Starting phenix.real_space_refine on Fri Oct 23 08:33:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xcm_66735/10_2026/9xcm_66735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xcm_66735/10_2026/9xcm_66735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xcm_66735/10_2026/9xcm_66735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xcm_66735/10_2026/9xcm_66735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xcm_66735/10_2026/9xcm_66735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xcm_66735/10_2026/9xcm_66735.map" } resolution = 2.52 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 48 5.16 5 C 5805 2.51 5 N 1528 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9126 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2789 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 4437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4437 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 534} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1869 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.04, per 1000 atoms: 0.22 Number of scatterers: 9126 At special positions: 0 Unit cell: (91, 85.15, 124.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 3 15.00 O 1742 8.00 N 1528 7.00 C 5805 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: 0.73 Conformation dependent library (CDL) restraints added in 314.1 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 48.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.707A pdb=" N LYS C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 92 " --> pdb=" O TRP C 88 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 93 " --> pdb=" O HIS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.616A pdb=" N GLU C 102 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS C 103 " --> pdb=" O PRO C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.598A pdb=" N GLU C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET C 125 " --> pdb=" O MET C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 146 Processing helix chain 'C' and resid 174 through 177 removed outlier: 3.812A pdb=" N ILE C 177 " --> pdb=" O PRO C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 177' Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.537A pdb=" N ASP C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.044A pdb=" N VAL C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.893A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.551A pdb=" N THR C 262 " --> pdb=" O CYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.682A pdb=" N PHE C 268 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 270 " --> pdb=" O SER C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 270' Processing helix chain 'C' and resid 277 through 285 Processing helix chain 'C' and resid 291 through 297 removed outlier: 3.661A pdb=" N ALA C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 4.491A pdb=" N GLN C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.513A pdb=" N ILE C 343 " --> pdb=" O TYR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.745A pdb=" N GLU C 366 " --> pdb=" O GLN C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 4.065A pdb=" N ARG C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.600A pdb=" N GLU A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.754A pdb=" N GLU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 190 through 202 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 206 through 215 removed outlier: 4.016A pdb=" N SER A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.530A pdb=" N SER A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 272 removed outlier: 3.545A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 removed outlier: 3.555A pdb=" N GLU A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.560A pdb=" N LYS A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.777A pdb=" N GLU A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.676A pdb=" N ARG A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.609A pdb=" N LEU A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.994A pdb=" N CYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 removed outlier: 4.181A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.989A pdb=" N VAL A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.854A pdb=" N GLN A 487 " --> pdb=" O TYR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 544 removed outlier: 4.516A pdb=" N LYS A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 540 " --> pdb=" O MET A 536 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 568 removed outlier: 3.794A pdb=" N GLN A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 