Starting phenix.real_space_refine on Sun Jun 8 17:29:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua6_42051/06_2025/8ua6_42051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua6_42051/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ua6_42051/06_2025/8ua6_42051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua6_42051/06_2025/8ua6_42051.map" model { file = "/net/cci-nas-00/data/ceres_data/8ua6_42051/06_2025/8ua6_42051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua6_42051/06_2025/8ua6_42051.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.21, per 1000 atoms: 0.74 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: 3.31 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 0.96 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: 2.39 Time building geometry restraints manager: 3.85 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP A 144 HIS 0.005 0.001 HIS A 280 PHE 0.026 0.002 PHE C 373 TYR 0.026 0.002 TYR C 334 ARG 0.015 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.29242 ( 346) hydrogen bonds : angle 9.55373 ( 963) covalent geometry : bond 0.00600 ( 9978) covalent geometry : angle 1.14222 (13473) *********************** 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 : 1.831 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: 0.1966 time to fit residues: 79.2588 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 : 1.090 ------------------------------------------------------------------------------- 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 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 chunk 94 optimal weight: 0.0060 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 109 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.184769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140084 restraints weight = 15053.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141296 restraints weight = 17553.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141158 restraints weight = 13183.383| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9978 Z= 0.155 Angle : 0.823 12.307 13473 Z= 0.431 Chirality : 0.047 0.198 1532 Planarity : 0.006 0.152 1739 Dihedral : 7.557 55.139 1330 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.70 % Favored : 87.48 % Rotamer: Outliers : 4.40 % Allowed : 30.43 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.23), residues: 1214 helix: -1.48 (0.20), residues: 608 sheet: 0.30 (0.50), residues: 121 loop : -2.92 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 88 HIS 0.005 0.001 HIS A 280 PHE 0.018 0.002 PHE C 324 TYR 0.015 0.001 TYR A 377 ARG 0.007 0.001 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 346) hydrogen bonds : angle 6.41959 ( 963) covalent geometry : bond 0.00346 ( 9978) covalent geometry : angle 0.82306 (13473) *********************** 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 239 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8052 (tm-30) REVERT: C 96 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6790 (tpm170) REVERT: C 127 THR cc_start: 0.5171 (OUTLIER) cc_final: 0.4916 (t) REVERT: C 348 PHE cc_start: 0.6642 (m-10) cc_final: 0.6325 (m-10) REVERT: D 22 LEU cc_start: 0.7400 (mm) cc_final: 0.6982 (pp) REVERT: D 124 GLN cc_start: 0.8161 (pm20) cc_final: 0.7706 (tm-30) REVERT: B 103 LEU cc_start: 0.9024 (mt) cc_final: 0.8719 (tp) REVERT: A 225 LEU cc_start: 0.8830 (pp) cc_final: 0.8581 (pp) REVERT: A 459 LYS cc_start: 0.8767 (mmtp) cc_final: 0.8351 (mmtm) REVERT: A 478 ASN cc_start: 0.7460 (m-40) cc_final: 0.7061 (p0) outliers start: 48 outliers final: 20 residues processed: 229 average time/residue: 0.1688 time to fit residues: 58.0097 Evaluate side-chains 175 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 D residue 14 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 36 VAL 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 49 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 187 ILE 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 409 THR Chi-restraints excluded: chain A residue 431 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** 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 = 0.4219 r_free = 0.4219 target = 0.181069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135337 restraints weight = 15194.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135752 restraints weight = 18828.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135833 restraints weight = 14346.673| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9978 Z= 0.168 Angle : 0.767 13.431 13473 Z= 0.404 Chirality : 0.046 0.238 1532 Planarity : 0.005 0.142 1739 Dihedral : 6.588 48.242 1320 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.82 % Allowed : 12.11 % Favored : 87.07 % Rotamer: Outliers : 5.13 % Allowed : 30.16 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.23), residues: 1214 helix: -1.31 (0.21), residues: 609 sheet: 0.42 (0.50), residues: 121 loop : -2.98 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 123 HIS 0.003 0.001 HIS A 280 PHE 0.013 0.002 PHE A 118 TYR 0.025 0.002 TYR C 104 ARG 0.004 0.001 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 346) hydrogen bonds : angle 5.78830 ( 963) covalent geometry : bond 0.00377 ( 9978) covalent geometry : angle 0.76674 (13473) *********************** 