b 17 PHE cc_start: 0.9514 (t80) cc_final: 0.8862 (m-10) REVERT: e 113 ASP cc_start: 0.9669 (t70) cc_final: 0.9392 (t0) REVERT: e 127 GLN cc_start: 0.9492 (mp10) cc_final: 0.9228 (mp10) REVERT: g 24 MET cc_start: 0.9647 (mmp) cc_final: 0.9181 (mmp) REVERT: g 26 MET cc_start: 0.9352 (ptp) cc_final: 0.8975 (ptp) REVERT: g 32 MET cc_start: 0.9065 (mmm) cc_final: 0.8831 (mmm) REVERT: g 39 MET cc_start: 0.9007 (mmp) cc_final: 0.8636 (mmm) REVERT: g 229 MET cc_start: 0.9759 (mmp) cc_final: 0.9210 (mmm) REVERT: p 82 ARG cc_start: 0.9261 (ttp-110) cc_final: 0.8886 (ttp80) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.1989 time to fit residues: 121.4085 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 : 1.386 ------------------------------------------------------------------------------- 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: 3.9990 chunk 306 optimal weight: 6.9990 chunk 417 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 415 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 366 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 248 ASN ** 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 139 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.038863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.028342 restraints weight = 362061.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.029274 restraints weight = 230440.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029947 restraints weight = 166167.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030425 restraints weight = 130182.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030776 restraints weight = 108060.803| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- 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 = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37735 Z= 0.148 Angle : 0.604 10.486 51158 Z= 0.317 Chirality : 0.042 0.229 5994 Planarity : 0.004 0.053 6634 Dihedral : 5.798 88.754 5369 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 0.66 (0.12), residues: 4856 helix: 1.40 (0.10), residues: 2728 sheet: -0.14 (0.21), residues: 556 loop : -1.00 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG e 51 TYR 0.024 0.001 TYR a 23 PHE 0.042 0.002 PHE P 53 TRP 0.056 0.002 TRP a 261 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00312 (37735) covalent geometry : angle 0.60445 (51158) hydrogen bonds : bond 0.04097 ( 2317) hydrogen bonds : angle 4.71155 ( 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 364 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.425 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: 0.9704 (pp) cc_final: 0.9367 (tp) REVERT: A 355 PHE cc_start: 0.9162 (t80) cc_final: 0.8911 (t80) REVERT: B 49 MET cc_start: 0.8922 (tpt) cc_final: 0.8186 (tpt) REVERT: B 179 MET cc_start: 0.9241 (mmp) cc_final: 0.8931 (mmm) REVERT: B 235 MET cc_start: 0.9411 (mmp) cc_final: 0.9178 (mmm) REVERT: B 432 MET cc_start: 0.9549 (mmm) cc_final: 0.9041 (mmt) REVERT: C 49 MET cc_start: 0.9575 (mtm) cc_final: 0.9195 (mpp) REVERT: C 157 MET cc_start: 0.9659 (mpp) cc_final: 0.9445 (mmm) REVERT: C 246 MET cc_start: 0.9634 (mmp) cc_final: 0.9415 (mmm) REVERT: C 432 MET cc_start: 0.9662 (mmp) cc_final: 0.8998 (mmp) REVERT: D 203 MET cc_start: 0.8589 (mpp) cc_final: 0.8366 (mpp) REVERT: D 245 PHE cc_start: 