Starting phenix.real_space_refine on Thu May 15 10:20:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uop_42435/05_2025/8uop_42435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uop_42435/05_2025/8uop_42435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uop_42435/05_2025/8uop_42435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uop_42435/05_2025/8uop_42435.map" model { file = "/net/cci-nas-00/data/ceres_data/8uop_42435/05_2025/8uop_42435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uop_42435/05_2025/8uop_42435.cif" } resolution = 3.8 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= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 4182 2.51 5 N 1122 2.21 5 O 1318 1.98 5 H 6544 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13188 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 6.55, per 1000 atoms: 0.50 Number of scatterers: 13188 At special positions: 0 Unit cell: (99.176, 76.538, 89.474, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 1318 8.00 N 1122 7.00 C 4182 6.00 H 6544 1.00 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: 3.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 40.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 93 through 99 removed outlier: 4.030A pdb=" N LEU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.731A pdb=" N VAL A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.768A pdb=" N SER A 156 " --> pdb=" O GLY A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 176 through 197 removed outlier: 4.340A pdb=" N ARG A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 185 " --> pdb=" O TRP A 181 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.892A pdb=" N LEU A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 271 through 286 removed outlier: 4.555A pdb=" N VAL A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.618A pdb=" N GLU A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.826A pdb=" N ASP A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 416 removed outlier: 4.837A pdb=" N LYS A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.856A pdb=" N ASN B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.538A pdb=" N ILE B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET B 94 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 124 removed outlier: 3.656A pdb=" N SER B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 134 removed outlier: 4.098A pdb=" N LEU B 134 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 174 through 188 removed outlier: 5.006A pdb=" N ARG B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 219 through 228 removed outlier: 3.619A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 removed outlier: 3.803A pdb=" N LEU B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.791A pdb=" N VAL B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 306' Processing helix chain 'B' and resid 325 through 336 removed outlier: 4.176A pdb=" N ILE B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.555A pdb=" N ILE B 348 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 Processing helix chain 'B' and resid 380 through 389 Processing helix chain 'B' and resid 401 through 419 removed outlier: 3.640A pdb=" N LYS B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 14 removed outlier: 3.641A pdb=" N ASN A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 21 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 151 removed outlier: 6.480A pdb=" N ASN A 148 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 167 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE A 150 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 164 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE A 240 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 291 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE A 242 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A 289 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 317 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 291 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 316 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 342 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY A 318 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA A 368 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LYS A 395 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 370 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR A 144 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 8 through 12 Processing sheet with id=AA5, first strand: chain 'B' and resid 239 through 243 removed outlier: 4.523A pdb=" N MET B 239 " --> pdb=" O MET B 168 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 168 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 164 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE B 165 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 393 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 341 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER B 371 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.673A pdb=" N ILE B 291 " --> pdb=" O VAL B 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 206 hydrogen bonds defined for protein. 