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 218 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7403 (mmp80) REVERT: C 90 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 96 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7051 (tpp-160) REVERT: C 348 PHE cc_start: 0.6618 (m-10) cc_final: 0.6303 (m-10) REVERT: D 85 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7143 (tp30) REVERT: D 125 PHE cc_start: 0.5345 (t80) cc_final: 0.4848 (t80) REVERT: B 103 LEU cc_start: 0.9077 (mt) cc_final: 0.8760 (tp) REVERT: A 154 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7792 (mttm) REVERT: A 225 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8571 (pp) REVERT: A 297 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6707 (tm-30) REVERT: A 315 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7910 (mmtp) REVERT: A 494 GLN cc_start: 0.7955 (tp40) cc_final: 0.7504 (tm-30) outliers start: 56 outliers final: 25 residues processed: 199 average time/residue: 0.2081 time to fit residues: 58.6144 Evaluate side-chains 170 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 275 VAL 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 115 VAL Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 156 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 279 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 315 LYS 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 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 HIS C 188 GLN ** 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 = 0.4235 r_free = 0.4235 target = 0.182569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141984 restraints weight = 15049.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136157 restraints weight = 20495.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131388 restraints weight = 14528.004| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9978 Z= 0.154 Angle : 0.740 11.230 13473 Z= 0.387 Chirality : 0.045 0.239 1532 Planarity : 0.005 0.135 1739 Dihedral : 6.157 47.987 1316 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.74 % Allowed : 11.61 % Favored : 87.64 % Rotamer: Outliers : 4.77 % Allowed : 30.71 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1214 helix: -1.21 (0.21), residues: 612 sheet: 0.45 (0.49), residues: 120 loop : -2.94 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 123 HIS 0.004 0.001 HIS A 280 PHE 0.015 0.002 PHE A 307 TYR 0.018 0.002 TYR C 104 ARG 0.004 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 346) hydrogen bonds : angle 5.48911 ( 963) covalent geometry : bond 0.00355 ( 9978) covalent geometry : angle 0.73991 (13473) *********************** 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 206 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 269 ASP cc_start: 0.7357 (t0) cc_final: 0.6874 (t0) REVERT: C 319 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8581 (t) REVERT: C 347 LYS cc_start: 0.8164 (tptm) cc_final: 0.7913 (ttpp) REVERT: C 348 PHE cc_start: 0.6839 (m-10) cc_final: 0.6570 (m-10) REVERT: D 125 PHE cc_start: 0.5291 (t80) cc_final: 0.4870 (t80) REVERT: B 103 LEU cc_start: 0.9071 (mt) cc_final: 0.8821 (tp) REVERT: A 87 GLU cc_start: 0.7276 (tt0) cc_final: 0.7032 (tm-30) REVERT: A 225 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8540 (pp) REVERT: A 382 MET cc_start: 0.7779 (ttt) cc_final: 0.7499 (ttm) REVERT: A 410 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8407 (ttmt) REVERT: A 494 GLN cc_start: 0.8186 (tp40) cc_final: 0.7751 (tm-30) outliers start: 52 outliers final: 34 residues processed: 194 average time/residue: 0.1847 time to fit residues: 52.4085 Evaluate side-chains 176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL 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 148 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain B residue 62 CYS 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 49 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 187 ILE 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 344 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 VAL 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 24 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN A 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.193233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3945 r_free = 0.3945 target = 0.145634 restraints weight = 16249.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143948 restraints weight = 13911.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.145641 restraints weight = 11527.381| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9978 Z= 0.168 Angle : 0.733 14.164 13473 Z= 0.382 Chirality : 0.046 0.203 1532 Planarity : 0.005 0.152 1739 Dihedral : 6.054 48.512 1316 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.74 % Allowed : 12.19 % Favored : 87.07 % Rotamer: Outliers : 5.32 % Allowed : 31.16 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.24), residues: 1214 helix: -1.05 (0.21), residues: 613 sheet: 0.31 (0.49), residues: 122 loop : -2.91 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 123 HIS 0.003 0.001 HIS A 280 PHE 0.020 0.002 PHE B 92 TYR 0.016 0.002 TYR A 46 ARG 0.006 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 346) hydrogen bonds : angle 5.31565 ( 963) covalent geometry : bond 0.00389 ( 