Starting phenix.real_space_refine on Fri Oct 10 23:19:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua6_42051/10_2025/8ua6_42051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua6_42051/10_2025/8ua6_42051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ua6_42051/10_2025/8ua6_42051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua6_42051/10_2025/8ua6_42051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ua6_42051/10_2025/8ua6_42051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua6_42051/10_2025/8ua6_42051.map" } resolution = 3.9 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= -0.001 sd= 0.050 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 6219 2.51 5 N 1665 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9806 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2919 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 15, 'TRANS': 360} Chain breaks: 1 Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "B" Number of atoms: 1216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1216 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 1 Chain: "A" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3738 Classifications: {'peptide': 459} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 452} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.23, per 1000 atoms: 0.23 Number of scatterers: 9806 At special positions: 0 Unit cell: (97.44, 113.4, 147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1869 8.00 N 1665 7.00 C 6219 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: 0.91 Conformation dependent library (CDL) restraints added in 376.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 9 sheets defined 48.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.517A pdb=" N VAL C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 49 through 60 removed outlier: 3.659A pdb=" N ARG C 53 " --> pdb=" O CYS C 49 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.898A pdb=" N GLU C 75 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 76 " --> pdb=" O LEU C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 76' Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.593A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.829A pdb=" N GLN C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C 243 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.603A pdb=" N LEU C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.521A pdb=" N PHE C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 30 removed outlier: 3.622A pdb=" N VAL D 20 " --> pdb=" O HIS D 16 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.610A pdb=" N ALA D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 94 removed outlier: 3.600A pdb=" N PHE D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 101 through 112 removed outlier: 4.574A pdb=" N GLU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 29 Processing helix chain 'E' and resid 51 through 56 removed outlier: 4.218A pdb=" N SER E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 64 removed outlier: 3.719A pdb=" N VAL E 64 " --> pdb=" O HIS E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 94 removed outlier: 3.541A pdb=" N ILE E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 24 through 33 Processing helix chain 'B' and resid 51 through 65 removed outlier: 3.548A pdb=" N LYS B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 4.219A pdb=" N GLN B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 111 removed outlier: 3.563A pdb=" N LEU B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.613A pdb=" N ASP A 22 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU A 24 " --> pdb=" O TRP A 21 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG A 25 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.773A pdb=" N MET A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 95 removed outlier: 3.571A pdb=" N PHE A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.571A pdb=" N PHE A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 132 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.922A pdb=" N HIS A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 removed outlier: 3.568A pdb=" N VAL A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.565A pdb=" N LEU A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 4.194A pdb=" N ILE A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 4.170A pdb=" N LYS A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.707A pdb=" N ALA A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 256 through 271 removed outlier: 3.963A pdb=" N TYR A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 