Starting phenix.real_space_refine on Thu Mar 13 11:52:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsp_41597/03_2025/8tsp_41597.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsp_41597/03_2025/8tsp_41597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tsp_41597/03_2025/8tsp_41597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsp_41597/03_2025/8tsp_41597.map" model { file = "/net/cci-nas-00/data/ceres_data/8tsp_41597/03_2025/8tsp_41597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsp_41597/03_2025/8tsp_41597.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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 54 5.16 5 C 5630 2.51 5 N 1548 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8888 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4444 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 13, 'TRANS': 559} Chain: "B" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4444 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 13, 'TRANS': 559} Time building chain proxies: 5.71, per 1000 atoms: 0.64 Number of scatterers: 8888 At special positions: 0 Unit cell: (67.095, 122.475, 136.32, 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 54 16.00 O 1656 8.00 N 1548 7.00 C 5630 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 6 sheets defined 69.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 10 through 21 removed outlier: 4.044A pdb=" N ARG A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 23 through 47 removed outlier: 3.678A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.685A pdb=" N LEU A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 109 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 112 through 119 removed outlier: 4.286A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 163 removed outlier: 3.899A pdb=" N LEU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 213 removed outlier: 3.774A pdb=" N SER A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 224 through 272 Proline residue: A 253 - end of helix removed outlier: 3.681A pdb=" N PHE A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.594A pdb=" N ILE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 323 removed outlier: 3.526A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.634A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 471 Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 512 through 526 Processing helix chain 'A' and resid 538 through 544 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 10 through 21 removed outlier: 4.048A pdb=" N ARG B 14 " --> pdb=" O TRP B 10 " (cutoff:3.500A) Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 23 through 47 removed outlier: 3.674A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.702A pdb=" N LEU B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 109 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 112 through 119 removed outlier: 4.153A pdb=" N PHE B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 163 removed outlier: 3.587A pdb=" N LEU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 213 removed outlier: 3.632A pdb=" N SER B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 224 through 272 Proline residue: B 253 - end of helix removed outlier: 3.661A pdb=" N PHE B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 4.012A pdb=" N THR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 323 removed outlier: 3.538A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 468 through 471 Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 512 through 526 Processing helix chain 'B' and resid 538 through 544 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 570 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366 removed outlier: 6.390A pdb=" N ARG A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THR A 348 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE A 362 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 346 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 342 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE A 344 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 401 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASN A 346 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU A 399 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422 removed outlier: 3.788A pdb=" N ILE A 503 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 422 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 535 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 504 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 558 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLU A 552 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 366 removed outlier: 5.082A pdb=" N ARG B 360 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE B 349 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU B 364 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG B 345 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE B 366 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU B 343 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL B 347 