9978) covalent geometry : angle 0.73334 (13473) *********************** 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 208 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 150 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 109 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6504 (pm20) REVERT: C 269 ASP cc_start: 0.7485 (t0) cc_final: 0.6844 (t0) REVERT: C 348 PHE cc_start: 0.6952 (m-10) cc_final: 0.6596 (m-10) REVERT: D 63 ILE cc_start: 0.5756 (OUTLIER) cc_final: 0.5458 (tp) REVERT: D 125 PHE cc_start: 0.5256 (t80) cc_final: 0.4839 (t80) REVERT: B 103 LEU cc_start: 0.9103 (mt) cc_final: 0.8830 (tp) REVERT: A 115 VAL cc_start: 0.8934 (m) cc_final: 0.8533 (t) REVERT: A 154 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7557 (mtmm) REVERT: A 190 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: A 224 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.6925 (t) REVERT: A 225 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8598 (pp) REVERT: A 382 MET cc_start: 0.7742 (ttt) cc_final: 0.7442 (ttm) REVERT: A 410 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8447 (ttmt) REVERT: A 494 GLN cc_start: 0.8283 (tp40) cc_final: 0.7930 (tm-30) outliers start: 58 outliers final: 31 residues processed: 193 average time/residue: 0.1879 time to fit residues: 54.7051 Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL 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 275 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 93 THR 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 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 225 LEU Chi-restraints excluded: chain A residue 226 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 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 91 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 48 HIS ** 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 = 0.4438 r_free = 0.4438 target = 0.193683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.148318 restraints weight = 16304.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.150587 restraints weight = 18218.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.151189 restraints weight = 12025.983| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9978 Z= 0.156 Angle : 0.732 15.620 13473 Z= 0.376 Chirality : 0.045 0.219 1532 Planarity : 0.005 0.157 1739 Dihedral : 5.984 46.595 1316 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.78 % Favored : 87.56 % Rotamer: Outliers : 4.67 % Allowed : 32.45 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.24), residues: 1214 helix: -0.90 (0.21), residues: 613 sheet: 0.19 (0.49), residues: 124 loop : -2.86 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 123 HIS 0.003 0.001 HIS A 280 PHE 0.021 0.002 PHE B 92 TYR 0.019 0.002 TYR A 260 ARG 0.006 0.000 ARG D 62 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 346) hydrogen bonds : angle 5.28965 ( 963) covalent geometry : bond 0.00363 ( 9978) covalent geometry : angle 0.73153 (13473) *********************** 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 194 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7902 (tm-30) REVERT: C 109 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6669 (pm20) REVERT: C 269 ASP cc_start: 0.7454 (t0) cc_final: 0.6956 (t0) REVERT: C 348 PHE cc_start: 0.6913 (m-10) cc_final: 0.6533 (m-10) REVERT: D 63 ILE cc_start: 0.5672 (OUTLIER) cc_final: 0.5428 (tp) REVERT: D 125 PHE cc_start: 0.5310 (t80) cc_final: 0.4856 (t80) REVERT: B 103 LEU cc_start: 0.9070 (mt) cc_final: 0.8791 (tp) REVERT: A 190 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6840 (mt-10) REVERT: A 224 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.6887 (t) REVERT: A 225 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8686 (pp) REVERT: A 382 MET cc_start: 0.7825 (ttt) cc_final: 0.7517 (ttm) REVERT: A 410 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8516 (mttt) REVERT: A 459 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8319 (mmtm) REVERT: A 494 GLN cc_start: 0.8139 (tp40) cc_final: 0.7786 (tm-30) outliers start: 51 outliers final: 32 residues processed: 181 average time/residue: 0.1769 time to fit residues: 47.8663 Evaluate side-chains 173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL 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 360 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 95 VAL 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 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 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 392 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 48 HIS ** 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 = 0.4408 r_free = 0.4408 target = 0.190601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144340 restraints weight = 16532.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.146260 restraints weight = 19317.