289 through 292 Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.618A pdb=" N ASN A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 removed outlier: 3.796A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 355 removed outlier: 4.190A pdb=" N HIS A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.564A pdb=" N LEU A 360 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.977A pdb=" N TYR A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 removed outlier: 3.635A pdb=" N ALA A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.862A pdb=" N GLU A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 removed outlier: 3.529A pdb=" N LEU A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.545A pdb=" N MET A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 495 removed outlier: 4.134A pdb=" N GLU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.693A pdb=" N TYR C 104 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 148 " --> pdb=" O TYR C 104 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 106 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 145 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 261 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY C 147 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 257 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 166 through 168 removed outlier: 5.977A pdb=" N GLY C 321 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N PHE C 357 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N MET C 323 " --> pdb=" O PHE C 357 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY C 359 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA C 325 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 193 removed outlier: 3.768A pdb=" N GLY C 274 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY C 224 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 217 through 220 removed outlier: 3.780A pdb=" N VAL C 219 " --> pdb=" O PHE C 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 362 through 363 removed outlier: 3.667A pdb=" N GLU C 362 " --> pdb=" O HIS C 388 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS C 388 " --> pdb=" O GLU C 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 373 through 374 Processing sheet with id=AA7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.702A pdb=" N VAL D 36 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR D 37 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU D 75 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE D 39 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 36 through 40 Processing sheet with id=AA9, first strand: chain 'B' and resid 13 through 16 346 hydrogen bonds defined for protein. 963 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: 1.29 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1693 1.29 - 1.42: 2454 1.42 - 1.55: 5753 1.55 - 1.68: 4 1.68 - 1.82: 74 Bond restraints: 9978 Sorted by residual: bond pdb=" CG PRO D 86 " pdb=" CD PRO D 86 " ideal model delta sigma weight residual 1.503 1.157 0.346 3.40e-02 8.65e+02 1.04e+02 bond pdb=" N CYS B 159 " pdb=" CA CYS B 159 " ideal model delta sigma weight residual 1.457 1.375 0.082 1.29e-02 6.01e+03 4.08e+01 bond pdb=" N PRO D 86 " pdb=" CD PRO D 86 " ideal model delta sigma weight residual 1.473 1.552 -0.079 1.40e-02 5.10e+03 3.18e+01 bond pdb=" CA PHE B 158 " pdb=" C PHE B 158 " ideal model delta sigma weight residual 1.523 1.457 0.067 1.34e-02 5.57e+03 2.47e+01 bond pdb=" CA ASP B 144 " pdb=" C ASP B 144 " ideal model delta sigma weight residual 1.525 1.462 0.064 1.34e-02 5.57e+03 2.25e+01 ... (remaining 9973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 13337 4.36 - 8.72: 115 8.72 - 13.08: 12 13.08 - 17.44: 6 17.44 - 21.80: 3 Bond angle restraints: 13473 Sorted by residual: angle pdb=" N ASP B 144 " pdb=" CA ASP B 144 " pdb=" C ASP B 144 " ideal model delta sigma weight residual 108.34 130.14 -21.80 1.31e+00 5.83e-01 2.77e+02 angle pdb=" CA PRO D 86 " pdb=" N PRO D 86 " pdb=" CD PRO D 86 " ideal model delta sigma weight residual 112.00 94.95 17.05 1.40e+00 5.10e-01 1.48e+02 angle pdb=" N PRO D 86 " pdb=" CD PRO D 86 " pdb=" CG PRO D 86 " ideal model delta sigma weight residual 103.20 85.24 17.96 1.50e+00 4.44e-01 1.43e+02 angle pdb=" N VAL A 165 " pdb=" CA VAL A 165 " pdb=" C VAL A 165 " ideal model delta sigma weight residual 113.71 105.57 8.14 9.50e-01 1.11e+00 7.34e+01 angle pdb=" N THR C 20 " pdb=" CA THR C 20 " pdb=" C THR C 20 " ideal model delta sigma weight residual 113.41 104.37 9.04 1.22e+00 6.72e-01 5.49e+01 ... (remaining 13468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 4935 16.95 - 33.90: 