0.9467 (m-80) cc_final: 0.8878 (m-80) REVERT: D 280 MET cc_start: 0.9530 (tpt) cc_final: 0.9165 (tpt) REVERT: D 319 HIS cc_start: 0.9402 (m90) cc_final: 0.8823 (m90) REVERT: E 1 MET cc_start: 0.8846 (tmm) cc_final: 0.8332 (ppp) REVERT: E 87 MET cc_start: 0.9272 (mpp) cc_final: 0.8504 (mpp) REVERT: E 159 MET cc_start: 0.9744 (mmp) cc_final: 0.9428 (mmp) REVERT: E 203 MET cc_start: 0.9486 (mmm) cc_final: 0.8981 (mmm) REVERT: E 225 MET cc_start: 0.9499 (mmt) cc_final: 0.9242 (mmm) REVERT: E 280 MET cc_start: 0.9392 (tpp) cc_final: 0.8916 (tpp) REVERT: E 319 HIS cc_start: 0.9098 (m90) cc_final: 0.8426 (m-70) REVERT: E 450 MET cc_start: 0.9438 (mmp) cc_final: 0.9038 (mmm) REVERT: F 158 MET cc_start: 0.9729 (tpt) cc_final: 0.9398 (mmp) REVERT: F 225 MET cc_start: 0.9602 (mmp) cc_final: 0.9337 (mmm) REVERT: F 266 MET cc_start: 0.9074 (mpp) cc_final: 0.8771 (mpp) REVERT: F 299 GLN cc_start: 0.9582 (mt0) cc_final: 0.9203 (mp-120) REVERT: F 402 GLN cc_start: 0.9532 (mt0) cc_final: 0.9294 (mt0) REVERT: G 18 PHE cc_start: 0.8774 (t80) cc_final: 0.8477 (t80) REVERT: H 1 MET cc_start: 0.8787 (mmm) cc_final: 0.8256 (tpp) REVERT: H 64 MET cc_start: 0.9448 (mmp) cc_final: 0.9194 (mmp) REVERT: J 14 ILE cc_start: 0.9427 (mm) cc_final: 0.8655 (pt) REVERT: K 18 PHE cc_start: 0.9239 (m-80) cc_final: 0.8937 (m-80) REVERT: K 73 PHE cc_start: 0.9074 (m-10) cc_final: 0.8787 (m-80) REVERT: L 18 PHE cc_start: 0.9046 (t80) cc_final: 0.8794 (t80) REVERT: L 27 PHE cc_start: 0.9529 (m-80) cc_final: 0.8993 (m-80) REVERT: L 30 LEU cc_start: 0.9251 (pp) cc_final: 0.9010 (pp) REVERT: L 60 ASP cc_start: 0.8669 (m-30) cc_final: 0.8266 (m-30) REVERT: O 55 ILE cc_start: 0.7956 (mm) cc_final: 0.7731 (mm) REVERT: O 64 MET cc_start: 0.8976 (mmp) cc_final: 0.8746 (mmm) REVERT: P 52 MET cc_start: 0.8503 (ppp) cc_final: 0.8282 (ppp) REVERT: P 67 VAL cc_start: 0.8785 (p) cc_final: 0.8463 (m) REVERT: Q 73 PHE cc_start: 0.9459 (m-10) cc_final: 0.9132 (m-80) REVERT: R 23 THR cc_start: 0.9082 (p) cc_final: 0.8718 (p) REVERT: R 27 PHE cc_start: 0.7698 (m-10) cc_final: 0.7076 (m-80) REVERT: R 52 MET cc_start: 0.9617 (tmm) cc_final: 0.9332 (ptm) REVERT: a 87 GLU cc_start: 0.9644 (mt-10) cc_final: 0.9381 (mp0) REVERT: a 88 MET cc_start: 0.9453 (mtt) cc_final: 0.9060 (mmm) REVERT: a 236 MET cc_start: 0.8522 (tmm) cc_final: 0.7933 (ppp) REVERT: a 275 ILE cc_start: 0.9744 (pt) cc_final: 0.9538 (pt) REVERT: a 278 MET cc_start: 0.9726 (mmp) cc_final: 0.9361 (mmm) REVERT: a 286 MET cc_start: 0.9702 (tmm) cc_final: 0.9261 (ptp) REVERT: b 17 PHE cc_start: 0.9520 (t80) cc_final: 0.8918 (m-80) REVERT: e 113 ASP cc_start: 0.9663 (t70) cc_final: 0.9393 (t0) REVERT: e 127 GLN cc_start: 0.9498 (mp10) cc_final: 0.9248 (mp10) REVERT: g 24 MET cc_start: 0.9675 (mmp) cc_final: 0.9208 (mmp) REVERT: g 26 MET cc_start: 0.9331 (ptp) cc_final: 0.8983 (ptp) REVERT: g 39 MET cc_start: 0.9008 (mmp) cc_final: 0.8638 (mmm) REVERT: g 49 MET cc_start: 0.9463 (ttt) cc_final: 0.9092 (tmm) REVERT: g 229 MET cc_start: 0.9763 (mmp) cc_final: 0.9185 (mmm) REVERT: p 82 ARG cc_start: 0.9278 (ttp-110) cc_final: 0.8916 (ttp80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2123 time to fit residues: 130.1781 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 : 1.238 ------------------------------------------------------------------------------- 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: 9.9990 chunk 381 optimal weight: 3.9990 chunk 393 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 447 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 295 HIS ** 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.028571 restraints weight = 356546.