4.469A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.505A pdb=" N PHE A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 608 through 637 removed outlier: 3.667A pdb=" N LEU A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 621 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 Processing helix chain 'B' and resid 27 through 36 removed outlier: 3.673A pdb=" N ASN B 32 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 removed outlier: 4.116A pdb=" N VAL B 57 " --> pdb=" O PRO B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 74 removed outlier: 3.548A pdb=" N LEU B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 101 through 107 removed outlier: 3.597A pdb=" N VAL B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.959A pdb=" N ILE B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 141 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.583A pdb=" N LEU B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 187' Processing helix chain 'B' and resid 209 through 231 removed outlier: 3.855A pdb=" N LEU B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.216A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N CYS C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 39 removed outlier: 4.306A pdb=" N VAL C 37 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS C 70 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA5, first strand: chain 'C' and resid 171 through 172 removed outlier: 6.552A pdb=" N ILE C 153 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N SER C 302 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C 155 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C 299 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 240 through 243 removed outlier: 3.769A pdb=" N LYS C 240 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 252 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 242 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 443 through 444 Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 470 294 hydrogen bonds defined for protein. 819 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: 1.33 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2943 1.34 - 1.46: 2023 1.46 - 1.58: 4257 1.58 - 1.70: 6 1.70 - 1.82: 81 Bond restraints: 9310 Sorted by residual: bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 bond pdb=" C5 ATP C 401 " pdb=" C6 ATP C 401 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C8 ATP C 401 " pdb=" N7 ATP C 401 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.08e+01 bond pdb=" C5 ATP C 401 " pdb=" N7 ATP C 401 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.90e+01 bond pdb=" C4 ATP C 401 " pdb=" N9 ATP C 401 " ideal model delta sigma weight residual 1.374 1.332 0.042 1.00e-02 1.00e+04 1.74e+01 ... (remaining 9305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 12419 2.99 - 5.98: 139 5.98 - 8.98: 19 8.98 - 11.97: 2 11.97 - 14.96: 2 Bond angle restraints: 12581 Sorted by residual: angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 124.91 14.96 1.00e+00 1.00e+00 2.24e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 122.82 14.01 1.00e+00 1.00e+00 1.96e+02 angle pdb=" C5 ATP C 401 " pdb=" C4 ATP C 401 " pdb=" N3 ATP C 401 " ideal model delta sigma weight residual 126.80 118.56 8.24 1.00e+00 1.00e+00 6.79e+01 angle pdb=" N3 ATP C 401 " pdb=" C4 ATP C 401 " pdb=" N9 ATP C 401 " ideal model delta sigma weight residual 127.04 135.17 -8.13 1.15e+00 7.59e-01 5.02e+01 angle pdb=" N1 ATP C 401 " pdb=" C2 ATP C 401 " pdb=" N3 ATP C 401 " ideal model delta sigma weight residual 128.69 123.69 5.00 1.00e+00 1.00e+00 2.50e+01 ... (remaining 12576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 5336 15.58 - 31.15: 282 31.15 - 46.72: 64 46.72 - 62.30: 1 62.30 - 77.87: 7 Dihedral angle restraints: 5690 sinusoidal: 2349 harmonic: 3341 Sorted by residual: dihedral pdb=" CA ARG A 441 " pdb=" C ARG A 441 " pdb=" N ASP A 442 " pdb=" CA ASP A 442 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA HIS A 438 " pdb=" C HIS A 438 " pdb=" N LYS A 439 " pdb=" CA LYS A 439 " ideal model delta harmonic sigma weight residual 180.00 152.39 27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ARG B 56 " pdb=" C ARG B 56 " pdb=" N VAL B 57 " pdb=" CA VAL B 57 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 5687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1201 0.073 - 0.146: 187 0.146 - 0.218: 14 0.218 - 0.291: 1 0.291 - 0.364: 1 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CB ILE B 246 " pdb=" CA ILE B 246 " pdb=" CG1 ILE B 246 " pdb=" CG2 ILE B 246 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE C 252 " pdb=" CA ILE C 252 " pdb=" CG1 ILE C 252 " pdb=" CG2 ILE C 252 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL B 23 " pdb=" CA VAL B 23 " pdb=" CG1 VAL B 23 " pdb=" CG2 VAL B 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1401 not shown) Planarity restraints: 1609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 358 " 0.027 2.00e-02 2.50e+03 2.00e-02 9.96e+00 pdb=" CG TRP C 358 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 358 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 358 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 358 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 358 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 358 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 358 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 358 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 358 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 369 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 370 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 119 " 0.013 2.00e-02 2.50e+03 1.88e-02 6.19e+00 pdb=" CG PHE B 119 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 119 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B 119 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 119 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 119 " 0.000 2.00e-02 2.50e+03 ... (remaining 1606 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2326 2.79 - 3.32: 7931 3.32 - 3.85: 14889 3.85 - 4.37: 18428 4.37 - 4.90: 30284 Nonbonded interactions: 73858 Sorted by model distance: nonbonded pdb=" OH TYR A 348 " pdb=" OD2 ASP A 618 " model vdw 2.267 3.040 nonbonded pdb=" O SER B 124 " pdb=" OH TYR B 181 " model vdw 2.284 3.040 nonbonded pdb=" OG SER C 302 " pdb=" OG SER C 340 " model vdw 2.286 3.040 nonbonded pdb=" OG SER C 241 " pdb=" O ILE C 250 " model vdw 2.298 3.040 nonbonded pdb=" O GLY C 158 " pdb=" OG1 THR C 305 " model vdw 2.312 3.040 ... (remaining 73853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 9.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9310 Z= 0.261 Angle : 0.867 14.959 12581 Z= 0.504 Chirality : 0.054 0.364 1404 Planarity : 0.007 0.063 1609 Dihedral : 10.581 77.874 3534 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.04 (0.18), residues: 1133 helix: -4.51 (0.09), residues: 560 sheet: -1.30 (0.56), residues: 70 loop : -1.99 (0.23), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 492 TYR 0.021 0.002 TYR C 296 PHE 0.042 0.003 PHE B 119 TRP 0.054 0.005 TRP C 358 HIS 0.009 0.002 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.26 ( 9310) covalent geometry : angle 0.86743 / 0.50 (12581) hydrogen bonds : bond 0.32900 / 22.23 ( 292) hydrogen bonds : angle 9.97590 / 6.94 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 THR cc_start: 0.6551 (p) cc_final: 0.6341 (m) REVERT: C 125 MET cc_start: 0.5973 (mmt) cc_final: 0.5411 (tpp) REVERT: C 229 MET cc_start: 0.6712 (mmm) cc_final: 0.6486 (mmm) REVERT: A 567 LYS cc_start: 0.7772 (ttpp) cc_final: 0.7461 (tttt) REVERT: A 630 LYS cc_start: 0.7085 (ttmt) cc_final: 0.6874 (ttmt) REVERT: B 114 GLU cc_start: 0.6623 (tp30) cc_final: 0.6420 (tp30) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.5585 time to fit residues: 135.4301 Evaluate side-chains 197 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 175 HIS A 84 GLN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 354 HIS A 470 ASN A 487 GLN A 532 ASN B 108 HIS B 115 GLN B 126 ASN B 137 ASN B 173 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.167912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.154900 restraints weight = 11398.145| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.60 r_work: 0.4069 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9310 Z= 0.132 Angle : 0.564 6.095 12581 Z= 0.298 Chirality : 0.043 0.150 1404 Planarity : 0.006 0.054 1609 Dihedral : 6.372 89.277 1263 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.19 % Allowed : 11.03 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.21), residues: 1133 helix: -2.58 (0.17), residues: 572 sheet: -0.71 (0.57), residues: 72 loop : -1.42 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 374 TYR 0.013 0.001 TYR C 296 PHE 0.017 0.002 PHE B 119 TRP 0.023 0.002 TRP C 358 HIS 0.007 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9310) covalent geometry : angle 0.56401 / 0.30 (12581) hydrogen bonds : bond 0.04919 / 3.28 ( 292) hydrogen bonds : angle 4.94209 / 3.51 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: C 180 LEU cc_start: 0.7061 (tp) cc_final: 0.6752 (mp) REVERT: C 229 MET cc_start: 0.7009 (mmm) cc_final: 0.6565 (tpt) REVERT: C 360 THR cc_start: 0.8078 (m) cc_final: 0.7622 (p) REVERT: A 426 GLU cc_start: 0.7915 (tt0) cc_final: 0.7404 (tm-30) REVERT: A 476 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7393 (mmm) REVERT: A 504 ASP cc_start: 0.6787 (p0) cc_final: 0.6429 (p0) REVERT: A 567 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7951 (tttt) REVERT: A 573 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6763 (tpp) REVERT: B 23 VAL cc_start: 0.7612 (p) cc_final: 0.7410 (t) REVERT: B 217 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7493 (mp) outliers start: 22 outliers final: 5 residues processed: 215 average time/residue: 0.4686 time to fit residues: 108.8589 Evaluate side-chains 191 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain B residue 217 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [90, 80, 22, 85, 58, 36, 17, 12, 72, 23, 16] chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 350 ASN A 434 HIS A 560 GLN A 605 ASN B 115 GLN B 126 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.168058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.155053 restraints weight = 11203.165| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.60 r_work: 0.4038 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9310 Z= 0.162 Angle : 0.558 6.425 12581 Z= 0.295 Chirality : 0.046 0.236 1404 Planarity : 0.005 0.052 1609 Dihedral : 6.170 66.192 1262 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.38 % Allowed : 13.72 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.23), residues: 1133 helix: -1.75 (0.19), residues: 586 sheet: -0.54 (0.60), residues: 67 loop : -1.05 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 250 TYR 0.016 0.002 TYR A 414 PHE 0.022 0.002 PHE B 119 TRP 0.020 0.002 TRP C 358 HIS 0.008 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 9310) covalent geometry : angle 0.55848 / 0.30 (12581) hydrogen bonds : bond 0.04450 / 2.98 ( 292) hydrogen bonds : angle 4.53453 / 3.23 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.348 Fit side-chains REVERT: C 229 MET cc_start: 0.7107 (mmm) cc_final: 0.6762 (tpt) REVERT: C 360 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7672 (p) REVERT: A 426 GLU cc_start: 0.7941 (tt0) cc_final: 0.7389 (tm-30) REVERT: A 476 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7325 (mmm) REVERT: A 492 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7442 (ttt90) REVERT: A 504 ASP cc_start: 0.6890 (p0) cc_final: 0.6487 (p0) REVERT: A 567 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7962 (tttt) REVERT: A 573 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.5860 (mpt) REVERT: B 217 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7448 (mp) outliers start: 34 outliers final: 10 residues processed: 202 average time/residue: 0.4844 time to fit residues: 105.3693 Evaluate side-chains 190 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 217 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [12, 45, 42, 25, 57, 11, 15, 81, 61, 85, 18] chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 0.0980 chunk 81 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 350 ASN A 560 GLN B 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.170126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.157310 restraints weight = 11321.504| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.59 r_work: 0.4064 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9310 Z= 0.104 Angle : 0.496 5.826 12581 Z= 0.260 Chirality : 0.043 0.253 1404 Planarity : 0.004 0.049 1609 Dihedral : 5.678 59.217 1262 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.28 % Allowed : 15.01 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.24), residues: 1133 helix: -1.14 (0.21), residues: 590 sheet: -0.21 (0.61), residues: 67 loop : -0.82 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 30 TYR 0.017 0.001 TYR A 414 PHE 0.013 0.001 PHE B 240 TRP 0.012 0.002 TRP C 342 HIS 0.003 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 9310) covalent geometry : angle 0.49602 / 0.26 (12581) hydrogen bonds : bond 0.03443 / 2.24 ( 292) hydrogen bonds : angle 4.21499 / 3.01 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.330 Fit side-chains REVERT: C 296 TYR cc_start: 0.7792 (m-80) cc_final: 0.7473 (m-80) REVERT: C 360 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7619 (p) REVERT: A 87 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.5874 (mt0) REVERT: A 134 MET cc_start: 0.4541 (ttp) cc_final: 0.3936 (ttt) REVERT: A 426 GLU cc_start: 0.7840 (tt0) cc_final: 0.7313 (tm-30) REVERT: A 476 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7332 (mmm) REVERT: A 504 ASP cc_start: 0.6794 (p0) cc_final: 0.6421 (p0) REVERT: A 534 VAL cc_start: 0.6885 (t) cc_final: 0.6449 (m) REVERT: B 137 ASN cc_start: 0.6226 (t0) cc_final: 0.5847 (m110) REVERT: B 217 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7440 (mp) outliers start: 33 outliers final: 10 residues processed: 198 average time/residue: 0.4851 time to fit residues: 103.5032 Evaluate side-chains 194 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 217 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [48, 13, 80, 58, 22, 57, 3, 59, 10, 86, 94] chunk 48 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN B 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.169236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.156373 restraints weight = 11292.470| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.59 r_work: 0.4053 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9310 Z= 0.123 Angle : 0.513 5.942 12581 Z= 0.268 Chirality : 0.044 0.242 1404 Planarity : 0.004 0.051 1609 Dihedral : 5.568 69.601 1262 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.78 % Allowed : 16.40 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.25), residues: 1133 helix: -0.83 (0.21), residues: 595 sheet: -0.06 (0.62), residues: 67 loop : -0.67 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 568 TYR 0.014 0.001 TYR A 414 PHE 0.016 0.001 PHE B 240 TRP 0.012 0.002 TRP C 358 HIS 0.005 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9310) covalent geometry : angle 0.51348 / 0.27 (12581) hydrogen bonds : bond 0.03566 / 2.36 ( 292) hydrogen bonds : angle 4.10410 / 2.92 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.344 Fit side-chains REVERT: C 331 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7573 (mm) REVERT: C 360 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7609 (p) REVERT: A 87 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.6079 (mp10) REVERT: A 426 GLU cc_start: 0.7832 (tt0) cc_final: 0.7333 (tm-30) REVERT: A 476 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7317 (mmm) REVERT: A 504 ASP cc_start: 0.6712 (p0) cc_final: 0.6334 (p0) REVERT: B 217 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7492 (mp) outliers start: 28 outliers final: 10 residues processed: 182 average time/residue: 0.4970 time to fit residues: 97.4692 Evaluate side-chains 179 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 217 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [24, 44, 98, 45, 56, 82, 30, 84, 20, 26, 109] chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN B 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.167669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.154745 restraints weight = 11319.489| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.59 r_work: 0.4030 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9310 Z= 0.150 Angle : 0.537 6.614 12581 Z= 0.280 Chirality : 0.045 0.257 1404 Planarity : 0.004 0.053 1609 Dihedral : 5.772 79.846 1262 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.68 % Allowed : 16.20 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.25), residues: 1133 helix: -0.70 (0.22), residues: 587 sheet: 0.00 (0.62), residues: 67 loop : -0.67 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 568 TYR 0.014 0.002 TYR A 414 PHE 0.014 0.002 PHE B 240 TRP 0.014 0.002 TRP C 358 HIS 0.007 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 9310) covalent geometry : angle 0.53714 / 0.28 (12581) hydrogen bonds : bond 0.03827 / 2.55 ( 292) hydrogen bonds : angle 4.14977 / 2.95 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.356 Fit side-chains REVERT: C 331 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7639 (mm) REVERT: C 360 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7613 (p) REVERT: A 87 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.6070 (mp10) REVERT: A 426 GLU cc_start: 0.7906 (tt0) cc_final: 0.7417 (tm-30) REVERT: A 476 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7312 (mmm) REVERT: A 504 ASP cc_start: 0.6813 (p0) cc_final: 0.6436 (p0) REVERT: A 568 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7367 (mmm-85) REVERT: B 217 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7490 (mp) outliers start: 37 outliers final: 14 residues processed: 195 average time/residue: 0.4942 time to fit residues: 103.8367 Evaluate side-chains 190 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 252 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [66, 3, 73, 108, 82, 37, 107, 84, 90, 0, 74] chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 117 ASN A 160 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 613 GLN B 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.168897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.156119 restraints weight = 11370.516| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.59 r_work: 0.4049 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9310 Z= 0.114 Angle : 