555 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: 4.06 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6542 1.03 - 1.23: 6 1.23 - 1.42: 2788 1.42 - 1.62: 3916 1.62 - 1.81: 42 Bond restraints: 13294 Sorted by residual: bond pdb=" C TYR A 286 " pdb=" N PRO A 287 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.34e-02 5.57e+03 5.46e+00 bond pdb=" CA TYR A 286 " pdb=" CB TYR A 286 " ideal model delta sigma weight residual 1.528 1.559 -0.031 1.41e-02 5.03e+03 4.91e+00 bond pdb=" CB ASP B 299 " pdb=" CG ASP B 299 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.76e+00 bond pdb=" CA ASN A 236 " pdb=" CB ASN A 236 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.39e-02 5.18e+03 4.60e+00 bond pdb=" N MET B 168 " pdb=" CA MET B 168 " ideal model delta sigma weight residual 1.453 1.469 -0.015 9.20e-03 1.18e+04 2.83e+00 ... (remaining 13289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 23444 1.95 - 3.89: 529 3.89 - 5.84: 46 5.84 - 7.79: 2 7.79 - 9.73: 1 Bond angle restraints: 24022 Sorted by residual: angle pdb=" N ASP B 6 " pdb=" CA ASP B 6 " pdb=" C ASP B 6 " ideal model delta sigma weight residual 108.46 114.83 -6.37 1.51e+00 4.39e-01 1.78e+01 angle pdb=" N VAL B 421 " pdb=" CA VAL B 421 " pdb=" C VAL B 421 " ideal model delta sigma weight residual 106.21 110.24 -4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N ALA B 48 " pdb=" CA ALA B 48 " pdb=" C ALA B 48 " ideal model delta sigma weight residual 110.70 105.07 5.63 1.55e+00 4.16e-01 1.32e+01 angle pdb=" N LEU B 97 " pdb=" CA LEU B 97 " pdb=" C LEU B 97 " ideal model delta sigma weight residual 113.18 108.37 4.81 1.33e+00 5.65e-01 1.31e+01 angle pdb=" N THR B 200 " pdb=" CA THR B 200 " pdb=" C THR B 200 " ideal model delta sigma weight residual 107.57 114.21 -6.64 1.94e+00 2.66e-01 1.17e+01 ... (remaining 24017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5396 17.46 - 34.91: 568 34.91 - 52.37: 182 52.37 - 69.83: 55 69.83 - 87.29: 11 Dihedral angle restraints: 6212 sinusoidal: 3390 harmonic: 2822 Sorted by residual: dihedral pdb=" CA GLU A 235 " pdb=" C GLU A 235 " pdb=" N ASN A 236 " pdb=" CA ASN A 236 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALA B 228 " pdb=" C ALA B 228 " pdb=" N ALA B 229 " pdb=" CA ALA B 229 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ALA B 225 " pdb=" C ALA B 225 " pdb=" N ILE B 226 " pdb=" CA ILE B 226 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 6209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 646 0.036 - 0.072: 267 0.072 - 0.109: 87 0.109 - 0.145: 23 0.145 - 0.181: 3 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CB VAL A 219 " pdb=" CA VAL A 219 " pdb=" CG1 VAL A 219 " pdb=" CG2 VAL A 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CG LEU B 198 " pdb=" CB LEU B 198 " pdb=" CD1 LEU B 198 " pdb=" CD2 LEU B 198 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1023 not shown) Planarity restraints: 2046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 225 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.53e+00 pdb=" C ALA B 225 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA B 225 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE B 226 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 286 " 0.020 2.00e-02 2.50e+03 1.21e-02 4.39e+00 pdb=" CG TYR A 286 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 286 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 286 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 286 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 286 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 286 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 286 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 286 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR A 286 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 286 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 286 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 193 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C LEU B 193 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 193 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS B 194 " 0.011 2.00e-02 2.50e+03 ... (remaining 2043 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 348 2.09 - 