Starting phenix.real_space_refine on Tue Sep 24 01:26:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/09_2024/8ga0_29883.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/09_2024/8ga0_29883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/09_2024/8ga0_29883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/09_2024/8ga0_29883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/09_2024/8ga0_29883.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga0_29883/09_2024/8ga0_29883.cif" } resolution = 3.5 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= 0.003 sd= 0.052 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 40 5.16 5 C 4348 2.51 5 N 1095 2.21 5 O 1115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6598 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3287 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 420} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3311 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 19, 'TRANS': 422} Time building chain proxies: 4.56, per 1000 atoms: 0.69 Number of scatterers: 6598 At special positions: 0 Unit cell: (72.092, 88.232, 114.056, 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 40 16.00 O 1115 8.00 N 1095 7.00 C 4348 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: 1.60 Conformation dependent library (CDL) restraints added in 968.4 milliseconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 66.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.520A pdb=" N GLU A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 55 through 67 removed outlier: 3.934A pdb=" N GLN A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 71 removed outlier: 3.549A pdb=" N THR A 71 " --> pdb=" O LEU A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.542A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.502A pdb=" N GLY A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 165 removed outlier: 4.131A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.884A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 202 removed outlier: 3.671A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.669A pdb=" N LYS A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.026A pdb=" N MET A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.552A pdb=" N THR A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 252 " --> pdb=" O LEU A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 252' Processing helix chain 'A' and resid 253 through 274 removed outlier: 3.933A pdb=" N GLY A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 284 removed outlier: 3.856A pdb=" N HIS A 284 " --> pdb=" O HIS A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 287 through 292 removed outlier: 4.028A pdb=" N VAL A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 309 removed outlier: 3.553A pdb=" N ALA A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE A 298 " --> pdb=" O MET A 294 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.585A pdb=" N VAL A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 379 removed outlier: 4.603A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 removed outlier: 3.777A pdb=" N HIS A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.683A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.944A pdb=" N ILE A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 422 removed outlier: 3.793A pdb=" N ILE A 422 " --> pdb=" O TYR A 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 423 through 440 removed outlier: 3.548A pdb=" N THR A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 removed outlier: 4.347A pdb=" N LEU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 removed outlier: 3.612A pdb=" N LEU B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 52 removed outlier: 3.503A pdb=" N PHE B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 69 removed outlier: 4.019A pdb=" N TRP B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 82 removed outlier: 3.507A pdb=" N THR B 80 " --> pdb=" O PRO B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 3.631A pdb=" N PHE B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE B 95 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 removed outlier: 3.945A pdb=" N LEU