Starting phenix.real_space_refine on Thu Jul 2 16:54:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x47_66532/07_2026/9x47_66532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x47_66532/07_2026/9x47_66532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x47_66532/07_2026/9x47_66532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x47_66532/07_2026/9x47_66532.map" model { file = "/net/cci-nas-00/data/ceres_data/9x47_66532/07_2026/9x47_66532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x47_66532/07_2026/9x47_66532.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 5830 2.51 5 N 1523 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9041 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4514 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain: "B" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4527 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 13, 'TRANS': 556} Time building chain proxies: 1.56, per 1000 atoms: 0.17 Number of scatterers: 9041 At special positions: 0 Unit cell: (74.304, 99.072, 136.224, 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 1648 8.00 N 1523 7.00 C 5830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 420.7 milliseconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 72.3% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.994A pdb=" N LEU A 5 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 6 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 7 " --> pdb=" O LEU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 42 Proline residue: A 19 - end of helix Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 48 through 98 removed outlier: 3.599A pdb=" N VAL A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.526A pdb=" N GLY A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 134 removed outlier: 4.515A pdb=" N ASP A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 155 through 201 removed outlier: 3.685A pdb=" N PHE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 210 through 237 removed outlier: 3.780A pdb=" N ILE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 265 Processing helix chain 'A' and resid 268 through 280 Processing helix chain 'A' and resid 281 through 311 removed outlier: 4.067A pdb=" N GLU A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 424 through 430 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 473 through 488 removed outlier: 4.566A pdb=" N ARG A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.557A pdb=" N LEU A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 560 through 572 removed outlier: 3.615A pdb=" N GLN A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 20 through 51 removed outlier: 3.710A pdb=" N PHE B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 56 through 106 Proline residue: B 83 - end of helix removed outlier: 3.902A pdb=" N SER B 92 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 117 through 161 removed outlier: 4.390A pdb=" N ASP B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE B 144 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 207 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 208 through 209 No H-bonds generated for 'chain 'B' and resid 208 through 209' Processing helix chain 'B' and resid 210 through 211 No H-bonds generated for 'chain 'B' and resid 210 through 211' Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 219 through 247 removed outlier: 3.806A pdb=" N MET B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 240 " --> pdb=" O ASN B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 273 Processing helix chain 'B' and resid 278 through 321 removed outlier: 4.182A pdb=" N THR B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Proline residue: B 295 - end of helix removed outlier: 4.927A pdb=" N SER B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 417 Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 444 through 455 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.606A pdb=" N ILE B 492 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 559 through 