2.72: 22698 2.72 - 3.34: 37656 3.34 - 3.97: 45929 3.97 - 4.60: 72127 Nonbonded interactions: 178758 Sorted by model distance: nonbonded pdb=" HH TYR B 257 " pdb=" OD2 ASP B 299 " model vdw 1.459 2.450 nonbonded pdb=" H ASP B 293 " pdb=" O VAL B 317 " model vdw 1.486 2.450 nonbonded pdb=" OG SER B 246 " pdb=" H MET B 295 " model vdw 1.530 2.450 nonbonded pdb=" O ASN B 298 " pdb=" H TRP B 300 " model vdw 1.555 2.450 nonbonded pdb="HH11 ARG B 180 " pdb=" OE2 GLU B 184 " model vdw 1.573 2.450 ... (remaining 178753 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.560 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: 0.230 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.460 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1503 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6750 Z= 0.245 Angle : 0.905 9.735 9128 Z= 0.547 Chirality : 0.045 0.181 1026 Planarity : 0.005 0.055 1198 Dihedral : 16.453 87.286 2470 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.67 % Favored : 83.64 % Rotamer: Outliers : 0.73 % Allowed : 17.45 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.60 (0.25), residues: 868 helix: -1.37 (0.30), residues: 264 sheet: -2.50 (0.61), residues: 64 loop : -3.09 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP A 300 HIS 0.009 0.002 HIS B 0 PHE 0.018 0.003 PHE A 175 TYR 0.034 0.003 TYR A 286 ARG 0.010 0.001 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.18619 ( 206) hydrogen bonds : angle 8.03634 ( 555) covalent geometry : bond 0.00468 ( 6750) covalent geometry : angle 0.90511 ( 9128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.0860 (p90) cc_final: 0.0132 (p90) REVERT: A 359 GLU cc_start: 0.1655 (tm-30) cc_final: -0.0744 (mt-10) REVERT: B 6 ASP cc_start: 0.5409 (p0) cc_final: 0.5123 (p0) REVERT: B 92 ARG cc_start: 0.3431 (mmt180) cc_final: 0.2180 (tpt90) REVERT: B 239 MET cc_start: 0.2235 (mmp) cc_final: 0.1922 (mmt) REVERT: B 360 MET cc_start: 0.0955 (tpt) cc_final: 0.0245 (mtp) outliers start: 5 outliers final: 2 residues processed: 95 average time/residue: 0.4121 time to fit residues: 52.1069 Evaluate side-chains 68 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5341 r_free = 0.5341 target = 0.345076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5254 r_free = 0.5254 target = 0.334775 restraints weight = 40662.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5285 r_free = 0.5285 target = 0.338494 restraints weight = 22237.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.340934 restraints weight = 12833.565| |-----------------------------------------------------------------------------| r_work (final): 0.5293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2010 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6750 Z= 0.174 Angle : 0.707 7.640 9128 Z= 0.382 Chirality : 0.043 0.152 1026 Planarity : 0.005 0.055 1198 Dihedral : 7.009 50.885 950 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.79 % Favored : 86.87 % Rotamer: Outliers : 2.20 % Allowed : 18.62 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.56 (0.25), residues: 868 helix: -1.31 (0.29), residues: 274 sheet: -2.67 (0.61), residues: 63 loop : -3.08 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 181 HIS 0.008 0.002 HIS B 0 PHE 0.017 0.002 PHE B 322 TYR 0.021 0.002 TYR A 278 ARG 0.003 0.000 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 206) hydrogen bonds : angle 6.23523 ( 555) covalent geometry : bond 0.00376 ( 6750) covalent geometry : angle 0.70661 ( 9128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.2617 (tpp) cc_final: 0.2275 (ttm) REVERT: A 131 TYR cc_start: 0.0865 (p90) cc_final: 0.0249 (p90) REVERT: A 166 MET cc_start: 0.1000 (mmm) cc_final: -0.0059 (mpp) REVERT: A 359 GLU cc_start: 0.1791 (OUTLIER) cc_final: -0.1055 (mt-10) REVERT: A 376 GLU cc_start: 0.0496 (mm-30) cc_final: -0.0293 (mp0) REVERT: B 92 ARG cc_start: 0.2654 (mmt180) cc_final: 0.1340 (tpt90) REVERT: B 239 MET cc_start: 0.3592 (mmp) cc_final: 0.2887 (mmt) REVERT: B 360 MET cc_start: 0.1751 (tpt) cc_final: 0.0786 (mtp) outliers start: 15 outliers final: 12 residues processed: 86 average time/residue: 0.3655 time to fit residues: 43.0734 Evaluate side-chains 75 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 26 optimal weight: 0.0270 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 chunk 77 optimal weight: 5.9990 overall best weight: 1.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5332 r_free = 0.5332 target = 0.345226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.340648 restraints weight = 42012.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.5308 r_free = 0.5308 target = 0.342350 restraints weight = 23802.