B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.664A pdb=" N GLY B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 removed outlier: 4.143A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.694A pdb=" N LEU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.637A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 231 removed outlier: 3.557A pdb=" N GLY B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 277 removed outlier: 3.837A pdb=" N ILE B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 3.787A pdb=" N LEU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 297 Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.597A pdb=" N GLY B 306 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 removed outlier: 4.032A pdb=" N SER B 313 " --> pdb=" O PRO B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.562A pdb=" N VAL B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 removed outlier: 4.750A pdb=" N ARG B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 379 removed outlier: 3.521A pdb=" N ALA B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 removed outlier: 3.565A pdb=" N HIS B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 393 through 397 removed outlier: 3.657A pdb=" N ALA B 396 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 397 " --> pdb=" O MET B 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 393 through 397' Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 422 through 439 removed outlier: 3.844A pdb=" N ILE B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 437 " --> pdb=" O THR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 448 through 457 removed outlier: 4.029A pdb=" N ALA B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2059 1.34 - 1.46: 1333 1.46 - 1.58: 3278 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6744 Sorted by residual: bond pdb=" C ALA A 358 " pdb=" N PRO A 359 " ideal model delta sigma weight residual 1.334 1.379 -0.046 8.40e-03 1.42e+04 2.98e+01 bond pdb=" N GLU B 235 " pdb=" CA GLU B 235 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.54e-02 4.22e+03 2.01e+00 bond pdb=" CA THR A 31 " pdb=" C THR A 31 " ideal model delta sigma weight residual 1.524 1.539 -0.016 1.26e-02 6.30e+03 1.53e+00 bond pdb=" C LEU A 423 " pdb=" N PRO A 424 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.23e-02 6.61e+03 1.47e+00 bond pdb=" C LEU B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.25e-02 6.40e+03 1.40e+00 ... (remaining 6739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 8833 1.84 - 3.68: 249 3.68 - 5.52: 47 5.52 - 7.36: 20 7.36 - 9.20: 11 Bond angle restraints: 9160 Sorted by residual: angle pdb=" N ILE B 213 " pdb=" CA ILE B 213 " pdb=" C ILE B 213 " ideal model delta sigma weight residual 113.71 104.51 9.20 9.50e-01 1.11e+00 9.38e+01 angle pdb=" N THR B 251 " pdb=" CA THR B 251 " pdb=" C THR B 251 " ideal model delta sigma weight residual 114.56 106.62 7.94 1.27e+00 6.20e-01 3.91e+01 angle pdb=" N ILE B 336 " pdb=" CA ILE B 336 " pdb=" C ILE B 336 " ideal model delta sigma weight residual 111.91 106.45 5.46 8.90e-01 1.26e+00 3.77e+01 angle pdb=" N ILE A 35 " pdb=" CA ILE A 35 " pdb=" C ILE A 35 " ideal model delta sigma weight residual 112.29 108.55 3.74 9.40e-01 1.13e+00 1.59e+01 angle pdb=" C HIS A 234 " pdb=" N GLU A 235 " pdb=" CA GLU A 235 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 ... (remaining 9155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3458 17.57 - 35.14: 380 35.14 - 52.71: 52 52.71 - 70.28: 5 70.28 - 87.85: 3 Dihedral angle restraints: 3898 sinusoidal: 1462 harmonic: 2436 Sorted by residual: dihedral pdb=" CA THR B 211 " pdb=" C THR B 211 " pdb=" N LEU B 212 " pdb=" CA LEU B 212 " ideal model delta harmonic sigma weight residual 180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LEU B 212 " pdb=" C LEU B 212 " pdb=" N ILE B 213 " pdb=" CA ILE B 213 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA B 358 " pdb=" C ALA B 358 " pdb=" N PRO B 359 " pdb=" CA PRO B 359 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 790 0.051 - 0.102: 233 0.102 - 0.153: 46 0.153 - 0.204: 8 0.204 - 0.255: 3 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CB ILE B 410 " pdb=" CA ILE B 410 " pdb=" CG1 ILE B 410 " pdb=" CG2 ILE B 410 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE A 336 " pdb=" CA ILE A 336 " pdb=" CG1 ILE A 336 " pdb=" CG2 ILE A 336 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1077 not shown) Planarity restraints: 1146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 358 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO B 359 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 359 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 359 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 109 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO A 110 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 149 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO A 150 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.038 5.00e-02 4.00e+02 ... (remaining 1143 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1885 2.80 - 3.32: 5441 3.32 - 3.85: 10899 3.85 - 4.37: 13154 4.37 - 4.90: 22231 Nonbonded interactions: 53610 Sorted by model distance: nonbonded pdb=" O LEU A 345 " pdb=" OG SER A 349 " model vdw 2.274 3.040 nonbonded pdb=" O VAL B 412 " pdb=" OG1 THR B 416 " model vdw 2.333 3.040 nonbonded pdb=" O ARG B 147 " pdb=" OG1 THR B 151 " model vdw 2.335 3.040 nonbonded pdb=" O VAL A 412 " pdb=" OG1 THR A 416 " model vdw 2.337 3.040 nonbonded pdb=" OG SER B 86 " pdb=" O GLY B 299 " model vdw 2.346 3.040 ... (remaining 53605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 22 through 458 or (resid 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 or (resid 461 and (name N or name CA or \ name C or name O or name CB )))) } 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.100 Find NCS groups from input model: 0.440 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.004 0.053 6744 Z= 0.246 Angle : 0.840 9.202 9160 Z= 0.460 Chirality : 0.051 0.255 1080 Planarity : 0.007 0.072 1146 Dihedral : 14.181 87.846 2362 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % 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: -6.86 (0.16), residues: 878 helix: -4.82 (0.08), residues: 586 sheet: None (None), residues: 0 loop : -3.41 (0.28), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 291 HIS 0.007 0.001 HIS A 284 PHE 0.015 0.001 PHE A 357 TYR 0.017 0.001 TYR B 419 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.731 Fit side-chains REVERT: A 45 LEU cc_start: 0.7827 (mt) cc_final: 0.7549 (mt) REVERT: A 213 ILE cc_start: 0.7488 (tp) cc_final: 0.7076 (tp) REVERT: A 276 MET cc_start: 0.5353 (mtt) cc_final: 0.5098 (mtt) REVERT: B 38 MET cc_start: 0.7578 (mmt) cc_final: 0.7359 (mmt) REVERT: B 55 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7921 (mtpp) REVERT: B 201 ILE cc_start: 0.8935 (mt) cc_final: 0.8668 (mt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2016 time to fit residues: 38.2194 Evaluate side-chains 117 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS B 62 ASN B 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6744 Z= 0.245 Angle : 0.621 6.231 9160 Z= 0.321 Chirality : 0.041 0.117 1080 Planarity : 0.006 0.059 1146 Dihedral : 5.635 24.167 936 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.66 % Allowed : 14.35 % Favored : 83.99 % 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: -5.53 (0.20), residues: 878 helix: -3.65 (0.14), residues: 603 sheet: None (None), residues: 0 loop : -3.16 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 291 HIS 0.001 0.000 HIS B 284 PHE 0.027 0.001 PHE A 95 TYR 0.007 0.001 TYR B 94 ARG 0.005 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.693 Fit side-chains REVERT: A 45 LEU cc_start: 0.8042 (mt) cc_final: 0.7664 (mt) REVERT: A 213 ILE cc_start: 0.7584 (tp) cc_final: 0.7092 (tp) REVERT: A 256 LEU cc_start: 0.7884 (tp) cc_final: 0.7399 (tp) REVERT: A 294 MET cc_start: 0.8017 (tmm) cc_final: 0.7654 (tpp) REVERT: B 55 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7929 (mtpp) REVERT: B 201 ILE cc_start: 0.9062 (mt) cc_final: 0.8859 (mt) REVERT: B 228 MET cc_start: 0.6951 (tpp) cc_final: 0.6607 (tpt) REVERT: B 254 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7716 (mp) REVERT: B 357 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7052 (m-10) outliers start: 11 outliers final: 8 