567 removed outlier: 3.696A pdb=" N LYS B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 355 removed outlier: 5.240A pdb=" N GLN A 351 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE A 340 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A 355 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP A 336 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE A 335 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR A 392 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS A 337 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER A 390 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 413 removed outlier: 6.452A pdb=" N ALA A 411 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP A 496 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 413 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 493 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 495 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 363 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY A 364 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU A 542 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 366 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 549 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASP A 543 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA4, first strand: chain 'B' and resid 358 through 364 removed outlier: 5.845A pdb=" N VAL B 347 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER B 362 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 345 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 364 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN B 343 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 347 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS B 396 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 418 through 420 removed outlier: 6.370A pdb=" N GLY B 419 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASP B 503 " --> pdb=" O GLY B 419 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 500 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 372 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N MET B 549 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 374 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 546 " --> pdb=" O HIS B 557 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 548 " --> pdb=" O VAL B 555 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1788 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: 1.36 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2923 1.34 - 1.46: 1568 1.46 - 1.58: 4632 1.58 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 9200 Sorted by residual: bond pdb=" CG1 ILE A 526 " pdb=" CD1 ILE A 526 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.46e-01 bond pdb=" CB MET A 34 " pdb=" CG MET A 34 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.19e-01 bond pdb=" CB ILE B 489 " pdb=" CG2 ILE B 489 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.02e-01 bond pdb=" C ILE A 139 " pdb=" O ILE A 139 " ideal model delta sigma weight residual 1.237 1.228 0.009 1.12e-02 7.97e+03 6.04e-01 bond pdb=" CG LEU A 275 " pdb=" CD1 LEU A 275 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.61e-01 ... (remaining 9195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 12235 1.46 - 2.93: 179 2.93 - 4.39: 28 4.39 - 5.86: 16 5.86 - 7.32: 3 Bond angle restraints: 12461 Sorted by residual: angle pdb=" C SER A 522 " pdb=" N LEU A 523 " pdb=" CA LEU A 523 " ideal model delta sigma weight residual 121.56 125.53 -3.97 1.56e+00 4.11e-01 6.47e+00 angle pdb=" CB MET A 147 " pdb=" CG MET A 147 " pdb=" SD MET A 147 " ideal model delta sigma weight residual 112.70 119.58 -6.88 3.00e+00 1.11e-01 5.26e+00 angle pdb=" C ASN A 396 " pdb=" N GLN A 397 " pdb=" CA GLN A 397 " ideal model delta sigma weight residual 121.54 125.79 -4.25 1.91e+00 2.74e-01 4.94e+00 angle pdb=" N GLU B 335 " pdb=" CA GLU B 335 " pdb=" CB GLU B 335 " ideal model delta sigma weight residual 113.65 110.68 2.97 1.47e+00 4.63e-01 4.10e+00 angle pdb=" N ASN A 248 " pdb=" CA ASN A 