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.343350 restraints weight = 13970.772| |-----------------------------------------------------------------------------| r_work (final): 0.5318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2104 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6750 Z= 0.140 Angle : 0.609 5.938 9128 Z= 0.331 Chirality : 0.042 0.150 1026 Planarity : 0.004 0.041 1198 Dihedral : 6.526 56.342 950 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.67 % Favored : 86.98 % Rotamer: Outliers : 4.25 % Allowed : 16.72 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.33 (0.26), residues: 868 helix: -1.09 (0.29), residues: 281 sheet: -2.90 (0.53), residues: 83 loop : -2.88 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 300 HIS 0.007 0.001 HIS A 372 PHE 0.015 0.001 PHE B 242 TYR 0.018 0.001 TYR A 278 ARG 0.004 0.000 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 206) hydrogen bonds : angle 5.90060 ( 555) covalent geometry : bond 0.00295 ( 6750) covalent geometry : angle 0.60863 ( 9128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.2862 (OUTLIER) cc_final: 0.2216 (mm) REVERT: A 94 MET cc_start: 0.3389 (tpp) cc_final: 0.2990 (ttm) REVERT: A 131 TYR cc_start: 0.1416 (p90) cc_final: 0.0780 (p90) REVERT: A 166 MET cc_start: 0.1500 (mmm) cc_final: 0.0411 (mpp) REVERT: A 235 GLU cc_start: 0.0876 (OUTLIER) cc_final: -0.0609 (tt0) REVERT: A 331 ARG cc_start: 0.0707 (ttt180) cc_final: -0.1081 (ttm-80) REVERT: A 362 LYS cc_start: 0.2771 (OUTLIER) cc_final: 0.2432 (tptt) REVERT: A 376 GLU cc_start: 0.1149 (mm-30) cc_final: 0.0452 (mp0) REVERT: A 378 GLU cc_start: -0.2512 (OUTLIER) cc_final: -0.2920 (pm20) REVERT: B 239 MET cc_start: 0.2793 (mmp) cc_final: 0.1987 (mmt) REVERT: B 360 MET cc_start: 0.1213 (tpt) cc_final: -0.0250 (mtt) outliers start: 29 outliers final: 17 residues processed: 90 average time/residue: 0.3328 time to fit residues: 42.0597 Evaluate side-chains 80 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 19 optimal weight: 0.0570 chunk 13 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.344800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.335181 restraints weight = 41139.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.338662 restraints weight = 23063.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.340935 restraints weight = 13230.683| |-----------------------------------------------------------------------------| r_work (final): 0.5298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2046 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6750 Z= 0.103 Angle : 0.550 4.305 9128 Z= 0.299 Chirality : 0.041 0.141 1026 Planarity : 0.003 0.039 1198 Dihedral : 6.107 57.424 950 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.37 % Favored : 89.17 % Rotamer: Outliers : 3.37 % Allowed : 17.01 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.09 (0.27), residues: 868 helix: -0.65 (0.31), residues: 271 sheet: -2.80 (0.49), residues: 97 loop : -2.82 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 303 HIS 0.007 0.001 HIS A 372 PHE 0.011 0.001 PHE B 242 TYR 0.015 0.001 TYR A 278 ARG 0.002 0.000 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 206) hydrogen bonds : angle 5.52469 ( 555) covalent geometry : bond 0.00222 ( 6750) covalent geometry : angle 0.54981 ( 9128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.2951 (tpp) cc_final: 0.2640 (ttm) REVERT: A 130 LEU cc_start: 0.1260 (tp) cc_final: 0.0593 (pt) REVERT: A 131 TYR cc_start: 0.1067 (p90) cc_final: 0.0282 (p90) REVERT: A 166 MET cc_start: 0.1461 (mmm) cc_final: 0.0767 (mpp) REVERT: A 168 MET cc_start: 0.1902 (mmt) cc_final: 0.1556 (mmt) REVERT: A 331 ARG cc_start: 0.0107 (ttt180) cc_final: -0.1838 (ttm-80) REVERT: A 362 LYS cc_start: 0.2006 (OUTLIER) cc_final: 0.1083 (tptt) REVERT: A 376 GLU cc_start: 0.0823 (mm-30) cc_final: 0.0056 (mp0) REVERT: B 239 MET cc_start: 0.3620 (mmp) cc_final: 0.2778 (mmt) REVERT: B 360 MET cc_start: 0.2457 (tpt) cc_final: 0.0786 (mtt) outliers start: 23 outliers final: 17 residues processed: 79 average time/residue: 0.3364 time to fit residues: 37.2993 Evaluate side-chains 76 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.342841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5293 r_free = 0.5293 target = 0.338765 restraints weight = 41628.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.340814 restraints weight = 23883.