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLU B 397 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 402 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS B 405 " --> pdb=" O MET B 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.726A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP B 505 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 422 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 372 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 547 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 558 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU B 552 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 431 through 432 581 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2781 1.34 - 1.46: 1587 1.46 - 1.58: 4546 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 9018 Sorted by residual: bond pdb=" N VAL B 555 " pdb=" CA VAL B 555 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N ILE B 250 " pdb=" CA ILE B 250 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.09e-02 8.42e+03 9.88e+00 bond pdb=" N ASP B 252 " pdb=" CA ASP B 252 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.67e+00 bond pdb=" N VAL A 551 " pdb=" CA VAL A 551 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.67e+00 bond pdb=" N ILE B 177 " pdb=" CA ILE B 177 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.42e+00 ... (remaining 9013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 12027 2.59 - 5.19: 142 5.19 - 7.78: 15 7.78 - 10.38: 2 10.38 - 12.97: 2 Bond angle restraints: 12188 Sorted by residual: angle pdb=" N ILE B 250 " pdb=" CA ILE B 250 " pdb=" C ILE B 250 " ideal model delta sigma weight residual 113.43 108.13 5.30 1.09e+00 8.42e-01 2.37e+01 angle pdb=" CB MET A 295 " pdb=" CG MET A 295 " pdb=" SD MET A 295 " ideal model delta sigma weight residual 112.70 125.67 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" N ASN A 477 " pdb=" CA ASN A 477 " pdb=" C ASN A 477 " ideal model delta sigma weight residual 111.81 106.25 5.56 1.54e+00 4.22e-01 1.30e+01 angle pdb=" CA ASP A 553 " pdb=" C ASP A 553 " pdb=" O ASP A 553 " ideal model delta sigma weight residual 121.84 117.67 4.17 1.16e+00 7.43e-01 1.29e+01 angle pdb=" N ASN B 477 " pdb=" CA ASN B 477 " pdb=" C ASN B 477 " ideal model delta sigma weight residual 111.81 106.32 5.49 1.54e+00 4.22e-01 1.27e+01 ... (remaining 12183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4718 17.83 - 35.65: 594 35.65 - 53.48: 143 53.48 - 71.31: 29 71.31 - 89.14: 8 Dihedral angle restraints: 5492 sinusoidal: 2178 harmonic: 3314 Sorted by residual: dihedral pdb=" CA ARG B 391 " pdb=" C ARG B 391 " pdb=" N PHE B 392 " pdb=" CA PHE B 392 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER A 249 " pdb=" C SER A 249 " pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP A 471 " pdb=" CB ASP A 471 " pdb=" CG ASP A 471 " pdb=" OD1 ASP A 471 " ideal model delta sinusoidal sigma weight residual -30.00 -87.41 57.41 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1016 0.042 - 0.085: 313 0.085 - 0.127: 86 0.127 - 0.170: 27 0.170 - 0.212: 10 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CA ILE A 556 " pdb=" N ILE A 556 " pdb=" C ILE A 556 " pdb=" CB ILE A 556 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE B 255 " pdb=" N ILE B 255 " pdb=" C ILE B 255 " pdb=" CB ILE B 255 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA ILE B 180 " pdb=" N ILE B 180 " pdb=" C ILE B 180 " pdb=" CB ILE B 180 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 1449 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 186 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C SER A 186 " 0.036 2.00e-02 2.50e+03 pdb=" O SER A 186 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 187 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 184 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C VAL A 184 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL A 184 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 185 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 184 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C VAL B 184 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL B 184 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL B 185 " -0.012 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 788 2.74 - 3.28: 9452 3.28 - 3.82: 14911 3.82 - 4.36: 16760 4.36 - 4.90: 28594 Nonbonded interactions: 70505 Sorted by model distance: nonbonded pdb=" O THR B 9 " pdb=" OG1 THR B 12 " model vdw 2.201 3.040 nonbonded pdb=" O THR A 9 " pdb=" OG1 THR A 12 " model vdw 2.205 3.040 nonbonded pdb=" ND2 ASN A 430 " pdb=" OE1 GLN B 209 " model vdw 2.261 3.120 nonbonded pdb=" NH1 ARG A 102 " pdb=" OD1 ASP B 231 " model vdw 2.283 3.120 nonbonded pdb=" O GLU A 224 " pdb=" OG1 THR A 227 " model vdw 2.299 3.040 ... (remaining 70500 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.600 Find NCS groups from input model: 0.290 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 0.038 9018 Z= 0.278 Angle : 0.752 12.969 12188 Z= 0.470 Chirality : 0.048 0.212 1452 Planarity : 0.005 0.066 1542 Dihedral : 16.525 89.137 3348 