248 " pdb=" C ASN A 248 " ideal model delta sigma weight residual 111.36 113.54 -2.18 1.09e+00 8.42e-01 4.02e+00 ... (remaining 12456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5041 17.97 - 35.94: 426 35.94 - 53.91: 77 53.91 - 71.88: 8 71.88 - 89.85: 7 Dihedral angle restraints: 5559 sinusoidal: 2228 harmonic: 3331 Sorted by residual: dihedral pdb=" CA ILE B 533 " pdb=" C ILE B 533 " pdb=" N ALA B 534 " pdb=" CA ALA B 534 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP B 393 " pdb=" CB ASP B 393 " pdb=" CG ASP B 393 " pdb=" OD1 ASP B 393 " ideal model delta sinusoidal sigma weight residual -30.00 -82.70 52.70 1 2.00e+01 2.50e-03 9.45e+00 dihedral pdb=" CG ARG A 132 " pdb=" CD ARG A 132 " pdb=" NE ARG A 132 " pdb=" CZ ARG A 132 " ideal model delta sinusoidal sigma weight residual -90.00 -131.48 41.48 2 1.50e+01 4.44e-03 9.36e+00 ... (remaining 5556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 892 0.028 - 0.055: 390 0.055 - 0.083: 126 0.083 - 0.111: 48 0.111 - 0.139: 17 Chirality restraints: 1473 Sorted by residual: chirality pdb=" CA PHE B 493 " pdb=" N PHE B 493 " pdb=" C PHE B 493 " pdb=" CB PHE B 493 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 533 " pdb=" N ILE B 533 " pdb=" C ILE B 533 " pdb=" CB ILE B 533 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CB VAL B 302 " pdb=" CA VAL B 302 " pdb=" CG1 VAL B 302 " pdb=" CG2 VAL B 302 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1470 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 41 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" CG ASP A 41 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP A 41 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 41 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 342 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 343 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 343 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 343 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 493 " -0.011 2.00e-02 2.50e+03 8.96e-03 1.40e+00 pdb=" CG PHE B 493 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 493 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 493 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 493 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 493 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 493 " 0.001 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1646 2.77 - 3.30: 9229 3.30 - 3.83: 15391 3.83 - 4.37: 17493 4.37 - 4.90: 31034 Nonbonded interactions: 74793 Sorted by model distance: nonbonded pdb=" OD1 ASP B 458 " pdb=" OH TYR B 468 " model vdw 2.234 3.040 nonbonded pdb=" O LEU A 557 " pdb=" NE2 GLN A 564 " model vdw 2.274 3.120 nonbonded pdb=" OH TYR A 504 " pdb=" NE2 GLN A 570 " model vdw 2.293 3.120 nonbonded pdb=" NH1 ARG B 12 " pdb=" OD1 ASP B 321 " model vdw 2.308 3.120 nonbonded pdb=" O THR A 423 " pdb=" OG SER A 426 " model vdw 2.317 3.040 ... (remaining 74788 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 2.190 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.003 0.034 9200 Z= 0.127 Angle : 0.487 7.324 12461 Z= 0.258 Chirality : 0.038 0.139 1473 Planarity : 0.003 0.032 1570 Dihedral : 13.620 89.848 3405 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.26), residues: 1138 helix: 2.20 (0.19), residues: 781 sheet: -1.70 (0.67), residues: 67 loop : -0.46 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 512 TYR 0.016 0.001 TYR B 190 PHE 0.020 0.001 PHE B 493 TRP 0.007 0.001 TRP A 228 HIS 0.004 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9200) covalent geometry : angle 0.48685 / 0.26 (12461) hydrogen bonds : bond 0.13381 / 9.10 ( 612) hydrogen bonds : angle 4.70169 / 3.41 ( 1788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.236 Fit side-chains REVERT: A 105 ASP cc_start: 0.7446 (m-30) cc_final: 0.7191 (m-30) REVERT: A 175 ARG cc_start: 0.7005 (mtt180) cc_final: 0.6786 (mpt180) REVERT: A 568 TYR cc_start: 0.8160 (t80) cc_final: 0.7726 (t80) REVERT: B 31 THR cc_start: 0.8538 (t) cc_final: 0.8330 (m) REVERT: B 116 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7456 (mm-40) REVERT: B 159 ARG cc_start: 0.6434 (ttt180) cc_final: 0.5436 (ttp80) REVERT: B 171 MET cc_start: 0.8348 (tpp) cc_final: 0.7555 (mmm) REVERT: B 346 HIS cc_start: 0.8153 (m-70) cc_final: 0.7852 (m-70) REVERT: B 395 ASP cc_start: 0.7550 (m-30) cc_final: 0.7195 (m-30) REVERT: B 495 ASN cc_start: 0.7229 (t0) cc_final: 0.5719 (p0) REVERT: B 512 ARG cc_start: 0.7408 (ptp90) cc_final: 0.6445 (tpt170) REVERT: B 525 MET cc_start: 0.8010 (mtm) cc_final: 0.7679 (mtm) REVERT: B 562 GLN cc_start: 0.7443 (mt0) cc_final: 0.6651 (tt0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0952 time to fit residues: 21.2511 Evaluate side-chains 112 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN B 215 GLN B 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109257 restraints weight = 11260.687| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.56 r_work: 0.3148 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9200 Z= 0.139 Angle : 0.516 7.823 12461 Z= 0.263 Chirality : 0.039 0.143 1473 Planarity : 0.004 0.031 1570 Dihedral : 3.520 17.484 1233 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.91 % Allowed : 5.74 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.26), residues: 1138 helix: 2.12 (0.19), residues: 789 sheet: -1.45 (0.76), residues: 57 loop : -0.62 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 565 TYR 0.012 0.001 TYR B 260 PHE 0.012 0.001 PHE B 493 TRP 0.008 0.001 TRP A 228 HIS 0.002 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9200) covalent geometry : angle 0.51624 / 0.26 (12461) hydrogen bonds : bond 0.04293 / 2.90 ( 612) hydrogen bonds : angle 3.81183 / 2.77 ( 1788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.342 Fit side-chains REVERT: A 175 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7798 (mpt180) REVERT: A 423 THR cc_start: 0.8454 (p) cc_final: 0.8154 (t) REVERT: A 568 TYR cc_start: 0.8390 (t80) cc_final: 0.8072 (t80) REVERT: A 570 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8325 (tp40) REVERT: B 116 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7809 (mm-40) REVERT: B 159 ARG cc_start: 0.7195 (ttt180) cc_final: 0.6428 (ttp80) REVERT: B 171 MET cc_start: 0.8701 (tpp) cc_final: 0.8040 (mmm) REVERT: B 346 HIS cc_start: 0.8557 (m-70) cc_final: 0.8347 (m-70) REVERT: B 395 ASP cc_start: 0.7560 (m-30) cc_final: 0.7332 (m-30) REVERT: B 495 ASN cc_start: 0.7675 (t0) cc_final: 0.6679 (p0) REVERT: B 512 ARG cc_start: 0.7512 (ptp90) cc_final: 0.6803 (tpt170) REVERT: B 525 MET cc_start: 0.8563 (mtm) cc_final: 0.8207 (mtm) REVERT: B 562 GLN cc_start: 0.7789 (mt0) cc_final: 0.6970 (tt0) outliers start: 9 outliers final: 6 residues processed: 124 average time/residue: 0.0795 time to fit residues: 14.0645 Evaluate side-chains 111 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.151425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121844 restraints weight = 11935.042| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.03 r_work: 0.3385 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9200 Z= 0.181 Angle : 0.530 7.798 12461 Z= 0.269 Chirality : 0.040 0.150 1473 Planarity : 0.004 0.033 1570 Dihedral : 3.590 19.393 1233 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.11 % Allowed : 7.75 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.25), residues: 1138 helix: 1.94 (0.18), residues: 791 sheet: -1.58 (0.76), residues: 57 loop : -0.76 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.011 0.001 TYR B 260 PHE 0.028 0.001 PHE A 453 TRP 0.008 0.001 TRP A 228 HIS 0.005 0.001 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 9200) covalent geometry : angle 0.52980 / 0.27 (12461) hydrogen bonds : bond 0.04219 / 2.82 ( 612) hydrogen bonds : angle 3.81988 / 2.79 ( 1788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.219 Fit side-chains REVERT: A 34 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.9095 (mmm) REVERT: A 175 ARG cc_start: 0.8166 (mtt180) cc_final: 0.7772 (mpt180) REVERT: A 423 THR cc_start: 0.8313 (p) cc_final: 0.7995 (t) REVERT: A 568 TYR cc_start: 0.8470 (t80) cc_final: 0.8071 (t80) REVERT: B 86 TYR cc_start: 0.8206 (m-10) cc_final: 0.7750 (m-10) REVERT: B 116 GLN cc_start: 0.8556 (mm-40) cc_final: 0.7900 (mm-40) REVERT: B 159 ARG cc_start: 0.7267 (ttt180) cc_final: 0.5691 (tpt-90) REVERT: B 171 MET cc_start: 0.8792 (tpp) cc_final: 0.8052 (mmm) REVERT: B 346 HIS cc_start: 0.8566 (m-70) cc_final: 0.8355 (m-70) REVERT: B 395 ASP cc_start: 0.7732 (m-30) cc_final: 0.7447 (m-30) REVERT: B 512 ARG cc_start: 0.7604 (ptp90) cc_final: 0.6791 (tpt170) REVERT: B 562 GLN cc_start: 0.7843 (mt0) cc_final: 0.6919 (tt0) outliers start: 11 outliers final: 7 residues processed: 121 average time/residue: 0.0912 time to fit residues: 15.5629 Evaluate side-chains 115 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.152671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123100 restraints weight = 12028.779| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.04 r_work: 0.3403 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9200 Z= 0.138 Angle : 0.491 7.838 12461 Z= 0.249 Chirality : 0.038 0.145 1473 Planarity : 0.003 0.032 1570 Dihedral : 3.592 19.301 1233 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.31 % Allowed : 9.87 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1138 helix: 2.00 (0.18), residues: 792 sheet: -1.44 (0.78), residues: 55 loop : -0.79 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 407 TYR 0.010 0.001 TYR B 260 PHE 0.025 0.001 PHE A 453 TRP 0.008 0.001 TRP A 228 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9200) covalent geometry : angle 0.49078 / 0.25 (12461) hydrogen bonds : bond 0.03938 / 2.62 ( 612) hydrogen bonds : angle 3.71926 / 2.72 ( 1788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.203 Fit side-chains REVERT: A 175 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7785 (mpt180) REVERT: A 423 THR cc_start: 0.8192 (p) cc_final: 0.7887 (t) REVERT: A 445 LEU cc_start: 0.7938 (mt) cc_final: 0.7701 (mt) REVERT: A 568 TYR cc_start: 0.8488 (t80) cc_final: 0.8122 (t80) REVERT: B 86 TYR cc_start: 0.8130 (m-10) cc_final: 0.7856 (m-10) REVERT: B 116 GLN cc_start: 0.8560 (mm-40) cc_final: 0.7914 (mm-40) REVERT: B 159 ARG cc_start: 0.7218 (ttt180) cc_final: 0.5684 (tpt-90) REVERT: B 171 MET cc_start: 0.8802 (tpp) cc_final: 0.8142 (mmm) REVERT: B 346 HIS cc_start: 0.8449 (m-70) cc_final: 0.8239 (m-70) REVERT: B 492 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8345 (mp) REVERT: B 512 ARG cc_start: 0.7558 (ptp90) cc_final: 0.6738 (tpt170) REVERT: B 562 GLN cc_start: 0.7841 (mt0) cc_final: 0.6924 (tt0) outliers start: 13 outliers final: 9 residues processed: 125 average time/residue: 0.0871 time to fit residues: 15.3456 Evaluate side-chains 119 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 GLN B 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122627 restraints weight = 11955.184| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.02 r_work: 0.3407 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9200 Z= 0.135 Angle : 0.489 7.993 12461 Z= 0.247 Chirality : 0.038 0.152 1473 Planarity : 0.003 0.034 1570 Dihedral : 3.555 18.745 1233 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.41 % Allowed : 10.88 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.25), residues: 1138 helix: 2.04 (0.18), residues: 792 sheet: -1.58 (0.77), residues: 55 loop : -0.76 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.009 0.001 TYR B 260 PHE 0.027 0.001 PHE A 453 TRP 0.008 0.001 TRP A 228 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 9200) covalent geometry : angle 0.48902 / 0.25 (12461) hydrogen bonds : bond 0.03875 / 2.60 ( 612) hydrogen bonds : angle 3.69002 / 2.72 ( 1788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.325 Fit side-chains REVERT: A 175 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7782 (mpt180) REVERT: A 423 THR cc_start: 0.8198 (p) cc_final: 0.7961 (t) REVERT: A 445 LEU cc_start: 0.8013 (mt) cc_final: 0.7760 (mt) REVERT: A 568 TYR cc_start: 0.8487 (t80) cc_final: 0.8085 (t80) REVERT: B 86 TYR cc_start: 0.8125 (m-10) cc_final: 0.7824 (m-10) REVERT: B 116 GLN cc_start: 