818 33.90 - 50.85: 224 50.85 - 67.80: 56 67.80 - 84.75: 16 Dihedral angle restraints: 6049 sinusoidal: 2450 harmonic: 3599 Sorted by residual: dihedral pdb=" CA TYR A 278 " pdb=" C TYR A 278 " pdb=" N LEU A 279 " pdb=" CA LEU A 279 " ideal model delta harmonic sigma weight residual -180.00 -137.26 -42.74 0 5.00e+00 4.00e-02 7.31e+01 dihedral pdb=" CA ILE A 296 " pdb=" C ILE A 296 " pdb=" N GLU A 297 " pdb=" CA GLU A 297 " ideal model delta harmonic sigma weight residual 180.00 149.85 30.15 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA ARG A 173 " pdb=" C ARG A 173 " pdb=" N PRO A 174 " pdb=" CA PRO A 174 " ideal model delta harmonic sigma weight residual 180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 6046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1322 0.067 - 0.134: 185 0.134 - 0.200: 20 0.200 - 0.267: 2 0.267 - 0.334: 3 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA ASP B 144 " pdb=" N ASP B 144 " pdb=" C ASP B 144 " pdb=" CB ASP B 144 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA PHE B 145 " pdb=" N PHE B 145 " pdb=" C PHE B 145 " pdb=" CB PHE B 145 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CG LEU B 160 " pdb=" CB LEU B 160 " pdb=" CD1 LEU B 160 " pdb=" CD2 LEU B 160 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1529 not shown) Planarity restraints: 1739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 173 " 0.112 5.00e-02 4.00e+02 1.65e-01 4.37e+01 pdb=" N PRO A 174 " -0.286 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 85 " -0.112 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO D 86 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 157 " 0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLN B 157 " -0.079 2.00e-02 2.50e+03 pdb=" O GLN B 157 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE B 158 " 0.027 2.00e-02 2.50e+03 ... (remaining 1736 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 152 2.59 - 3.17: 8573 3.17 - 3.74: 14729 3.74 - 4.32: 19808 4.32 - 4.90: 31605 Nonbonded interactions: 74867 Sorted by model distance: nonbonded pdb=" N ASP B 144 " pdb=" OD1 ASP B 144 " model vdw 2.010 3.120 nonbonded pdb=" OG SER B 8 " pdb=" OD1 ASP B 10 " model vdw 2.136 3.040 nonbonded pdb=" OD1 ASP C 107 " pdb=" N SER C 108 " model vdw 2.166 3.120 nonbonded pdb=" OE1 GLN A 254 " pdb=" ND2 ASN A 255 " model vdw 2.176 3.120 nonbonded pdb=" OG SER C 263 " pdb=" OD1 ASN C 266 " model vdw 2.197 3.040 ... (remaining 74862 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 'D' and resid 7 through 127) selection = chain 'E' } 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 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: 4.200 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.840 Find NCS groups from input model: 0.060 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 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 0.346 9978 Z= 0.297 Angle : 1.142 21.797 13473 Z= 0.702 Chirality : 0.049 0.334 1532 Planarity : 0.008 0.165 1739 Dihedral : 18.634 84.749 3709 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.99 % Allowed : 12.03 % Favored : 86.99 % Rotamer: Outliers : 1.28 % Allowed : 32.63 % Favored : 66.09 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -3.13 (0.23), residues: 1214 helix: -1.71 (0.21), residues: 565 sheet: -0.08 (0.55), residues: 106 loop : -2.88 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 335 TYR 0.026 0.002 TYR C 334 PHE 0.026 0.002 PHE C 373 TRP 0.014 0.002 TRP A 144 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 9978) covalent geometry : angle 1.14222 (13473) hydrogen bonds : bond 0.29242 ( 346) hydrogen bonds : angle 9.55373 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 268 time to evaluate : 0.388 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: C 48 VAL cc_start: 0.8529 (t) cc_final: 0.8321 (t) REVERT: C 186 LYS cc_start: 0.8707 (tmtt) cc_final: 0.7474 (tttt) REVERT: C 207 THR cc_start: 0.8486 (m) cc_final: 0.8186 (t) REVERT: D 22 LEU cc_start: 0.7168 (mm) cc_final: 0.6933 (pp) REVERT: B 153 VAL cc_start: 0.8537 (t) cc_final: 0.8284 (t) REVERT: A 118 PHE cc_start: 0.8304 (t80) cc_final: 0.8076 (t80) REVERT: A 259 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 301 GLU cc_start: 0.8169 (tp30) cc_final: 0.7800 (tt0) REVERT: A 322 MET cc_start: 0.8803 (tmm) cc_final: 0.8594 (tmm) outliers start: 14 outliers final: 6 residues processed: 278 average time/residue: 0.0870 time to fit residues: 35.0188 Evaluate side-chains 182 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 82 HIS C 188 GLN C 205 GLN C 313 ASN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN E 27 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.181546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141833 restraints weight = 15287.