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.341488 restraints weight = 11404.133| |-----------------------------------------------------------------------------| r_work (final): 0.5279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2208 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6750 Z= 0.182 Angle : 0.677 6.555 9128 Z= 0.367 Chirality : 0.044 0.156 1026 Planarity : 0.004 0.047 1198 Dihedral : 6.675 53.043 950 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.67 % Favored : 86.75 % Rotamer: Outliers : 4.40 % Allowed : 17.16 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.20 (0.26), residues: 868 helix: -0.79 (0.30), residues: 262 sheet: -2.98 (0.51), residues: 84 loop : -2.83 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 303 HIS 0.007 0.002 HIS A 0 PHE 0.023 0.002 PHE B 322 TYR 0.024 0.002 TYR A 278 ARG 0.005 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 206) hydrogen bonds : angle 5.83822 ( 555) covalent geometry : bond 0.00388 ( 6750) covalent geometry : angle 0.67664 ( 9128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.2447 (OUTLIER) cc_final: 0.2176 (tp) REVERT: A 94 MET cc_start: 0.2839 (tpp) cc_final: 0.2366 (ttm) REVERT: A 131 TYR cc_start: 0.1209 (p90) cc_final: 0.0679 (p90) REVERT: A 166 MET cc_start: 0.1572 (mmm) cc_final: 0.0616 (mpp) REVERT: A 295 MET cc_start: 0.3712 (tmm) cc_final: 0.3446 (tmm) REVERT: A 331 ARG cc_start: 0.0295 (ttt180) cc_final: -0.1286 (ttt180) REVERT: A 376 GLU cc_start: 0.0821 (mm-30) cc_final: -0.0114 (mp0) REVERT: B 360 MET cc_start: 0.2572 (tpt) cc_final: 0.1058 (mtt) outliers start: 30 outliers final: 25 residues processed: 89 average time/residue: 0.3351 time to fit residues: 41.9676 Evaluate side-chains 87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.339601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5206 r_free = 0.5206 target = 0.328650 restraints weight = 41165.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.334039 restraints weight = 29419.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5268 r_free = 0.5268 target = 0.336447 restraints weight = 12356.340| |-----------------------------------------------------------------------------| r_work (final): 0.5275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2361 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6750 Z= 0.170 Angle : 0.638 5.339 9128 Z= 0.348 Chirality : 0.043 0.156 1026 Planarity : 0.004 0.039 1198 Dihedral : 6.711 52.906 950 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.67 % Favored : 86.87 % Rotamer: Outliers : 4.55 % Allowed : 18.77 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.21 (0.27), residues: 868 helix: -0.80 (0.30), residues: 263 sheet: -2.90 (0.52), residues: 84 loop : -2.86 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 303 HIS 0.006 0.001 HIS A 372 PHE 0.024 0.002 PHE B 165 TYR 0.020 0.002 TYR A 278 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 206) hydrogen bonds : angle 5.93726 ( 555) covalent geometry : bond 0.00365 ( 6750) covalent geometry : angle 0.63816 ( 9128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 1.020 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: A 79 ILE cc_start: 0.3206 (OUTLIER) cc_final: 0.2756 (tp) REVERT: A 94 MET cc_start: 0.3177 (tpp) cc_final: 0.2705 (ttm) REVERT: A 130 LEU cc_start: 0.0693 (tp) cc_final: 0.0184 (pt) REVERT: A 131 TYR cc_start: 0.1154 (p90) cc_final: 0.0588 (p90) REVERT: A 157 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6376 (t0) REVERT: A 184 GLU cc_start: 0.3784 (OUTLIER) cc_final: 0.3373 (pt0) REVERT: A 295 MET cc_start: 0.3775 (tmm) cc_final: 0.3504 (tmm) REVERT: A 331 ARG cc_start: 0.0595 (ttt180) cc_final: -0.1112 (ttt180) REVERT: A 376 GLU cc_start: 0.1198 (mm-30) cc_final: 0.0089 (mt-10) REVERT: B 94 MET cc_start: 0.5733 (mmp) cc_final: 0.5161 (mmp) REVERT: B 239 MET cc_start: 0.3182 (mmp) cc_final: 0.2187 (mmt) REVERT: B 360 MET cc_start: 0.2435 (tpt) cc_final: 0.0590 (mtt) outliers start: 31 outliers final: 20 residues processed: 85 average time/residue: 0.3215 time to fit residues: 39.0758 Evaluate side-chains 81 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 4 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 64 optimal weight: 0.0000 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 315 GLN ** B 315 GLN ** 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 = 0.5282 r_free = 0.5282 target = 0.337676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.331152 restraints weight = 41299.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5238 r_free = 0.5238 target = 0.332809 restraints weight = 24974.