0.8543 (mm-40) cc_final: 0.7900 (mm-40) REVERT: B 159 ARG cc_start: 0.7247 (ttt180) cc_final: 0.5804 (tpt-90) REVERT: B 171 MET cc_start: 0.8808 (tpp) cc_final: 0.8104 (mmm) REVERT: B 346 HIS cc_start: 0.8447 (m-70) cc_final: 0.8239 (m-70) REVERT: B 492 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 512 ARG cc_start: 0.7673 (ptp90) cc_final: 0.6819 (tpt170) REVERT: B 525 MET cc_start: 0.8605 (mtm) cc_final: 0.8285 (mtm) REVERT: B 562 GLN cc_start: 0.7884 (mt0) cc_final: 0.6965 (tt0) outliers start: 14 outliers final: 9 residues processed: 125 average time/residue: 0.0955 time to fit residues: 16.7268 Evaluate side-chains 119 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 82 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.153191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123594 restraints weight = 11929.674| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.02 r_work: 0.3421 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9200 Z= 0.117 Angle : 0.482 7.906 12461 Z= 0.242 Chirality : 0.038 0.150 1473 Planarity : 0.003 0.035 1570 Dihedral : 3.529 18.092 1233 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.71 % Allowed : 11.78 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.25), residues: 1138 helix: 2.15 (0.18), residues: 788 sheet: -1.62 (0.76), residues: 55 loop : -0.66 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.009 0.001 TYR B 260 PHE 0.027 0.001 PHE A 453 TRP 0.007 0.001 TRP A 228 HIS 0.002 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9200) covalent geometry : angle 0.48170 / 0.24 (12461) hydrogen bonds : bond 0.03768 / 2.52 ( 612) hydrogen bonds : angle 3.62595 / 2.67 ( 1788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.324 Fit side-chains REVERT: A 175 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7774 (mpt180) REVERT: A 423 THR cc_start: 0.8110 (p) cc_final: 0.7878 (t) REVERT: A 445 LEU cc_start: 0.7945 (mt) cc_final: 0.7683 (mt) REVERT: A 447 MET cc_start: 0.7764 (mtm) cc_final: 0.7395 (mtm) REVERT: A 463 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 470 ARG cc_start: 0.8099 (ptt90) cc_final: 0.7872 (ptt90) REVERT: A 568 TYR cc_start: 0.8482 (t80) cc_final: 0.8086 (t80) REVERT: B 86 TYR cc_start: 0.8067 (m-10) cc_final: 0.7822 (m-10) REVERT: B 116 GLN cc_start: 0.8522 (mm-40) cc_final: 0.7887 (mm-40) REVERT: B 159 ARG cc_start: 0.7231 (ttt180) cc_final: 0.5819 (tpt-90) REVERT: B 171 MET cc_start: 0.8790 (tpp) cc_final: 0.8082 (mmm) REVERT: B 492 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8211 (mp) REVERT: B 512 ARG cc_start: 0.7663 (ptp90) cc_final: 0.6806 (tpt170) REVERT: B 525 MET cc_start: 0.8626 (mtm) cc_final: 0.8261 (mtm) REVERT: B 562 GLN cc_start: 0.7883 (mt0) cc_final: 0.6962 (tt0) outliers start: 17 outliers final: 10 residues processed: 133 average time/residue: 0.0938 time to fit residues: 17.2877 Evaluate side-chains 125 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113823 restraints weight = 12005.440| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.05 r_work: 0.3299 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9200 Z= 0.130 Angle : 0.498 8.801 12461 Z= 0.249 Chirality : 0.038 0.163 1473 Planarity : 0.003 0.035 1570 Dihedral : 3.545 18.150 1233 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.51 % Allowed : 12.59 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.25), residues: 1138 helix: 2.14 (0.18), residues: 788 sheet: -1.61 (0.77), residues: 55 loop : -0.68 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 390 TYR 0.009 0.001 TYR B 260 PHE 0.028 0.001 PHE A 453 TRP 0.008 0.001 TRP A 228 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9200) covalent geometry : angle 0.49826 / 0.25 (12461) hydrogen bonds : bond 0.03802 / 2.55 ( 612) hydrogen bonds : angle 3.64432 / 2.68 ( 1788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.353 Fit side-chains REVERT: A 175 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7712 (mpt180) REVERT: A 423 THR cc_start: 0.8134 (p) cc_final: 0.7876 (t) REVERT: A 445 LEU cc_start: 0.7963 (mt) cc_final: 0.7717 (mt) REVERT: A 447 MET cc_start: 0.7825 (mtm) cc_final: 0.7521 (mtm) REVERT: A 463 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 470 ARG cc_start: 0.8078 (ptt90) cc_final: 0.7860 (ptt90) REVERT: A 568 TYR cc_start: 0.8527 (t80) cc_final: 0.8094 (t80) REVERT: B 86 TYR cc_start: 0.8014 (m-10) cc_final: 0.7617 (m-10) REVERT: B 116 GLN cc_start: 0.8433 (mm-40) cc_final: 0.7759 (mm-40) REVERT: B 159 ARG cc_start: 0.7203 (ttt180) cc_final: 0.5726 (tpt-90) REVERT: B 171 MET cc_start: 0.8876 (tpp) cc_final: 0.8192 (mmm) REVERT: B 345 ASP cc_start: 0.8022 (t0) cc_final: 0.7783 (t0) REVERT: B 492 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8092 (mp) REVERT: B 512 ARG cc_start: 0.7600 (ptp90) cc_final: 0.6698 (tpt170) REVERT: B 562 GLN cc_start: 0.7781 (mt0) cc_final: 0.6901 (tt0) outliers start: 15 outliers final: 10 residues processed: 124 average time/residue: 0.0965 time to fit residues: 16.7472 Evaluate side-chains 120 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 59 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 46 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115240 restraints weight = 11916.347| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.05 r_work: 0.3318 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9200 Z= 0.110 Angle : 0.489 7.764 12461 Z= 0.245 Chirality : 0.038 0.161 1473 Planarity : 0.003 0.035 1570 Dihedral : 3.516 18.225 1233 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.31 % Allowed : 12.99 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.25), residues: 1138 helix: 2.23 (0.18), residues: 789 sheet: -1.57 (0.77), residues: 55 loop : -0.65 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 390 TYR 0.008 0.001 TYR B 260 PHE 0.027 0.001 PHE A 453 TRP 0.007 0.001 TRP A 228 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9200) covalent geometry : angle 0.48910 / 0.24 (12461) hydrogen bonds : bond 0.03691 / 2.52 ( 612) hydrogen bonds : angle 3.60656 / 2.66 ( 1788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.344 Fit side-chains REVERT: A 175 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7704 (mpt180) REVERT: A 445 LEU cc_start: 0.7891 (mt) cc_final: 0.7636 (mt) REVERT: A 447 MET cc_start: 0.7758 (mtm) cc_final: 0.7521 (mtm) REVERT: A 470 ARG cc_start: 0.8047 (ptt90) cc_final: 0.7847 (ptt90) REVERT: A 568 TYR cc_start: 0.8541 (t80) cc_final: 0.8118 (t80) REVERT: B 86 TYR cc_start: 0.8006 (m-10) cc_final: 0.7570 (m-10) REVERT: B 116 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7738 (mm-40) REVERT: B 159 ARG cc_start: 0.7189 (ttt180) cc_final: 0.5722 (tpt-90) REVERT: B 171 MET cc_start: 0.8879 (tpp) cc_final: 0.8210 (mmm) REVERT: B 345 ASP cc_start: 0.7998 (t0) cc_final: 0.7651 (t0) REVERT: B 492 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 512 ARG cc_start: 0.7588 (ptp90) cc_final: 0.6662 (tpt170) REVERT: B 562 GLN cc_start: 0.7771 (mt0) cc_final: 0.6889 (tt0) outliers start: 13 outliers final: 10 residues processed: 124 average time/residue: 0.1056 time to fit residues: 18.1288 Evaluate side-chains 123 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 92 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114923 restraints weight = 11975.217| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.04 r_work: 0.3305 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9200 Z= 0.125 Angle : 0.499 8.293 12461 Z= 0.249 Chirality : 0.038 0.152 1473 Planarity : 0.003 0.035 1570 Dihedral : 3.517 18.119 1233 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 13.09 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.25), residues: 1138 helix: 2.19 (0.18), residues: 789 sheet: -1.52 (0.78), residues: 55 loop : -0.60 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 390 TYR 0.009 0.001 TYR B 260 PHE 0.027 0.001 PHE A 453 TRP 0.008 0.001 TRP A 228 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9200) covalent geometry : angle 0.49919 / 0.25 (12461) hydrogen bonds : bond 0.03749 / 2.55 ( 612) hydrogen bonds : angle 3.62243 / 2.68 ( 1788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.433 