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140714 restraints weight = 19401.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134309 restraints weight = 13597.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134990 restraints weight = 14523.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135917 restraints weight = 11456.094| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9978 Z= 0.181 Angle : 0.834 12.679 13473 Z= 0.437 Chirality : 0.048 0.209 1532 Planarity : 0.006 0.154 1739 Dihedral : 7.659 55.145 1330 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.94 % Favored : 87.23 % Rotamer: Outliers : 5.13 % Allowed : 30.06 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -2.88 (0.23), residues: 1214 helix: -1.52 (0.20), residues: 611 sheet: 0.21 (0.50), residues: 121 loop : -2.94 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 335 TYR 0.020 0.002 TYR A 377 PHE 0.018 0.002 PHE C 324 TRP 0.012 0.002 TRP A 123 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9978) covalent geometry : angle 0.83363 (13473) hydrogen bonds : bond 0.05005 ( 346) hydrogen bonds : angle 6.38560 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 VAL cc_start: 0.8659 (t) cc_final: 0.8361 (t) REVERT: C 96 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6809 (tpm170) REVERT: C 127 THR cc_start: 0.5288 (OUTLIER) cc_final: 0.5039 (t) REVERT: D 22 LEU cc_start: 0.7477 (mm) cc_final: 0.7040 (pp) REVERT: D 43 GLN cc_start: 0.5978 (mp10) cc_final: 0.5772 (mp10) REVERT: D 124 GLN cc_start: 0.8235 (pm20) cc_final: 0.7711 (tm-30) REVERT: B 49 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8439 (t0) REVERT: B 103 LEU cc_start: 0.9002 (mt) cc_final: 0.8715 (tp) REVERT: A 225 LEU cc_start: 0.8793 (pp) cc_final: 0.8471 (pp) REVERT: A 279 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6559 (mt) REVERT: A 459 LYS cc_start: 0.8763 (mmtp) cc_final: 0.8333 (mmtm) REVERT: A 478 ASN cc_start: 0.7509 (m-40) cc_final: 0.7045 (p0) outliers start: 56 outliers final: 27 residues processed: 233 average time/residue: 0.0748 time to fit residues: 26.0783 Evaluate side-chains 191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 67 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 313 ASN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.175685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130547 restraints weight = 15408.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132785 restraints weight = 22390.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132947 restraints weight = 13624.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132048 restraints weight = 12345.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132982 restraints weight = 10255.362| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9978 Z= 0.230 Angle : 0.811 13.640 13473 Z= 0.428 Chirality : 0.049 0.258 1532 Planarity : 0.006 0.144 1739 Dihedral : 6.865 53.574 1322 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.82 % Allowed : 13.10 % Favored : 86.08 % Rotamer: Outliers : 5.77 % Allowed : 30.61 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.23), residues: 1214 helix: -1.37 (0.21), residues: 600 sheet: 0.19 (0.50), residues: 121 loop : -2.98 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.019 0.002 TYR A 46 PHE 0.022 0.002 PHE B 101 TRP 0.016 0.002 TRP A 167 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 9978) covalent geometry : angle 0.81112 (13473) hydrogen bonds : bond 0.04436 ( 346) hydrogen bonds : angle 5.93614 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7442 (mmp80) REVERT: C 96 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6975 (tpp-160) REVERT: C 186 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8494 (tttt) REVERT: C 188 GLN cc_start: 0.7725 (mt0) cc_final: 0.7507 (mt0) REVERT: C 258 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8474 (tt) REVERT: C 269 ASP cc_start: 0.7182 (t0) cc_final: 0.6679 (t0) REVERT: D 43 GLN cc_start: 0.5950 (mp10) cc_final: 0.5747 (mp10) REVERT: B 103 LEU cc_start: 0.9151 (mt) cc_final: 0.8850 (tp) REVERT: A 156 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 224 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7058 (t) REVERT: A 225 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8593 (pp) REVERT: A 315 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8069 (mmtp) REVERT: A 382 MET cc_start: 0.7881 (ttt) cc_final: 0.7599 (ttm) REVERT: A 478 ASN cc_start: 0.7737 (m-40) cc_final: 0.7310 (p0) REVERT: A 494 GLN cc_start: 0.8131 (tp40) cc_final: 0.7694 (tm-30) outliers start: 63 outliers final: 30 residues processed: 199 average time/residue: 0.0893 time to fit residues: 25.6977 Evaluate side-chains 180 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 465 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 113 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 HIS C 313 ASN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 157 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.181410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.135971 restraints weight = 15255.