0.508 7.310 12581 Z= 0.263 Chirality : 0.043 0.251 1404 Planarity : 0.004 0.050 1609 Dihedral : 5.457 71.521 1262 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.88 % Allowed : 18.19 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.25), residues: 1133 helix: -0.51 (0.22), residues: 596 sheet: 0.06 (0.62), residues: 67 loop : -0.58 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 568 TYR 0.014 0.001 TYR A 414 PHE 0.014 0.001 PHE B 240 TRP 0.011 0.001 TRP C 358 HIS 0.005 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9310) covalent geometry : angle 0.50826 / 0.26 (12581) hydrogen bonds : bond 0.03414 / 2.26 ( 292) hydrogen bonds : angle 4.02349 / 2.86 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.353 Fit side-chains REVERT: C 331 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7607 (mm) REVERT: C 360 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7587 (p) REVERT: A 87 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.6113 (mp10) REVERT: A 426 GLU cc_start: 0.7822 (tt0) cc_final: 0.7370 (tm-30) REVERT: A 476 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7319 (mmm) REVERT: A 504 ASP cc_start: 0.6716 (p0) cc_final: 0.6364 (p0) REVERT: A 568 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7361 (mmm-85) REVERT: B 23 VAL cc_start: 0.7712 (m) cc_final: 0.7401 (t) REVERT: B 137 ASN cc_start: 0.6180 (t0) cc_final: 0.5874 (m110) REVERT: B 217 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7512 (mp) outliers start: 29 outliers final: 14 residues processed: 186 average time/residue: 0.4805 time to fit residues: 96.3868 Evaluate side-chains 185 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 252 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [112, 56, 53, 79, 45, 35, 76, 23, 19, 6, 7] chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 613 GLN B 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.168160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.155247 restraints weight = 11323.582| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.59 r_work: 0.4035 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9310 Z= 0.133 Angle : 0.550 12.861 12581 Z= 0.281 Chirality : 0.045 0.236 1404 Planarity : 0.004 0.055 1609 Dihedral : 5.510 74.040 1262 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.68 % Allowed : 18.89 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.25), residues: 1133 helix: -0.40 (0.22), residues: 591 sheet: 0.15 (0.62), residues: 67 loop : -0.53 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 230 TYR 0.034 0.001 TYR A 601 PHE 0.013 0.001 PHE B 240 TRP 0.012 0.002 TRP C 358 HIS 0.006 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 9310) covalent geometry : angle 0.54951 / 0.28 (12581) hydrogen bonds : bond 0.03627 / 2.41 ( 292) hydrogen bonds : angle 4.06363 / 2.89 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.363 Fit side-chains REVERT: C 331 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7626 (mm) REVERT: C 360 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7574 (p) REVERT: A 87 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.6157 (mp10) REVERT: A 372 ASP cc_start: 0.7133 (p0) cc_final: 0.6812 (m-30) REVERT: A 426 GLU cc_start: 0.7859 (tt0) cc_final: 0.7411 (tm-30) REVERT: A 476 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7299 (mmm) REVERT: A 504 ASP cc_start: 0.6809 (p0) cc_final: 0.6470 (p0) REVERT: A 568 ARG cc_start: 0.7773 (mmm-85) cc_final: 0.7344 (mmm-85) REVERT: B 23 VAL cc_start: 0.7715 (m) cc_final: 0.7420 (t) REVERT: B 217 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7523 (mp) outliers start: 27 outliers final: 15 residues processed: 189 average time/residue: 0.4794 time to fit residues: 97.6875 Evaluate side-chains 191 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 252 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [82, 5, 64, 44, 102, 41, 91, 49, 47, 62, 46] chunk 82 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.169164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.156274 restraints weight = 11360.983| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.60 r_work: 0.4048 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9310 Z= 0.116 Angle : 0.558 11.484 12581 Z= 0.279 Chirality : 0.044 0.234 1404 Planarity : 0.004 0.055 1609 Dihedral : 5.345 69.109 1262 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.68 % Allowed : 19.38 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.26), residues: 1133 helix: -0.24 (0.22), residues: 591 sheet: 0.26 (0.63), residues: 67 loop : -0.50 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 149 TYR 0.014 0.001 TYR A 414 PHE 0.013 0.001 PHE B 240 TRP 0.011 0.001 TRP C 358 