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5250 r_free = 0.5250 target = 0.334153 restraints weight = 16177.797| |-----------------------------------------------------------------------------| r_work (final): 0.5254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2532 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 6750 Z= 0.223 Angle : 0.750 6.722 9128 Z= 0.410 Chirality : 0.046 0.190 1026 Planarity : 0.005 0.056 1198 Dihedral : 7.320 52.963 950 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.29 % Favored : 85.37 % Rotamer: Outliers : 5.72 % Allowed : 18.18 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.68 (0.25), residues: 868 helix: -1.18 (0.29), residues: 263 sheet: -3.00 (0.53), residues: 84 loop : -3.20 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 181 HIS 0.006 0.001 HIS A 372 PHE 0.027 0.002 PHE B 165 TYR 0.022 0.002 TYR A 278 ARG 0.004 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 206) hydrogen bonds : angle 6.36988 ( 555) covalent geometry : bond 0.00481 ( 6750) covalent geometry : angle 0.75033 ( 9128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 56 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.1275 (p90) cc_final: 0.0844 (p90) REVERT: A 184 GLU cc_start: 0.4165 (OUTLIER) cc_final: 0.3717 (pt0) REVERT: B 85 ARG cc_start: 0.1679 (ttp-170) cc_final: 0.0478 (ttm170) REVERT: B 94 MET cc_start: 0.5582 (mmp) cc_final: 0.5207 (mmp) REVERT: B 297 GLU cc_start: 0.3013 (mm-30) cc_final: 0.2599 (mp0) outliers start: 39 outliers final: 29 residues processed: 87 average time/residue: 0.3450 time to fit residues: 41.8315 Evaluate side-chains 83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 63 optimal weight: 0.0270 chunk 81 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 overall best weight: 2.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.338188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.331972 restraints weight = 41568.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5247 r_free = 0.5247 target = 0.333661 restraints weight = 24275.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5257 r_free = 0.5257 target = 0.334871 restraints weight = 15149.793| |-----------------------------------------------------------------------------| r_work (final): 0.5260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2480 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6750 Z= 0.175 Angle : 0.650 5.221 9128 Z= 0.357 Chirality : 0.043 0.154 1026 Planarity : 0.004 0.042 1198 Dihedral : 7.029 53.107 950 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.48 % Favored : 86.18 % Rotamer: Outliers : 4.84 % Allowed : 19.06 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.62 (0.25), residues: 868 helix: -1.15 (0.29), residues: 264 sheet: -2.79 (0.58), residues: 74 loop : -3.19 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 181 HIS 0.006 0.001 HIS A 372 PHE 0.019 0.002 PHE B 165 TYR 0.017 0.002 TYR A 278 ARG 0.006 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 206) hydrogen bonds : angle 6.17356 ( 555) covalent geometry : bond 0.00378 ( 6750) covalent geometry : angle 0.64958 ( 9128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.1206 (p90) cc_final: 0.0727 (p90) REVERT: A 146 MET cc_start: 0.3328 (ptt) cc_final: 0.2944 (ptp) REVERT: A 157 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6575 (t70) REVERT: A 235 GLU cc_start: 0.1282 (OUTLIER) cc_final: -0.2250 (mt-10) REVERT: A 376 GLU cc_start: 0.0767 (mm-30) cc_final: -0.0006 (mt-10) REVERT: B 85 ARG cc_start: 0.1436 (ttp-170) cc_final: 0.0769 (ttp-170) REVERT: B 94 MET cc_start: 0.5280 (mmp) cc_final: 0.5066 (mmp) REVERT: B 239 MET cc_start: 0.3361 (mmp) cc_final: 0.2141 (mmt) REVERT: B 286 TYR cc_start: -0.1983 (OUTLIER) cc_final: -0.2360 (t80) REVERT: B 297 GLU cc_start: 0.2945 (mm-30) cc_final: 0.2413 (mp0) REVERT: B 360 MET cc_start: 0.2609 (tpt) cc_final: 0.1121 (mtt) outliers start: 33 outliers final: 27 residues processed: 87 average time/residue: 0.3151 time to fit residues: 39.3518 Evaluate side-chains 85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.0670 chunk 82 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 315 GLN ** 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 = 0.5290 r_free = 0.5290 target = 0.338860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.332364 restraints weight = 41247.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.334122 restraints weight = 24629.