Fit side-chains REVERT: A 175 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7712 (mpt180) REVERT: A 445 LEU cc_start: 0.7977 (mt) cc_final: 0.7730 (mt) REVERT: A 463 GLU cc_start: 0.8266 (tp30) cc_final: 0.8066 (tp30) REVERT: B 86 TYR cc_start: 0.8086 (m-10) cc_final: 0.7633 (m-10) REVERT: B 116 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7692 (mm-40) REVERT: B 159 ARG cc_start: 0.7178 (ttt180) cc_final: 0.5755 (tpt-90) REVERT: B 171 MET cc_start: 0.8882 (tpp) cc_final: 0.8203 (mmm) REVERT: B 345 ASP cc_start: 0.7998 (t0) cc_final: 0.7663 (t0) REVERT: B 492 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8071 (mp) REVERT: B 512 ARG cc_start: 0.7605 (ptp90) cc_final: 0.6687 (tpt170) REVERT: B 562 GLN cc_start: 0.7772 (mt0) cc_final: 0.6906 (tt0) outliers start: 15 outliers final: 13 residues processed: 118 average time/residue: 0.0931 time to fit residues: 15.5461 Evaluate side-chains 121 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115213 restraints weight = 11839.518| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.04 r_work: 0.3320 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9200 Z= 0.114 Angle : 0.497 8.912 12461 Z= 0.248 Chirality : 0.038 0.150 1473 Planarity : 0.003 0.035 1570 Dihedral : 3.505 18.045 1233 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 13.29 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1138 helix: 2.25 (0.18), residues: 790 sheet: -1.45 (0.79), residues: 55 loop : -0.55 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 390 TYR 0.009 0.001 TYR B 260 PHE 0.027 0.001 PHE A 453 TRP 0.007 0.001 TRP A 228 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9200) covalent geometry : angle 0.49723 / 0.25 (12461) hydrogen bonds : bond 0.03686 / 2.52 ( 612) hydrogen bonds : angle 3.59238 / 2.65 ( 1788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.356 Fit side-chains REVERT: A 175 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7708 (mpt180) REVERT: A 347 GLN cc_start: 0.8386 (mp10) cc_final: 0.8154 (tp40) REVERT: A 445 LEU cc_start: 0.7901 (mt) cc_final: 0.7661 (mt) REVERT: A 568 TYR cc_start: 0.8486 (t80) cc_final: 0.8205 (t80) REVERT: B 86 TYR cc_start: 0.8072 (m-10) cc_final: 0.7603 (m-10) REVERT: B 116 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7716 (mm-40) REVERT: B 155 ILE cc_start: 0.8874 (mm) cc_final: 0.8666 (mp) REVERT: B 159 ARG cc_start: 0.7145 (ttt180) cc_final: 0.5666 (tpt-90) REVERT: B 171 MET cc_start: 0.8888 (tpp) cc_final: 0.8216 (mmm) REVERT: B 345 ASP cc_start: 0.7967 (t0) cc_final: 0.7641 (t0) REVERT: B 492 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8015 (mp) REVERT: B 512 ARG cc_start: 0.7588 (ptp90) cc_final: 0.6669 (tpt170) REVERT: B 562 GLN cc_start: 0.7740 (mt0) cc_final: 0.6910 (tt0) outliers start: 15 outliers final: 12 residues processed: 120 average time/residue: 0.0856 time to fit residues: 14.6426 Evaluate side-chains 123 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 574 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.142488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112989 restraints weight = 11729.947| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.99 r_work: 0.3293 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9200 Z= 0.146 Angle : 0.509 7.836 12461 Z= 0.255 Chirality : 0.039 0.150 1473 Planarity : 0.003 0.035 1570 Dihedral : 3.514 18.261 1233 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.31 % Allowed : 13.29 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.25), residues: 1138 helix: 2.16 (0.18), residues: 789 sheet: -1.47 (0.79), residues: 55 loop : -0.56 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 390 TYR 0.010 0.001 TYR B 260 PHE 0.028 0.001 PHE A 453 TRP 0.008 0.001 TRP A 228 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9200) covalent geometry : angle 0.50923 / 0.26 (12461) hydrogen bonds : bond 0.03843 / 2.60 ( 612) hydrogen bonds : angle 3.65220 / 2.70 ( 1788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.92 seconds wall clock time: 36 minutes 53.59 seconds (2213.59 seconds total)