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138886 restraints weight = 19945.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140067 restraints weight = 12107.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139758 restraints weight = 8743.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.140483 restraints weight = 8468.937| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9978 Z= 0.123 Angle : 0.705 11.033 13473 Z= 0.373 Chirality : 0.044 0.228 1532 Planarity : 0.005 0.132 1739 Dihedral : 6.109 46.394 1316 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.74 % Allowed : 11.37 % Favored : 87.89 % Rotamer: Outliers : 4.49 % Allowed : 31.90 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.24), residues: 1214 helix: -1.13 (0.21), residues: 605 sheet: 0.34 (0.51), residues: 118 loop : -2.85 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.019 0.001 TYR B 109 PHE 0.025 0.001 PHE B 101 TRP 0.006 0.001 TRP A 167 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9978) covalent geometry : angle 0.70493 (13473) hydrogen bonds : bond 0.03373 ( 346) hydrogen bonds : angle 5.45246 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7280 (mmt-90) REVERT: C 109 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6216 (pm20) REVERT: C 258 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8494 (tt) REVERT: C 269 ASP cc_start: 0.7328 (t0) cc_final: 0.6775 (t0) REVERT: D 125 PHE cc_start: 0.5279 (t80) cc_final: 0.4925 (t80) REVERT: A 154 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7455 (mtmm) REVERT: A 224 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.6914 (t) REVERT: A 225 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8588 (pp) REVERT: A 382 MET cc_start: 0.7838 (ttt) cc_final: 0.7535 (ttm) REVERT: A 410 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8378 (mttt) REVERT: A 494 GLN cc_start: 0.8063 (tp40) cc_final: 0.7772 (tm-30) outliers start: 49 outliers final: 23 residues processed: 204 average time/residue: 0.0866 time to fit residues: 25.7711 Evaluate side-chains 172 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.0030 chunk 90 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN A 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.195420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.148587 restraints weight = 16394.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.146468 restraints weight = 13360.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.148176 restraints weight = 11287.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.148881 restraints weight = 7954.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.148939 restraints weight = 7335.011| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9978 Z= 0.134 Angle : 0.706 14.456 13473 Z= 0.368 Chirality : 0.044 0.198 1532 Planarity : 0.005 0.154 1739 Dihedral : 5.947 45.176 1316 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.37 % Favored : 87.97 % Rotamer: Outliers : 4.67 % Allowed : 32.26 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.24), residues: 1214 helix: -0.98 (0.21), residues: 611 sheet: 0.57 (0.51), residues: 116 loop : -2.87 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 142 TYR 0.020 0.002 TYR C 104 PHE 0.020 0.001 PHE B 101 TRP 0.006 0.001 TRP C 68 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9978) covalent geometry : angle 0.70642 (13473) hydrogen bonds : bond 0.03382 ( 346) hydrogen bonds : angle 5.33017 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: C 107 ASP cc_start: 0.6001 (t0) cc_final: 0.5692 (t0) REVERT: C 109 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6455 (pm20) REVERT: C 269 ASP cc_start: 0.7480 (t0) cc_final: 0.6970 (t0) REVERT: C 399 LEU cc_start: 0.8005 (mt) cc_final: 0.7777 (mp) REVERT: D 24 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.6972 (tp) REVERT: D 43 GLN cc_start: 0.5787 (mp10) cc_final: 0.5550 (mp10) REVERT: D 63 ILE cc_start: 0.5722 (OUTLIER) cc_final: 0.5438 (tp) REVERT: D 125 PHE cc_start: 0.5204 (t80) cc_final: 0.4812 (t80) REVERT: A 224 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.6887 (t) REVERT: A 301 GLU cc_start: 0.7462 (tp30) cc_final: 0.7211 (tt0) REVERT: A 314 ASP cc_start: 0.7937 (p0) cc_final: 0.7704 (p0) REVERT: A 382 MET cc_start: 0.7830 (ttt) cc_final: 0.7540 (ttm) REVERT: A 410 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8447 (ttmt) REVERT: A 459 LYS cc_start: 0.8944 (mmtp) cc_final: 0.8435 (mmtm) REVERT: A 463 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: A 494 GLN cc_start: 0.8375 (tp40) cc_final: 0.8010 (tm-30) outliers start: 51 outliers final: 28 residues processed: 186 average time/residue: 0.0798 time to fit residues: 22.2029 Evaluate side-chains 174 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 465 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.197126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.146088 restraints weight = 16068.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.144393 restraints weight = 12025.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146147 restraints weight = 9563.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.148041 restraints weight = 7276.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147779 restraints weight = 6503.326| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9978 Z= 0.161 Angle : 0.727 15.643 13473 Z= 0.374 Chirality : 0.046 0.222 1532 Planarity : 0.005 0.158 1739 Dihedral : 5.925 48.125 1316 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.78 % Favored : 87.56 % Rotamer: Outliers : 4.58 % Allowed : 32.17 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.24), residues: 1214 helix: -0.95 (0.21), residues: 622 sheet: 0.22 (0.50), residues: 122 loop : -2.82 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 142 TYR 0.020 0.002 TYR B 109 PHE 0.022 0.002 PHE B 92 TRP 0.007 0.001 TRP A 123 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9978) covalent geometry : angle 0.72668 (13473) hydrogen bonds : bond 0.03403 ( 346) hydrogen bonds : angle 5.30368 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 269 ASP cc_start: 0.7700 (t0) cc_final: 0.7162 (t0) REVERT: B 157 GLN cc_start: 0.6523 (mm-40) cc_final: 0.6248 (mm-40) REVERT: A 190 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: A 365 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7758 (ptp) REVERT: A 382 MET cc_start: 0.7880 (ttt) cc_final: 0.7563 (ttm) REVERT: A 410 LYS cc_start: 0.8765 (ttpp) cc_final: 0.8483 (ttmt) REVERT: A 459 LYS cc_start: 0.8995 (mmtp) cc_final: 0.8446 (mmtm) REVERT: A 463 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7151 (mp10) REVERT: A 494 GLN cc_start: 0.8392 (tp40) cc_final: 0.8020 (tm-30) outliers start: 50 outliers final: 36 residues processed: 180 average time/residue: 0.0835 time to fit residues: 22.4699 Evaluate side-chains 172 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 496 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.0000 chunk 3 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 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 = 0.4466 r_free = 0.4466 target = 0.196039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.149212 restraints weight = 16318.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146794 restraints weight = 14036.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148761 restraints weight = 11512.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.149230 restraints weight = 8572.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.149311 restraints weight = 8121.185| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9978 Z= 0.127 Angle : 0.719 11.375 13473 Z= 0.367 Chirality : 0.045 0.182 1532 Planarity : 0.005 0.141 1739 Dihedral : 5.774 43.833 1316 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.20 % Favored : 88.14 % Rotamer: Outliers : 4.12 % Allowed : 33.73 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.24), residues: 1214 helix: -0.84 (0.21), residues: 621 sheet: 0.14 (0.50), residues: 124 loop : -2.71 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.021 0.002 TYR C 104 PHE 0.016 0.001 PHE B 101 TRP 0.006 0.001 TRP C 68 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9978) covalent geometry : angle 0.71906 (13473) hydrogen bonds : bond 0.03166 ( 346) hydrogen bonds : angle 5.18792 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.406 Fit side-chains REVERT: C 109 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: C 269 ASP cc_start: 0.7672 (t0) cc_final: 0.7352 (t0) REVERT: C 354 LEU cc_start: 0.9061 (tt) cc_final: 0.8601 (mp) REVERT: C 375 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7742 (tt) REVERT: D 125 PHE cc_start: 0.5241 (t80) cc_final: 0.5037 (t80) REVERT: B 157 GLN