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.72 % Allowed : 23.26 % Favored : 76.02 % 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: 0.50 (0.25), residues: 1142 helix: 1.08 (0.20), residues: 714 sheet: 0.37 (0.61), residues: 78 loop : -1.15 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 66 HIS 0.008 0.001 HIS A 214 PHE 0.019 0.002 PHE A 115 TYR 0.015 0.001 TYR A 445 ARG 0.011 0.001 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 295 MET cc_start: 0.5770 (mmm) cc_final: 0.5148 (mtt) REVERT: B 111 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.5796 (mpp) REVERT: B 117 ASP cc_start: 0.5455 (m-30) cc_final: 0.5115 (m-30) REVERT: B 283 THR cc_start: 0.8056 (p) cc_final: 0.7597 (t) REVERT: B 312 MET cc_start: 0.8902 (mmt) cc_final: 0.8416 (mmt) REVERT: B 363 ASN cc_start: 0.5549 (m-40) cc_final: 0.5337 (t0) outliers start: 7 outliers final: 3 residues processed: 155 average time/residue: 0.2484 time to fit residues: 51.6615 Evaluate side-chains 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 356 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN B 107 HIS B 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.165478 restraints weight = 10050.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161777 restraints weight = 14920.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.159982 restraints weight = 16529.093| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9018 Z= 0.277 Angle : 0.627 7.546 12188 Z= 0.331 Chirality : 0.043 0.158 1452 Planarity : 0.004 0.037 1542 Dihedral : 4.515 44.255 1253 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.41 % Allowed : 22.44 % Favored : 73.16 % 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: 1.09 (0.25), residues: 1142 helix: 1.54 (0.19), residues: 728 sheet: 0.41 (0.57), residues: 78 loop : -0.96 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 66 HIS 0.005 0.001 HIS B 107 PHE 0.025 0.002 PHE B 56 TYR 0.010 0.002 TYR A 87 ARG 0.005 0.001 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7717 (tpp) cc_final: 0.7446 (ttm) REVERT: A 291 MET cc_start: 0.7916 (mmm) cc_final: 0.7574 (tmm) REVERT: B 301 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7466 (mp) outliers start: 43 outliers final: 22 residues processed: 176 average time/residue: 0.2172 time to fit residues: 52.5167 Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.0060 chunk 43 optimal weight: 0.4980 chunk 109 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.193947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 141)---------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163770 restraints weight = 10082.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.158972 restraints weight = 10171.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.159371 restraints weight = 9510.309| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9018 Z= 0.164 Angle : 0.523 6.231 12188 Z= 0.279 Chirality : 0.040 0.152 1452 Planarity : 0.004 0.033 1542 Dihedral : 3.993 21.043 1248 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.00 % Allowed : 23.67 % Favored : 72.34 % 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: 1.76 (0.26), residues: 1142 helix: 2.12 (0.20), residues: 716 sheet: 0.59 (0.55), residues: 78 loop : -0.73 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 66 HIS 0.007 0.001 HIS A 214 PHE 0.014 0.001 PHE B 189 TYR 0.009 0.001 TYR A 162 ARG 0.005 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7979 (tpp) cc_final: 0.7382 (ttm) REVERT: B 200 MET cc_start: 0.5687 (OUTLIER) cc_final: 0.5081 (tpt) outliers start: 39 outliers final: 20 residues processed: 172 average time/residue: 0.2303 time to fit residues: 54.0767 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 0.0040 chunk 68 optimal weight: 0.9980 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.185347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.167099 restraints weight = 10052.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162229 restraints weight = 14173.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.160998 restraints weight = 15739.316| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9018 Z= 0.223 Angle : 0.562 5.735 12188 Z= 0.295 Chirality : 0.041 0.146 1452 Planarity : 0.004 0.034 1542 Dihedral : 4.052 22.018 1248 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.12 % Allowed : 23.36 % Favored : 71.52 % 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: 1.82 (0.26), residues: 1142 helix: 2.08 (0.20), residues: 718 sheet: 0.67 (0.55), residues: 78 loop : -0.52 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 66 HIS 0.004 0.001 HIS A 214 PHE 0.018 0.002 PHE A 56 TYR 0.016 0.001 TYR B 130 ARG 0.003 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 1.040 Fit side-chains REVERT: A 44 MET cc_start: 0.8076 (tpp) cc_final: 0.7452 (ttm) REVERT: A 127 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7397 (ttm-80) REVERT: B 200 MET cc_start: 0.5634 (tpt) cc_final: 0.5092 (tpt) REVERT: B 301 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7357 (mp) outliers start: 50 outliers final: 35 residues processed: 174 average time/residue: 0.2204 time to fit residues: 52.6640 Evaluate side-chains 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 43 optimal weight: 0.0070 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS B 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.195804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157433 restraints weight = 10015.