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.029521 restraints weight = 225186.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.030185 restraints weight = 162364.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.030664 restraints weight = 127144.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.031018 restraints weight = 105815.686| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37735 Z= 0.125 Angle : 0.594 10.530 51158 Z= 0.310 Chirality : 0.042 0.314 5994 Planarity : 0.004 0.056 6634 Dihedral : 5.701 89.871 5369 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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: 0.77 (0.12), residues: 4856 helix: 1.47 (0.10), residues: 2728 sheet: -0.04 (0.21), residues: 545 loop : -0.93 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 51 TYR 0.047 0.001 TYR a 23 PHE 0.042 0.001 PHE S 18 TRP 0.055 0.002 TRP a 261 HIS 0.004 0.001 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00260 (37735) covalent geometry : angle 0.59409 (51158) hydrogen bonds : bond 0.03996 ( 2317) hydrogen bonds : angle 4.61273 ( 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 374 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.381 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: A 258 LEU cc_start: 0.9674 (pp) cc_final: 0.9322 (tp) REVERT: A 355 PHE cc_start: 0.9121 (t80) cc_final: 0.8901 (t80) REVERT: B 49 MET cc_start: 0.8821 (tpt) cc_final: 0.8009 (tpt) REVERT: B 179 MET cc_start: 0.9152 (mmp) cc_final: 0.8880 (mmp) REVERT: B 432 MET cc_start: 0.9480 (mmm) cc_final: 0.9010 (mmt) REVERT: C 49 MET cc_start: 0.9563 (mtm) cc_final: 0.9185 (mtm) REVERT: C 157 MET cc_start: 0.9652 (mpp) cc_final: 0.9451 (mmm) REVERT: C 246 MET cc_start: 0.9622 (mmp) cc_final: 0.9402 (mmm) REVERT: C 432 MET cc_start: 0.9644 (mmp) cc_final: 0.8885 (mmp) REVERT: D 245 PHE cc_start: 0.9441 (m-80) cc_final: 0.8852 (m-80) REVERT: D 280 MET cc_start: 0.9473 (tpt) cc_final: 0.9107 (tpt) REVERT: D 319 HIS cc_start: 0.9431 (m90) cc_final: 0.8874 (m90) REVERT: E 1 MET cc_start: 0.8854 (tmm) cc_final: 0.8333 (ppp) REVERT: E 87 MET cc_start: 0.9239 (mpp) cc_final: 0.8502 (mpp) REVERT: E 159 MET cc_start: 0.9719 (mmp) cc_final: 0.9305 (mmp) REVERT: E 203 MET cc_start: 0.9407 (mmm) cc_final: 0.8600 (mmm) REVERT: E 225 MET cc_start: 0.9451 (mmt) cc_final: 0.9172 (mmm) REVERT: E 450 MET cc_start: 0.9430 (mmp) cc_final: 0.9054 (mmm) REVERT: F 55 MET cc_start: 0.9516 (mmm) cc_final: 0.8821 (mmm) REVERT: F 158 MET cc_start: 0.9670 (tpt) cc_final: 0.9365 (mmp) REVERT: F 225 MET cc_start: 0.9570 (mmp) cc_final: 0.9333 (mmm) REVERT: F 266 MET cc_start: 0.9099 (mpp) cc_final: 0.8810 (mpp) REVERT: F 299 GLN cc_start: 0.9542 (mt0) cc_final: 0.9190 (mp-120) REVERT: F 402 GLN cc_start: 0.9520 (mt0) cc_final: 0.9270 (mt0) REVERT: G 18 PHE cc_start: 0.8947 (t80) cc_final: 0.8651 (t80) REVERT: H 64 MET cc_start: 0.9430 (mmp) cc_final: 0.8913 (mtp) REVERT: J 14 ILE cc_start: 0.9363 (mm) cc_final: 0.8610 (pt) REVERT: J 18 PHE cc_start: 0.8675 (m-10) cc_final: 0.8452 (m-80) REVERT: K 18 PHE cc_start: 0.9249 (m-80) cc_final: 0.8958 (m-80) REVERT: K 73 PHE cc_start: 0.9009 (m-10) cc_final: 0.8729 (m-80) REVERT: L 18 PHE cc_start: 0.9060 (t80) cc_final: 0.8742 (t80) REVERT: L 27 PHE cc_start: 0.9550 (m-80) cc_final: 0.8977 (m-80) REVERT: L 30 LEU cc_start: 0.9225 (pp) cc_final: 0.9005 (pp) REVERT: L 60 ASP cc_start: 0.8997 (m-30) cc_final: 0.8714 (m-30) REVERT: O 55 ILE cc_start: 0.7854 (mm) cc_final: 0.7631 (mm) REVERT: O 64 MET cc_start: 0.9009 (mmp) cc_final: 0.8727 (mmm) REVERT: P 36 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8413 (mt-10) REVERT: P 53 PHE cc_start: 0.8905 (m-80) cc_final: 0.8536 (m-80) REVERT: P 67 VAL cc_start: 0.8779 (p) cc_final: 0.8507 (m) REVERT: Q 73 PHE cc_start: 0.9441 (m-10) cc_final: 0.9110 (m-80) REVERT: R 23 THR cc_start: 0.9015 (p) cc_final: 0.8650 (p) REVERT: R 27 PHE cc_start: 0.7684 (m-10) cc_final: 0.7118 (m-80) REVERT: R 52 MET cc_start: 0.9598 (tmm) cc_final: 0.9345 (ptm) REVERT: R 73 PHE cc_start: 0.9045 (m-80) cc_final: 0.8820 (m-80) REVERT: a 87 GLU cc_start: 0.9636 (mt-10) cc_final: 0.9272 (mp0) REVERT: a 88 MET cc_start: 0.9451 (mtt) cc_final: 0.8967 (mtt) REVERT: a 91 GLU cc_start: 0.9396 (tt0) cc_final: 0.9143 (pt0) REVERT: a 122 MET cc_start: 0.8806 (tpt) cc_final: 0.8605 (tpt) REVERT: a 126 ASP cc_start: 0.8625 (m-30) cc_final: 0.8243 (m-30) REVERT: a 236 MET cc_start: 0.8177 (tmm) cc_final: 0.7917 (ppp) REVERT: a 277 MET cc_start: 0.9560 (ppp) cc_final: 0.9210 (ppp) REVERT: a 278 MET cc_start: 0.9713 (mmp) cc_final: 0.9263 (mmm) REVERT: a 286 MET cc_start: 0.9689 (tmm) cc_final: 0.9203 (ptp) REVERT: b 17 PHE cc_start: 0.9529 (t80) cc_final: 0.9120 (m-10) REVERT: b 22 MET cc_start: 0.5891 (mmm) cc_final: 0.5597 (mmm) REVERT: e 113 ASP cc_start: 0.9669 (t70) cc_final: 0.9417 (t0) REVERT: e 127 GLN cc_start: 0.9427 (mp10) cc_final: 0.9185 (mp10) REVERT: g 24 MET cc_start: 0.9687 (mmp) cc_final: 0.9206 (mmp) REVERT: g 26 MET cc_start: 0.9338 (ptp) cc_final: 0.8955 (ptp) REVERT: g 39 MET cc_start: 0.9007 (mmp) cc_final: 0.8636 (mmm) REVERT: g 49 MET cc_start: 0.9442 (ttt) cc_final: 0.9075 (tmm) REVERT: g 229 MET cc_start: 0.9762 (mmp) cc_final: 0.9200 (mmm) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2118 time to fit residues: 133.0055 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 : 1.300 ------------------------------------------------------------------------------- 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: 0.9990 chunk 236 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 458 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 333 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 193 optimal weight: 0.0970 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.038962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.028424 restraints weight = 358853.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.029377 restraints weight = 226837.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030005 restraints weight = 163064.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030468 restraints weight = 128629.