residues processed: 128 average time/residue: 0.1689 time to fit residues: 29.4885 Evaluate side-chains 132 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 357 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6744 Z= 0.209 Angle : 0.572 5.642 9160 Z= 0.293 Chirality : 0.040 0.115 1080 Planarity : 0.005 0.049 1146 Dihedral : 5.264 24.129 936 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.87 % Allowed : 16.01 % Favored : 81.12 % 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: -4.47 (0.24), residues: 878 helix: -2.86 (0.17), residues: 603 sheet: None (None), residues: 0 loop : -2.75 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 291 HIS 0.002 0.000 HIS A 284 PHE 0.021 0.001 PHE A 208 TYR 0.006 0.001 TYR B 94 ARG 0.004 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8013 (tp) cc_final: 0.7566 (mm) REVERT: A 92 PHE cc_start: 0.7777 (t80) cc_final: 0.7564 (t80) REVERT: A 213 ILE cc_start: 0.7516 (tp) cc_final: 0.7098 (tp) REVERT: A 256 LEU cc_start: 0.7757 (tp) cc_final: 0.7479 (tp) REVERT: A 293 LEU cc_start: 0.8056 (mm) cc_final: 0.7675 (mm) REVERT: A 294 MET cc_start: 0.8206 (tmm) cc_final: 0.7689 (tpp) REVERT: B 55 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8148 (mtpp) REVERT: B 168 LEU cc_start: 0.8215 (mt) cc_final: 0.8002 (mt) REVERT: B 201 ILE cc_start: 0.8918 (mt) cc_final: 0.8717 (mt) REVERT: B 228 MET cc_start: 0.6950 (tpp) cc_final: 0.6609 (tpt) REVERT: B 357 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.7046 (m-10) outliers start: 19 outliers final: 13 residues processed: 137 average time/residue: 0.1772 time to fit residues: 32.6622 Evaluate side-chains 132 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 80 optimal weight: 0.0040 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6744 Z= 0.172 Angle : 0.548 5.794 9160 Z= 0.279 Chirality : 0.040 0.141 1080 Planarity : 0.004 0.044 1146 Dihedral : 4.976 24.654 936 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 18.43 % Favored : 79.00 % 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: -3.80 (0.25), residues: 878 helix: -2.34 (0.19), residues: 599 sheet: None (None), residues: 0 loop : -2.52 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 291 HIS 0.002 0.000 HIS A 284 PHE 0.029 0.001 PHE A 95 TYR 0.005 0.001 TYR B 94 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8078 (mt) cc_final: 0.7837 (mp) REVERT: A 84 LEU cc_start: 0.7900 (tp) cc_final: 0.7500 (mm) REVERT: A 213 ILE cc_start: 0.7372 (tp) cc_final: 0.6990 (tp) REVERT: A 294 MET cc_start: 0.8172 (tmm) cc_final: 0.7575 (tpp) REVERT: B 55 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8072 (mtpp) REVERT: B 201 ILE cc_start: 0.8837 (mt) cc_final: 0.8614 (mt) REVERT: B 384 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7451 (pp) outliers start: 17 outliers final: 13 residues processed: 134 average time/residue: 0.1775 time to fit residues: 31.7313 Evaluate side-chains 130 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6744 Z= 0.192 Angle : 0.550 5.536 9160 Z= 0.278 Chirality : 0.041 0.143 1080 Planarity : 0.004 0.044 1146 Dihedral : 4.872 24.514 936 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.17 % Allowed : 20.54 % Favored : 76.28 % 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: -3.45 (0.26), residues: 878 helix: -2.08 (0.20), residues: 611 sheet: None (None), residues: 0 loop : -2.35 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 124 HIS 0.003 0.000 HIS A 284 PHE 0.023 0.001 PHE A 95 TYR 0.005 0.001 TYR B 229 ARG 0.008 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8173 (mt) cc_final: 0.7848 (mp) REVERT: A 84 LEU cc_start: 0.7905 (tp) cc_final: 0.7522 (mm) REVERT: A 213 ILE cc_start: 0.7378 (tp) cc_final: 0.7028 (tp) REVERT: A 294 MET cc_start: 0.8254 (tmm) cc_final: 0.7775 (tpp) REVERT: B 55 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8073 (mtpp) REVERT: B 201 ILE cc_start: 0.8814 (mt) cc_final: 0.8598 (mt) REVERT: B 357 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: B 384 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7343 (pp) outliers start: 21 outliers final: 16 residues processed: 132 average time/residue: 0.2195 time to fit residues: 38.5478 Evaluate side-chains 131 