cc_start: 0.6301 (mm-40) cc_final: 0.5971 (mm110) REVERT: A 190 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6179 (mt-10) REVERT: A 365 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7636 (ptp) REVERT: A 382 MET cc_start: 0.7749 (ttt) cc_final: 0.7475 (ttm) REVERT: A 459 LYS cc_start: 0.8898 (mmtp) cc_final: 0.8373 (mmtm) REVERT: A 463 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: A 494 GLN cc_start: 0.8264 (tp40) cc_final: 0.7894 (tm-30) outliers start: 45 outliers final: 29 residues processed: 178 average time/residue: 0.0841 time to fit residues: 22.3091 Evaluate side-chains 165 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.198107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.147794 restraints weight = 15875.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145533 restraints weight = 11367.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.147530 restraints weight = 9459.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.148022 restraints weight = 7217.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.148114 restraints weight = 7003.874| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9978 Z= 0.141 Angle : 0.736 10.192 13473 Z= 0.372 Chirality : 0.045 0.183 1532 Planarity : 0.005 0.135 1739 Dihedral : 5.733 43.665 1316 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.94 % Favored : 87.48 % Rotamer: Outliers : 4.12 % Allowed : 33.27 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.24), residues: 1214 helix: -0.75 (0.21), residues: 621 sheet: 0.07 (0.50), residues: 124 loop : -2.59 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 62 TYR 0.021 0.002 TYR B 109 PHE 0.017 0.001 PHE B 92 TRP 0.006 0.001 TRP C 68 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9978) covalent geometry : angle 0.73599 (13473) hydrogen bonds : bond 0.03231 ( 346) hydrogen bonds : angle 5.11691 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.399 Fit side-chains REVERT: C 269 ASP cc_start: 0.7779 (t0) cc_final: 0.7441 (t0) REVERT: C 375 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7695 (tt) REVERT: C 386 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 190 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6142 (mt-10) REVERT: A 322 MET cc_start: 0.8274 (tmm) cc_final: 0.8041 (tmm) REVERT: A 365 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7694 (ptp) REVERT: A 382 MET cc_start: 0.7827 (ttt) cc_final: 0.7528 (ttm) REVERT: A 459 LYS cc_start: 0.8955 (mmtp) cc_final: 0.8485 (mmtm) REVERT: A 463 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: A 494 GLN cc_start: 0.8332 (tp40) cc_final: 0.7931 (tm-30) outliers start: 45 outliers final: 37 residues processed: 169 average time/residue: 0.0791 time to fit residues: 20.3291 Evaluate side-chains 170 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 496 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 54 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.183259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142256 restraints weight = 15111.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145746 restraints weight = 25723.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148303 restraints weight = 11209.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150217 restraints weight = 7764.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.150616 restraints weight = 6628.144| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9978 Z= 0.126 Angle : 0.731 11.976 13473 Z= 0.368 Chirality : 0.045 0.192 1532 Planarity : 0.005 0.134 1739 Dihedral : 5.653 41.072 1316 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.79 % Favored : 88.63 % Rotamer: Outliers : 4.31 % Allowed : 33.18 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.25), residues: 1214 helix: -0.68 (0.21), residues: 620 sheet: 0.10 (0.50), residues: 124 loop : -2.50 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 34 TYR 0.023 0.002 TYR C 104 PHE 0.017 0.001 PHE B 92 TRP 0.006 0.001 TRP C 68 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9978) covalent geometry : angle 0.73100 (13473) hydrogen bonds : bond 0.03100 ( 346) hydrogen bonds : angle 5.05528 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.353 Fit side-chains REVERT: C 90 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 269 ASP cc_start: 0.7701 (t0) cc_final: 0.7421 (t0) REVERT: C 354 LEU cc_start: 0.9037 (tt) cc_final: 0.8541 (mp) REVERT: C 386 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7936 (mp) REVERT: D 24 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.6942 (tp) REVERT: D 87 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7877 (tt) REVERT: A 190 