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030802 restraints weight = 107278.170| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- 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 = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37735 Z= 0.150 Angle : 0.612 9.907 51158 Z= 0.321 Chirality : 0.042 0.223 5994 Planarity : 0.004 0.055 6634 Dihedral : 5.687 88.090 5369 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.78 (0.12), residues: 4856 helix: 1.46 (0.10), residues: 2723 sheet: -0.02 (0.21), residues: 554 loop : -0.90 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 82 TYR 0.046 0.001 TYR a 23 PHE 0.037 0.002 PHE Q 18 TRP 0.055 0.002 TRP a 261 HIS 0.004 0.001 HIS p 145 Details of bonding type rmsd covalent geometry : bond 0.00312 (37735) covalent geometry : angle 0.61242 (51158) hydrogen bonds : bond 0.04011 ( 2317) hydrogen bonds : angle 4.67817 ( 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 355 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 1.415 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: A 258 LEU cc_start: 0.9706 (pp) cc_final: 0.9357 (tp) REVERT: A 457 MET cc_start: 0.9370 (mmm) cc_final: 0.8589 (tpp) REVERT: B 49 MET cc_start: 0.8866 (tpt) cc_final: 0.8089 (tpt) REVERT: B 53 MET cc_start: 0.9428 (mtm) cc_final: 0.9191 (mtt) REVERT: B 179 MET cc_start: 0.9146 (mmp) cc_final: 0.8925 (mmm) REVERT: B 432 MET cc_start: 0.9523 (mmm) cc_final: 0.8933 (mmt) REVERT: C 49 MET cc_start: 0.9563 (mtm) cc_final: 0.9139 (mtm) REVERT: C 246 MET cc_start: 0.9622 (mmp) cc_final: 0.9400 (mmm) REVERT: C 432 MET cc_start: 0.9663 (mmp) cc_final: 0.8993 (mmp) REVERT: D 245 PHE cc_start: 0.9390 (m-80) cc_final: 0.8908 (m-80) REVERT: D 280 MET cc_start: 0.9496 (tpt) cc_final: 0.9151 (tpt) REVERT: D 319 HIS cc_start: 0.9453 (m90) cc_final: 0.8922 (m90) REVERT: E 1 MET cc_start: 0.8926 (tmm) cc_final: 0.8428 (ppp) REVERT: E 87 MET cc_start: 0.9228 (mpp) cc_final: 0.8518 (mpp) REVERT: E 159 MET cc_start: 0.9717 (mmp) cc_final: 0.9455 (mmp) REVERT: E 203 MET cc_start: 0.9415 (mmm) cc_final: 0.8574 (mmm) REVERT: E 225 MET cc_start: 0.9483 (mmt) cc_final: 0.9210 (mmm) REVERT: E 280 MET cc_start: 0.9407 (ttm) cc_final: 0.9038 (ttm) REVERT: E 319 HIS cc_start: 0.9111 (m-70) cc_final: 0.8680 (m90) REVERT: E 450 MET cc_start: 0.9417 (mmp) cc_final: 0.9045 (mmm) REVERT: F 158 MET cc_start: 0.9685 (tpt) cc_final: 0.9377 (mmp) REVERT: F 225 MET cc_start: 0.9593 (mmp) cc_final: 0.9343 (mmm) REVERT: F 266 MET cc_start: 0.9111 (mpp) cc_final: 0.8809 (mpp) REVERT: F 299 GLN cc_start: 0.9551 (mt0) cc_final: 0.9209 (mp-120) REVERT: F 402 GLN cc_start: 0.9506 (mt0) cc_final: 0.9255 (mt0) REVERT: G 18 PHE cc_start: 0.9029 (t80) cc_final: 0.8786 (t80) REVERT: H 64 MET cc_start: 0.9418 (mmp) cc_final: 0.8918 (mtp) REVERT: J 14 ILE cc_start: 0.9367 (mm) cc_final: 0.8608 (pt) REVERT: J 18 PHE cc_start: 0.8688 (m-10) cc_final: 0.8428 (m-80) REVERT: K 18 PHE cc_start: 0.9243 (m-80) cc_final: 0.8983 (m-80) REVERT: K 73 PHE cc_start: 0.9054 (m-10) cc_final: 0.8769 (m-80) REVERT: L 18 PHE cc_start: 0.9031 (t80) cc_final: 0.8735 (t80) REVERT: L 27 PHE cc_start: 0.9559 (m-80) cc_final: 0.8968 (m-80) REVERT: L 60 ASP cc_start: 0.9169 (m-30) cc_final: 0.8878 (m-30) REVERT: O 55 ILE cc_start: 0.7888 (mm) cc_final: 0.7662 (mm) REVERT: O 64 MET cc_start: 0.9030 (mmp) cc_final: 0.8770 (mmm) REVERT: P 36 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8436 (mt-10) REVERT: P 52 