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 70 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.0060 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6744 Z= 0.148 Angle : 0.522 6.405 9160 Z= 0.263 Chirality : 0.040 0.126 1080 Planarity : 0.004 0.049 1146 Dihedral : 4.621 24.126 936 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.02 % Allowed : 19.79 % Favored : 77.19 % 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: 878 helix: -1.83 (0.20), residues: 603 sheet: None (None), residues: 0 loop : -2.16 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 253 HIS 0.002 0.000 HIS A 284 PHE 0.021 0.001 PHE A 95 TYR 0.004 0.001 TYR B 94 ARG 0.010 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.6660 (mtt) cc_final: 0.6399 (tpp) REVERT: A 45 LEU cc_start: 0.8035 (mt) cc_final: 0.7660 (mp) REVERT: A 84 LEU cc_start: 0.7857 (tp) cc_final: 0.7486 (mm) REVERT: A 213 ILE cc_start: 0.7223 (tp) cc_final: 0.6899 (tp) REVERT: A 276 MET cc_start: 0.5164 (mtt) cc_final: 0.4902 (mtt) REVERT: A 294 MET cc_start: 0.8276 (tmm) cc_final: 0.7603 (tpp) REVERT: B 55 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8114 (mtpp) REVERT: B 201 ILE cc_start: 0.8795 (mt) cc_final: 0.8549 (mt) REVERT: B 357 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6897 (m-10) REVERT: B 384 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7272 (pp) outliers start: 20 outliers final: 13 residues processed: 123 average time/residue: 0.1954 time to fit residues: 32.0380 Evaluate side-chains 122 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6744 Z= 0.167 Angle : 0.538 6.860 9160 Z= 0.267 Chirality : 0.041 0.268 1080 Planarity : 0.004 0.037 1146 Dihedral : 4.552 23.530 936 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.02 % Allowed : 20.85 % Favored : 76.13 % 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: -2.88 (0.27), residues: 878 helix: -1.65 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -2.11 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 124 HIS 0.003 0.000 HIS A 284 PHE 0.031 0.001 PHE A 95 TYR 0.005 0.001 TYR B 100 ARG 0.008 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.6683 (mtt) cc_final: 0.6403 (tpp) REVERT: A 45 LEU cc_start: 0.8057 (mt) cc_final: 0.7696 (mp) REVERT: A 84 LEU cc_start: 0.7871 (tp) cc_final: 0.7489 (mm) REVERT: A 148 GLU cc_start: 0.6888 (pp20) cc_final: 0.6400 (pp20) REVERT: A 213 ILE cc_start: 0.7234 (tp) cc_final: 0.6902 (tp) REVERT: A 294 MET cc_start: 0.8317 (tmm) cc_final: 0.7816 (tpp) REVERT: B 55 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8054 (mtpp) REVERT: B 201 ILE cc_start: 0.8765 (mt) cc_final: 0.8508 (mt) REVERT: B 357 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: B 384 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7259 (pp) outliers start: 20 outliers final: 15 residues processed: 127 average time/residue: 0.1873 time to fit residues: 31.8521 Evaluate side-chains 128 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6744 Z= 0.169 Angle : 0.544 7.375 9160 Z= 0.268 Chirality : 0.041 0.272 1080 Planarity : 0.004 0.040 1146 Dihedral : 4.491 23.185 936 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.87 % Allowed : 21.15 % Favored : 75.98 % 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: -2.62 (0.28), residues: 878 helix: -1.46 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -2.01 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 124 HIS 0.002 0.000 HIS A 284 PHE 0.027 0.001 PHE A 95 TYR 0.005 0.001 TYR B 202 ARG 0.008 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.6715 (mtt) cc_final: 0.6457 (tpp) REVERT: A 45 LEU cc_start: 0.8009 (mt) cc_final: 0.7676 (mp) REVERT: A 84 LEU cc_start: 0.7870 (tp) cc_final: 0.7487 (mm) REVERT: A 213 ILE cc_start: 0.7227 (tp) cc_final: 0.6883 (tp) REVERT: A 294 MET cc_start: 0.8335 (tmm) cc_final: 0.7829 (tpp) REVERT: B 55 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8172 (mtpp) REVERT: B 201 ILE cc_start: 0.8824 (mt) cc_final: 0.8559 (mt) REVERT: B 207 GLN cc_start: 0.7785 (pm20) cc_final: 0.7463 (pm20) REVERT: B 357 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6954 (m-10) REVERT: B 384 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7289 (pp) outliers start: 19 outliers