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.158411 restraints weight = 8519.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.159180 restraints weight = 7664.306| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9018 Z= 0.192 Angle : 0.553 7.183 12188 Z= 0.289 Chirality : 0.040 0.147 1452 Planarity : 0.003 0.033 1542 Dihedral : 4.020 21.642 1248 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.71 % Allowed : 24.18 % Favored : 71.11 % 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: 1.90 (0.26), residues: 1142 helix: 2.13 (0.20), residues: 718 sheet: 0.69 (0.55), residues: 78 loop : -0.47 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 66 HIS 0.002 0.001 HIS A 107 PHE 0.017 0.001 PHE B 189 TYR 0.013 0.001 TYR B 130 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 1.029 Fit side-chains REVERT: A 44 MET cc_start: 0.8049 (tpp) cc_final: 0.7345 (ttm) REVERT: A 127 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7178 (ttm-80) REVERT: A 301 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7617 (mp) REVERT: B 200 MET cc_start: 0.5534 (tpt) cc_final: 0.5066 (tpt) REVERT: B 301 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7186 (mp) outliers start: 46 outliers final: 34 residues processed: 163 average time/residue: 0.2252 time to fit residues: 50.0142 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 GLN B 405 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.186565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.163011 restraints weight = 10364.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157146 restraints weight = 14699.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.154412 restraints weight = 15254.404| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9018 Z= 0.199 Angle : 0.562 12.413 12188 Z= 0.290 Chirality : 0.041 0.143 1452 Planarity : 0.003 0.033 1542 Dihedral : 4.037 21.705 1248 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.12 % Allowed : 24.08 % Favored : 70.80 % 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: 1.78 (0.26), residues: 1142 helix: 2.00 (0.19), residues: 730 sheet: 0.45 (0.56), residues: 80 loop : -0.45 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 66 HIS 0.009 0.001 HIS B 405 PHE 0.018 0.001 PHE B 189 TYR 0.012 0.001 TYR B 162 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8171 (tpp) cc_final: 0.7440 (ttm) REVERT: A 75 MET cc_start: 0.7763 (tpp) cc_final: 0.7439 (mmm) REVERT: A 127 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7289 (ttm-80) REVERT: A 301 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 200 MET cc_start: 0.5633 (tpt) cc_final: 0.5121 (tpt) REVERT: B 301 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7060 (mp) outliers start: 50 outliers final: 37 residues processed: 171 average time/residue: 0.2283 time to fit residues: 52.5160 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 491 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.192654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153513 restraints weight = 10371.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154998 restraints weight = 8657.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155719 restraints weight = 7746.169| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9018 Z= 0.192 Angle : 0.559 8.234 12188 Z= 0.287 Chirality : 0.040 0.145 1452 Planarity : 0.004 0.045 1542 Dihedral : 4.017 21.611 1248 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.82 % Allowed : 24.28 % Favored : 70.90 % 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: 1.78 (0.26), residues: 1142 helix: 2.00 (0.19), residues: 734 sheet: 0.36 (0.60), residues: 70 loop : -0.42 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 66 HIS 0.005 0.001 HIS A 405 PHE 0.018 0.001 PHE B 189 TYR 0.014 0.001 TYR A 162 ARG 0.004 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8165 (tpp) cc_final: 0.7285 (ttm) REVERT: A 75 MET cc_start: 0.7663 (tpp) cc_final: 0.7392 (mmm) REVERT: A 127 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7279 (ttm-80) REVERT: A 301 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 200 MET cc_start: 0.5808 (tpt) cc_final: 0.5334 (tpt) REVERT: B 301 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7128 (mp) outliers start: 47 outliers final: 37 residues processed: 159 average time/residue: 0.2298 time to fit residues: 49.7253 Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 8.9990 chunk 43 optimal weight: 0.0980 chunk 83 optimal weight: 0.0030 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN ** B 430 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 = 0.4055 r_free = 0.4055 target = 0.184814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160799 restraints weight = 10491.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153706 restraints weight = 14457.