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.146256 restraints weight = 12584.661| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9978 Z= 0.208 Angle : 0.765 11.433 13473 Z= 0.395 Chirality : 0.047 0.195 1532 Planarity : 0.005 0.139 1739 Dihedral : 6.078 47.796 1316 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.66 % Allowed : 12.85 % Favored : 86.49 % Rotamer: Outliers : 4.40 % Allowed : 32.45 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.24), residues: 1214 helix: -0.97 (0.21), residues: 618 sheet: 0.17 (0.50), residues: 122 loop : -2.76 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 123 HIS 0.003 0.001 HIS A 280 PHE 0.023 0.002 PHE C 349 TYR 0.025 0.002 TYR A 260 ARG 0.008 0.001 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 346) hydrogen bonds : angle 5.33043 ( 963) covalent geometry : bond 0.00486 ( 9978) covalent geometry : angle 0.76483 (13473) *********************** 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 198 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: C 90 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7920 (tm-30) REVERT: C 109 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: C 269 ASP cc_start: 0.7608 (t0) cc_final: 0.7315 (t0) REVERT: C 348 PHE cc_start: 0.6725 (m-10) cc_final: 0.6454 (m-10) REVERT: B 103 LEU cc_start: 0.9123 (mt) cc_final: 0.8876 (tp) REVERT: A 190 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: A 224 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.6938 (t) REVERT: A 225 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8737 (pp) REVERT: A 382 MET cc_start: 0.7836 (ttt) cc_final: 0.7562 (ttm) REVERT: A 459 LYS cc_start: 0.8915 (mmtp) cc_final: 0.8407 (mmtm) REVERT: A 463 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: A 494 GLN cc_start: 0.8202 (tp40) cc_final: 0.7803 (tm-30) outliers start: 48 outliers final: 35 residues processed: 185 average time/residue: 0.1734 time to fit residues: 47.9905 Evaluate side-chains 179 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL 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 148 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain B residue 17 ASP 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 28 ILE 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 190 GLU 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 240 THR Chi-restraints excluded: chain A residue 269 LEU 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 496 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN C 307 GLN D 19 ASN ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.178692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136647 restraints weight = 15432.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132972 restraints weight = 22087.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126505 restraints weight = 14802.796| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9978 Z= 0.151 Angle : 0.736 11.731 13473 Z= 0.378 Chirality : 0.046 0.223 1532 Planarity : 0.005 0.134 1739 Dihedral : 5.962 43.664 1316 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.86 % Favored : 87.48 % Rotamer: Outliers : 3.76 % Allowed : 33.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.24), residues: 1214 helix: -0.89 (0.21), residues: 612 sheet: 0.07 (0.50), residues: 124 loop : -2.66 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 123 HIS 0.003 0.001 HIS A 280 PHE 0.025 0.002 PHE C 348 TYR 0.021 0.002 TYR A 260 ARG 0.004 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 346) hydrogen bonds : angle 5.24407 ( 963) covalent geometry : bond 0.00351 ( 9978) covalent geometry : angle 0.73603 (13473) *********************** 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 181 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 1.011 Fit side-chains REVERT: C 90 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7952 (tm-30) REVERT: C 109 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7007 (pp20) REVERT: C 269 ASP cc_start: 0.7689 (t0) cc_final: 0.7405 (t0) REVERT: A 225 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8714 (pp) REVERT: A 382 MET cc_start: 0.7701 (ttt) cc_final: 0.7456 (ttm) REVERT: A 463 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6897 (mp10) REVERT: A 494 GLN cc_start: 0.8163 (tp40) cc_final: 0.7746 (tm-30) outliers start: 41 outliers final: 31 residues processed: 168 average time/residue: 0.1760 time to fit residues: 44.5296 Evaluate side-chains 164 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 360 ASN Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 28 ILE 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 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 240 THR Chi-restraints excluded: chain A residue 269 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 76 optimal weight: 0.0020 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 48 HIS ** 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 = 0.4210 r_free = 0.4210 target = 0.180152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135492 restraints weight = 15300.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138352 restraints weight = 22233.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138834 restraints weight = 12331.178| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5303 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= 0.143 Angle : 0.738 10.571 13473 Z= 0.378 Chirality : 0.046 0.182 1532 Planarity : 0.005 0.129 1739 Dihedral : 5.859 41.200 1316 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.11 % Favored : 87.31 % Rotamer: Outliers : 3.39 % Allowed : 34.