final: 14 residues processed: 128 average time/residue: 0.1780 time to fit residues: 30.6606 Evaluate side-chains 126 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6744 Z= 0.176 Angle : 0.547 6.772 9160 Z= 0.268 Chirality : 0.041 0.295 1080 Planarity : 0.004 0.043 1146 Dihedral : 4.466 24.665 936 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.17 % Allowed : 21.00 % Favored : 75.83 % 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: -2.44 (0.28), residues: 878 helix: -1.32 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -1.95 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 124 HIS 0.002 0.000 HIS A 284 PHE 0.026 0.001 PHE A 95 TYR 0.004 0.001 TYR A 419 ARG 0.007 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.6762 (mtt) cc_final: 0.6541 (tpp) REVERT: A 45 LEU cc_start: 0.8063 (mt) cc_final: 0.7683 (mp) REVERT: A 84 LEU cc_start: 0.7901 (tp) cc_final: 0.7498 (mm) REVERT: B 55 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8078 (mtpp) REVERT: B 201 ILE cc_start: 0.8829 (mt) cc_final: 0.8593 (mt) REVERT: B 207 GLN cc_start: 0.7800 (pm20) cc_final: 0.7489 (pm20) REVERT: B 254 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7786 (mp) REVERT: B 357 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6916 (m-10) REVERT: B 384 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7252 (pp) outliers start: 21 outliers final: 15 residues processed: 131 average time/residue: 0.1914 time to fit residues: 34.0482 Evaluate side-chains 131 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6744 Z= 0.186 Angle : 0.558 6.762 9160 Z= 0.275 Chirality : 0.042 0.302 1080 Planarity : 0.004 0.048 1146 Dihedral : 4.464 23.964 936 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.02 % Allowed : 20.85 % Favored : 76.13 % 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: -2.28 (0.28), residues: 878 helix: -1.22 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -1.85 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 124 HIS 0.002 0.000 HIS A 284 PHE 0.025 0.001 PHE A 95 TYR 0.004 0.001 TYR A 419 ARG 0.008 0.000 ARG B 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.6770 (mtt) cc_final: 0.6558 (tpp) REVERT: A 45 LEU cc_start: 0.8065 (mt) cc_final: 0.7687 (mp) REVERT: A 84 LEU cc_start: 0.7955 (tp) cc_final: 0.7535 (mm) REVERT: A 276 MET cc_start: 0.5093 (mtt) cc_final: 0.4887 (mtt) REVERT: A 294 MET cc_start: 0.8237 (tmm) cc_final: 0.7896 (tpp) REVERT: B 55 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7964 (mtpp) REVERT: B 201 ILE cc_start: 0.8799 (mt) cc_final: 0.8539 (mt) REVERT: B 207 GLN cc_start: 0.7736 (pm20) cc_final: 0.7438 (pm20) REVERT: B 254 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7739 (mp) REVERT: B 357 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6930 (m-10) REVERT: B 384 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7217 (pp) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 0.1737 time to fit residues: 29.0208 Evaluate side-chains 128 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 398 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.0770 chunk 64 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 0.2980 chunk 29 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.188660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.170360 restraints weight = 7623.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.172153 restraints weight = 5234.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.174045 restraints weight = 4152.619| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6744 Z= 0.150 Angle : 0.541 6.560 9160 Z= 0.266 Chirality : 0.041 0.288 1080 Planarity : 0.004 0.042 1146 Dihedral : 4.290 23.594 936 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.72 % Allowed : 20.85 % Favored : 76.44 % 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: -1.99 (0.28), residues: 878 helix: -0.98 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -1.79 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 253 HIS 0.002 0.000 HIS A 284 PHE 0.025 0.001 PHE A 95 TYR 0.004 0.001 TYR B 445 ARG 0.007 0.000 ARG B 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1609.85 seconds wall clock time: 29 minutes 7.15 seconds (1747.15 seconds total)