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9310) covalent geometry : angle 0.55838 / 0.28 (12581) hydrogen bonds : bond 0.03394 / 2.25 ( 292) hydrogen bonds : angle 3.97822 / 2.83 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.354 Fit side-chains REVERT: C 331 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7634 (mm) REVERT: C 360 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7589 (p) REVERT: A 87 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.6158 (mp10) REVERT: A 372 ASP cc_start: 0.7094 (p0) cc_final: 0.6774 (m-30) REVERT: A 426 GLU cc_start: 0.7815 (tt0) cc_final: 0.7373 (tm-30) REVERT: A 476 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7322 (mmm) REVERT: A 504 ASP cc_start: 0.6717 (p0) cc_final: 0.6398 (p0) REVERT: A 568 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7317 (mmm-85) REVERT: A 601 TYR cc_start: 0.7580 (t80) cc_final: 0.7309 (t80) REVERT: B 23 VAL cc_start: 0.7735 (m) cc_final: 0.7444 (t) REVERT: B 137 ASN cc_start: 0.6139 (t0) cc_final: 0.5873 (m110) REVERT: B 217 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7520 (mp) outliers start: 27 outliers final: 14 residues processed: 187 average time/residue: 0.4814 time to fit residues: 97.2317 Evaluate side-chains 188 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 252 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [112, 83, 2, 47, 40, 31, 86, 11, 0, 4, 59] chunk 112 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS B 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.167587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.154787 restraints weight = 11330.493| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.58 r_work: 0.4031 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9310 Z= 0.146 Angle : 0.597 10.843 12581 Z= 0.298 Chirality : 0.046 0.294 1404 Planarity : 0.004 0.056 1609 Dihedral : 5.533 73.174 1262 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.09 % Allowed : 20.38 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1133 helix: -0.22 (0.22), residues: 583 sheet: 0.35 (0.64), residues: 67 loop : -0.45 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.014 0.001 TYR A 348 PHE 0.012 0.002 PHE B 175 TRP 0.013 0.002 TRP C 358 HIS 0.006 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9310) covalent geometry : angle 0.59672 / 0.30 (12581) hydrogen bonds : bond 0.03722 / 2.49 ( 292) hydrogen bonds : angle 4.06349 / 2.88 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.278 Fit side-chains REVERT: C 331 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7639 (mm) REVERT: C 360 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7614 (p) REVERT: A 87 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.6125 (mp10) REVERT: A 372 ASP cc_start: 0.7065 (p0) cc_final: 0.6740 (m-30) REVERT: A 426 GLU cc_start: 0.7832 (tt0) cc_final: 0.7404 (tm-30) REVERT: A 476 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7316 (mmm) REVERT: A 504 ASP cc_start: 0.6747 (p0) cc_final: 0.6442 (p0) REVERT: A 601 TYR cc_start: 0.7626 (t80) cc_final: 0.7422 (t80) REVERT: A 634 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6940 (tm-30) REVERT: B 23 VAL cc_start: 0.7718 (m) cc_final: 0.7431 (t) REVERT: B 217 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7555 (mp) outliers start: 21 outliers final: 13 residues processed: 182 average time/residue: 0.4526 time to fit residues: 88.8622 Evaluate side-chains 186 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 252 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [20, 82, 44, 62, 104, 35, 38, 42, 7, 109, 78] chunk 20 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.167629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.154811 restraints weight = 11278.843| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.58 r_work: 0.4029 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9310 Z= 0.156 Angle : 0.604 12.766 12581 Z= 0.303 Chirality : 0.047 0.324 1404 Planarity : 0.004 0.056 1609 Dihedral : 5.638 72.923 1262 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.29 % Allowed : 20.58 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.25), residues: 1133 helix: -0.27 (0.22), residues: 583 sheet: 0.35 (0.64), residues: 67 loop : -0.49 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 174 TYR 0.015 0.002 TYR A 348 PHE 0.017 0.002 PHE A 512 TRP 0.016 0.002 TRP A 513 HIS 0.007 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 9310) covalent geometry : angle 0.60383 / 0.30 (12581) hydrogen bonds : bond 0.03793 / 2.53 ( 292) hydrogen bonds : angle 4.13909 / 2.93 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3552.00 seconds wall clock time: 61 minutes 12.20 seconds (3672.20 seconds total)