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.25), residues: 1214 helix: -0.83 (0.21), residues: 617 sheet: 0.12 (0.50), residues: 124 loop : -2.54 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 123 HIS 0.003 0.001 HIS A 280 PHE 0.018 0.001 PHE B 92 TYR 0.026 0.002 TYR A 260 ARG 0.009 0.000 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 346) hydrogen bonds : angle 5.15466 ( 963) covalent geometry : bond 0.00334 ( 9978) covalent geometry : angle 0.73762 (13473) *********************** 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 177 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: C 90 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7900 (tm-30) REVERT: C 109 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6914 (pp20) REVERT: C 269 ASP cc_start: 0.7683 (t0) cc_final: 0.7427 (t0) REVERT: C 375 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7948 (tt) REVERT: A 225 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8666 (pp) REVERT: A 382 MET cc_start: 0.7784 (ttt) cc_final: 0.7496 (ttm) REVERT: A 459 LYS cc_start: 0.8555 (mmtp) cc_final: 0.8126 (mmtm) REVERT: A 463 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6881 (mp10) REVERT: A 494 GLN cc_start: 0.8060 (tp40) cc_final: 0.7628 (tm-30) outliers start: 37 outliers final: 28 residues processed: 165 average time/residue: 0.2178 time to fit residues: 54.4116 Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 D residue 14 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 28 ILE 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 137 CYS 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 240 THR Chi-restraints excluded: chain A residue 269 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 0.0070 chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4231 r_free = 0.4231 target = 0.182297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.142058 restraints weight = 15354.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144712 restraints weight = 27183.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147854 restraints weight = 13610.180| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5510 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= 0.124 Angle : 0.743 10.645 13473 Z= 0.376 Chirality : 0.044 0.177 1532 Planarity : 0.005 0.130 1739 Dihedral : 5.648 36.212 1316 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.70 % Favored : 87.81 % Rotamer: Outliers : 2.47 % Allowed : 34.83 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.25), residues: 1214 helix: -0.76 (0.21), residues: 624 sheet: 0.21 (0.50), residues: 124 loop : -2.43 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 68 HIS 0.003 0.001 HIS A 304 PHE 0.018 0.001 PHE B 92 TYR 0.025 0.001 TYR A 260 ARG 0.009 0.000 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 346) hydrogen bonds : angle 5.05027 ( 963) covalent geometry : bond 0.00285 ( 9978) covalent geometry : angle 0.74306 (13473) ********************** 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 185 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8246 (tm-30) REVERT: C 269 ASP cc_start: 0.7667 (t0) cc_final: 0.7411 (t0) REVERT: C 315 PRO cc_start: 0.7654 (Cg_exo) cc_final: 0.7438 (Cg_endo) REVERT: C 375 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7948 (tt) REVERT: A 225 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8617 (pp) REVERT: A 382 MET cc_start: 0.7662 (ttt) cc_final: 0.7392 (ttm) REVERT: A 459 LYS cc_start: 0.8307 (mmtp) cc_final: 0.8027 (mmtm) REVERT: A 494 GLN cc_start: 0.7931 (tp40) cc_final: 0.7510 (tm-30) outliers start: 27 outliers final: 20 residues processed: 176 average time/residue: 0.2145 time to fit residues: 57.3916 Evaluate side-chains 164 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR 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 D residue 14 SER Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 138 THR 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 224 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 465 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 chunk 68 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** 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 = 0.4221 r_free = 0.4221 target = 0.181233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139773 restraints weight = 15290.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143697 restraints weight = 24211.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145110 restraints weight = 10268.817| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9978 Z= 0.140 Angle : 0.760 13.070 13473 Z= 0.382 Chirality : 0.046 0.375 1532 Planarity : 0.005 0.130 1739 Dihedral : 5.624 38.658 1316 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.78 % Favored : 87.73 % Rotamer: Outliers : 2.66 % Allowed : 34.65 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.25), residues: 1214 helix: -0.69 (0.21), residues: 622 sheet: -0.01 (0.49), residues: 124 loop : -2.40 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 68 HIS 0.003 0.001 HIS C 191 PHE 0.019 0.001 PHE B 92 TYR 0.026 0.002 TYR A 260 ARG 0.009 0.000 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 346) hydrogen bonds : angle 5.04917 ( 963) covalent geometry : bond 0.00327 ( 9978) covalent geometry : angle 0.76029 (13473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3687.07 seconds wall clock time: 66 minutes 16.33 seconds (3976.33 seconds total)