MET cc_start: 0.8551 (ppp) cc_final: 0.8305 (ppp) REVERT: P 67 VAL cc_start: 0.8777 (p) cc_final: 0.8477 (m) REVERT: Q 73 PHE cc_start: 0.9468 (m-10) cc_final: 0.9144 (m-80) REVERT: R 23 THR cc_start: 0.9090 (p) cc_final: 0.8690 (p) REVERT: R 27 PHE cc_start: 0.7661 (m-10) cc_final: 0.7083 (m-80) REVERT: R 52 MET cc_start: 0.9596 (tmm) cc_final: 0.9343 (ptm) REVERT: R 73 PHE cc_start: 0.9097 (m-80) cc_final: 0.8879 (m-80) REVERT: a 87 GLU cc_start: 0.9660 (mt-10) cc_final: 0.9401 (mt-10) REVERT: a 88 MET cc_start: 0.9458 (mtt) cc_final: 0.9073 (mmm) REVERT: a 118 TRP cc_start: 0.7936 (t60) cc_final: 0.7525 (t60) REVERT: a 126 ASP cc_start: 0.8727 (m-30) cc_final: 0.8029 (m-30) REVERT: a 236 MET cc_start: 0.8638 (tmm) cc_final: 0.8040 (tmm) REVERT: a 240 GLU cc_start: 0.9270 (pt0) cc_final: 0.8868 (pt0) REVERT: a 274 PHE cc_start: 0.9608 (t80) cc_final: 0.9385 (t80) REVERT: a 275 ILE cc_start: 0.9713 (pt) cc_final: 0.9487 (pt) REVERT: a 277 MET cc_start: 0.9558 (ppp) cc_final: 0.9171 (ppp) REVERT: a 278 MET cc_start: 0.9712 (mmp) cc_final: 0.9244 (mmm) REVERT: a 286 MET cc_start: 0.9707 (tmm) cc_final: 0.9265 (ptp) REVERT: b 17 PHE cc_start: 0.9497 (t80) cc_final: 0.9018 (m-80) REVERT: b 22 MET cc_start: 0.5879 (mmm) cc_final: 0.5569 (mmm) REVERT: e 113 ASP cc_start: 0.9677 (t70) cc_final: 0.9430 (t0) REVERT: g 24 MET cc_start: 0.9703 (mmp) cc_final: 0.9225 (mmp) REVERT: g 26 MET cc_start: 0.9323 (ptp) cc_final: 0.8918 (ptp) REVERT: g 39 MET cc_start: 0.9031 (mmp) cc_final: 0.8665 (mmm) REVERT: g 229 MET cc_start: 0.9756 (mmp) cc_final: 0.9217 (mmm) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2043 time to fit residues: 123.1530 Evaluate side-chains 286 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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: 0.8980 chunk 26 optimal weight: 8.9990 chunk 461 optimal weight: 9.9990 chunk 288 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 419 optimal weight: 0.3980 chunk 246 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 466 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.028014 restraints weight = 360730.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.028940 restraints weight = 226387.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029598 restraints weight = 162829.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.030074 restraints weight = 127598.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030413 restraints weight = 105869.017| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37735 Z= 0.149 Angle : 0.609 11.340 51158 Z= 0.319 Chirality : 0.042 0.219 5994 Planarity : 0.004 0.055 6634 Dihedral : 5.675 88.229 5369 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.79 (0.12), residues: 4856 helix: 1.47 (0.10), residues: 2717 sheet: 0.06 (0.22), residues: 552 loop : -0.91 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 81 TYR 0.045 0.001 TYR a 23 PHE 0.044 0.002 PHE S 18 TRP 0.050 0.002 TRP a 261 HIS 0.004 0.001 HIS p 145 Details of bonding type rmsd covalent geometry : bond 0.00309 (37735) covalent geometry : angle 0.60860 (51158) hydrogen bonds : bond 0.03948 ( 2317) hydrogen bonds : angle 4.65972 ( 6804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6491.29 seconds wall clock time: 113 minutes 1.49 seconds (6781.49 seconds total)