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.151890 restraints weight = 15202.511| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9018 Z= 0.191 Angle : 0.563 10.944 12188 Z= 0.287 Chirality : 0.041 0.143 1452 Planarity : 0.004 0.046 1542 Dihedral : 4.018 21.628 1248 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.51 % Allowed : 24.59 % Favored : 70.90 % 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: 1.83 (0.26), residues: 1142 helix: 2.02 (0.19), residues: 734 sheet: 0.38 (0.61), residues: 70 loop : -0.37 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 66 HIS 0.006 0.001 HIS A 405 PHE 0.018 0.001 PHE B 189 TYR 0.012 0.001 TYR A 162 ARG 0.004 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8153 (tpp) cc_final: 0.7522 (tmm) REVERT: A 301 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7686 (mp) REVERT: B 200 MET cc_start: 0.5814 (tpt) cc_final: 0.5335 (tpt) REVERT: B 301 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7101 (mp) outliers start: 44 outliers final: 36 residues processed: 158 average time/residue: 0.2148 time to fit residues: 47.2324 Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 0.0470 chunk 102 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 0.0370 chunk 49 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.195917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.165907 restraints weight = 10352.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.163672 restraints weight = 18675.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165501 restraints weight = 14339.885| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9018 Z= 0.153 Angle : 0.562 10.444 12188 Z= 0.283 Chirality : 0.040 0.146 1452 Planarity : 0.004 0.041 1542 Dihedral : 3.937 20.620 1248 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.07 % Allowed : 26.84 % Favored : 70.08 % 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: 2.06 (0.26), residues: 1142 helix: 2.18 (0.20), residues: 734 sheet: 0.87 (0.61), residues: 66 loop : -0.33 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 66 HIS 0.003 0.001 HIS A 405 PHE 0.019 0.001 PHE B 189 TYR 0.017 0.001 TYR A 162 ARG 0.006 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8033 (tpp) cc_final: 0.7800 (ttp) REVERT: A 578 MET cc_start: 0.2947 (tmm) cc_final: 0.2022 (tpp) REVERT: B 200 MET cc_start: 0.5727 (tpt) cc_final: 0.5453 (tpt) REVERT: B 301 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6943 (mp) outliers start: 30 outliers final: 25 residues processed: 154 average time/residue: 0.2121 time to fit residues: 45.7194 Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 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 = 0.4042 r_free = 0.4042 target = 0.182591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.165240 restraints weight = 10308.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.161129 restraints weight = 13993.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.158357 restraints weight = 16750.857| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9018 Z= 0.285 Angle : 0.674 10.207 12188 Z= 0.334 Chirality : 0.043 0.138 1452 Planarity : 0.004 0.057 1542 Dihedral : 4.215 22.405 1248 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.18 % Allowed : 26.64 % Favored : 70.18 % 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: 1.72 (0.26), residues: 1142 helix: 1.90 (0.20), residues: 730 sheet: 0.43 (0.57), residues: 80 loop : -0.32 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 66 HIS 0.005 0.001 HIS A 405 PHE 0.018 0.002 PHE B 189 TYR 0.011 0.002 TYR B 410 ARG 0.005 0.000 ARG B 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8063 (tpp) cc_final: 0.7569 (tmm) REVERT: A 108 MET cc_start: 0.8527 (tpp) cc_final: 0.8292 (ttm) REVERT: A 578 MET cc_start: 0.2831 (tmm) cc_final: 0.1912 (tpp) REVERT: B 301 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7272 (mp) outliers start: 31 outliers final: 27 residues processed: 148 average time/residue: 0.2218 time to fit residues: 45.9879 Evaluate side-chains 146 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.191607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.178660 restraints weight = 10109.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175036 restraints weight = 16877.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.174735 restraints weight = 18778.607| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9018 Z= 0.193 Angle : 0.616 10.664 12188 Z= 0.305 Chirality : 0.041 0.184 1452 Planarity : 0.004 0.052 1542 Dihedral : 4.131 22.801 1248 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.07 % Allowed : 26.84 % Favored : 70.08 % 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: 1.88 (0.26), residues: 1142 helix: 2.02 (0.19), residues: 730 sheet: 0.43 (0.56), residues: 80 loop : -0.25 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 66 HIS 0.002 0.001 HIS A 405 PHE 0.019 0.001 PHE B 189 TYR 0.009 0.001 TYR B 445 ARG 0.005 0.000 ARG B 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2904.56 seconds wall clock time: 51 minutes 35.02 seconds (3095.02 seconds total)