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6513 (mt-10) REVERT: A 365 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7523 (ptp) REVERT: A 382 MET cc_start: 0.7771 (ttt) cc_final: 0.7506 (ttm) REVERT: A 459 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8275 (mmtm) REVERT: A 463 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: A 494 GLN cc_start: 0.8019 (tp40) cc_final: 0.7668 (tm-30) outliers start: 47 outliers final: 34 residues processed: 171 average time/residue: 0.0752 time to fit residues: 19.5875 Evaluate side-chains 169 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 496 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 104 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 107 optimal weight: 0.0270 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 65 optimal weight: 0.0000 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 overall best weight: 0.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.181766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141666 restraints weight = 15170.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143664 restraints weight = 27523.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.147243 restraints weight = 14212.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.147499 restraints weight = 9094.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.148448 restraints weight = 7882.174| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9978 Z= 0.121 Angle : 0.744 14.050 13473 Z= 0.372 Chirality : 0.045 0.352 1532 Planarity : 0.005 0.131 1739 Dihedral : 5.585 37.892 1316 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.79 % Favored : 88.71 % Rotamer: Outliers : 3.48 % Allowed : 34.01 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.25), residues: 1214 helix: -0.65 (0.22), residues: 620 sheet: 0.08 (0.50), residues: 124 loop : -2.41 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 34 TYR 0.040 0.001 TYR A 260 PHE 0.018 0.001 PHE B 92 TRP 0.007 0.001 TRP C 68 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9978) covalent geometry : angle 0.74450 (13473) hydrogen bonds : bond 0.03005 ( 346) hydrogen bonds : angle 5.01279 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: C 90 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7926 (tm-30) REVERT: C 269 ASP cc_start: 0.7660 (t0) cc_final: 0.7391 (t0) REVERT: C 354 LEU cc_start: 0.8985 (tt) cc_final: 0.8525 (mp) REVERT: C 386 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7865 (mp) REVERT: D 24 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.6946 (tp) REVERT: D 87 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7842 (tt) REVERT: A 190 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: A 382 MET cc_start: 0.7685 (ttt) cc_final: 0.7445 (ttm) REVERT: A 453 PHE cc_start: 0.8673 (t80) cc_final: 0.8327 (t80) REVERT: A 459 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8392 (mmtm) REVERT: A 494 GLN cc_start: 0.7894 (tp40) cc_final: 0.7490 (tm-30) outliers start: 38 outliers final: 33 residues processed: 163 average time/residue: 0.0756 time to fit residues: 18.7508 Evaluate side-chains 167 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 496 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.0060 chunk 95 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.181277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140827 restraints weight = 15366.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.145156 restraints weight = 28798.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.147009 restraints weight = 12765.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148498 restraints weight = 8928.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.148964 restraints weight = 7684.990| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9978 Z= 0.126 Angle : 0.743 13.126 13473 Z= 0.371 Chirality : 0.046 0.373 1532 Planarity : 0.005 0.132 1739 Dihedral : 5.535 36.662 1316 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.71 % Favored : 88.71 % Rotamer: Outliers : 3.48 % Allowed : 34.10 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.25), residues: 1214 helix: -0.57 (0.22), residues: 618 sheet: 0.04 (0.50), residues: 124 loop : -2.35 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 34 TYR 0.034 0.002 TYR A 260 PHE 0.027 0.001 PHE C 324 TRP 0.005 0.001 TRP C 68 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9978) covalent geometry : angle 0.74318 (13473) hydrogen bonds : bond 0.03080 ( 346) hydrogen bonds : angle 4.97793 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.88 seconds wall clock time: 31 minutes 35.95 seconds (1895.95 seconds total)