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.335394 restraints weight = 15759.343| |-----------------------------------------------------------------------------| r_work (final): 0.5230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2417 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6750 Z= 0.157 Angle : 0.632 5.138 9128 Z= 0.346 Chirality : 0.043 0.197 1026 Planarity : 0.004 0.038 1198 Dihedral : 6.873 52.603 950 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.36 % Favored : 86.29 % Rotamer: Outliers : 4.69 % Allowed : 20.09 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.53 (0.26), residues: 868 helix: -0.98 (0.30), residues: 257 sheet: -3.04 (0.52), residues: 86 loop : -3.10 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 181 HIS 0.006 0.001 HIS A 372 PHE 0.019 0.002 PHE B 242 TYR 0.020 0.001 TYR A 278 ARG 0.004 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 206) hydrogen bonds : angle 6.05259 ( 555) covalent geometry : bond 0.00343 ( 6750) covalent geometry : angle 0.63208 ( 9128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.2715 (ptt) cc_final: 0.2447 (ptp) REVERT: A 157 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6443 (t70) REVERT: A 235 GLU cc_start: 0.0783 (OUTLIER) cc_final: -0.2487 (mt-10) REVERT: A 376 GLU cc_start: 0.0357 (mm-30) cc_final: -0.0335 (mt-10) REVERT: B 85 ARG cc_start: 0.1059 (ttp-170) cc_final: 0.0266 (ttp-170) REVERT: B 239 MET cc_start: 0.3838 (mmp) cc_final: 0.2668 (mmt) REVERT: B 286 TYR cc_start: -0.2097 (OUTLIER) cc_final: -0.2372 (t80) REVERT: B 297 GLU cc_start: 0.2798 (mm-30) cc_final: 0.2093 (mp0) REVERT: B 360 MET cc_start: 0.2907 (tpt) cc_final: 0.1380 (mtt) outliers start: 32 outliers final: 28 residues processed: 84 average time/residue: 0.3216 time to fit residues: 38.7214 Evaluate side-chains 86 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 50 optimal weight: 0.0270 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 73 ASN ** B 315 GLN ** 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 = 0.5314 r_free = 0.5314 target = 0.341899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.331333 restraints weight = 40448.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.334592 restraints weight = 25702.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.337215 restraints weight = 15222.435| |-----------------------------------------------------------------------------| r_work (final): 0.5272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2339 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6750 Z= 0.105 Angle : 0.550 5.732 9128 Z= 0.300 Chirality : 0.041 0.147 1026 Planarity : 0.003 0.032 1198 Dihedral : 6.200 52.614 950 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.37 % Favored : 89.29 % Rotamer: Outliers : 2.64 % Allowed : 21.70 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.22 (0.26), residues: 868 helix: -0.64 (0.31), residues: 263 sheet: -2.89 (0.51), residues: 96 loop : -2.95 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 303 HIS 0.005 0.001 HIS A 372 PHE 0.013 0.001 PHE B 242 TYR 0.013 0.001 TYR A 278 ARG 0.002 0.000 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 206) hydrogen bonds : angle 5.52896 ( 555) covalent geometry : bond 0.00234 ( 6750) covalent geometry : angle 0.55022 ( 9128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ARG cc_start: 0.0343 (ttt180) cc_final: -0.1874 (ttm-80) REVERT: A 376 GLU cc_start: 0.0733 (mm-30) cc_final: -0.0232 (mt-10) REVERT: B 239 MET cc_start: 0.3275 (mmp) cc_final: 0.2053 (mmt) REVERT: B 297 GLU cc_start: 0.2851 (mm-30) cc_final: 0.1963 (mp0) REVERT: B 360 MET cc_start: 0.2762 (tpt) cc_final: 0.1339 (mtt) outliers start: 18 outliers final: 16 residues processed: 73 average time/residue: 0.3384 time to fit residues: 35.2923 Evaluate side-chains 70 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.0470 chunk 83 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 52 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5310 r_free = 0.5310 target = 0.341637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.335550 restraints weight = 41686.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.337431 restraints weight = 23896.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.5284 r_free = 0.5284 target = 0.338778 restraints weight = 14512.432| |-----------------------------------------------------------------------------| r_work (final): 0.5288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2304 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6750 Z= 0.102 Angle : 0.539 5.193 9128 Z= 0.291 Chirality : 0.040 0.140 1026 Planarity : 0.003 0.030 1198 Dihedral : 5.945 52.129 950 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.71 % Favored : 88.94 % Rotamer: Outliers : 2.79 % Allowed : 21.70 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.00 (0.27), residues: 868 helix: -0.37 (0.31), residues: 265 sheet: -2.81 (0.53), residues: 89 loop : -2.88 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.005 0.001 HIS A 372 PHE 0.015 0.001 PHE B 242 TYR 0.013 0.001 TYR A 278 ARG 0.003 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 206) hydrogen bonds : angle 5.37395 ( 555) covalent geometry : bond 0.00228 ( 6750) covalent geometry : angle 0.53871 ( 9128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3861.01 seconds wall clock time: 67 minutes 18.03 seconds (4038.03 seconds total)