Starting phenix.real_space_refine on Thu Jul 2 17:16:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x4a_66535/07_2026/9x4a_66535.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x4a_66535/07_2026/9x4a_66535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x4a_66535/07_2026/9x4a_66535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x4a_66535/07_2026/9x4a_66535.map" model { file = "/net/cci-nas-00/data/ceres_data/9x4a_66535/07_2026/9x4a_66535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x4a_66535/07_2026/9x4a_66535.cif" } resolution = 3.16 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 5839 2.51 5 N 1530 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 9087 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4496 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 20, 'TRANS': 549} 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} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.26, per 1000 atoms: 0.25 Number of scatterers: 9087 At special positions: 0 Unit cell: (73.272, 94.944, 137.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 6 15.00 Mg 2 11.99 O 1670 8.00 N 1530 7.00 C 5839 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: 0.90 Conformation dependent library (CDL) restraints added in 258.1 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 71.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.806A pdb=" N VAL A 6 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 7 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 9 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 47 Proline residue: A 19 - end of helix Proline residue: A 33 - end of helix removed outlier: 4.862A pdb=" N ILE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 48 through 99 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 118 through 134 removed outlier: 3.598A pdb=" N ARG A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.191A pdb=" N ILE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 201 removed outlier: 4.012A 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 209 Processing helix chain 'A' and resid 210 through 265 removed outlier: 4.103A pdb=" N GLU A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 268 through 288 Processing helix chain 'A' and resid 291 through 311 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 429 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 451 through 457 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.804A pdb=" N ASP A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 503 through 517 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 20 through 54 removed outlier: 4.329A pdb=" N PHE B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Proline residue: B 42 - end of helix removed outlier: 4.084A pdb=" N LEU B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 108 removed outlier: 4.069A pdb=" N LEU B 60 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 117 through 140 removed outlier: 3.976A pdb=" N MET B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 160 removed outlier: 3.710A pdb=" N GLY B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 210 removed outlier: 3.544A pdb=" N MET B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Proline residue: B 173 - end of helix removed outlier: 3.696A pdb=" N LYS B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 219 through 246 Processing helix chain 'B' and resid 247 through 274 removed outlier: 3.706A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 321 removed outlier: 3.994A pdb=" N LYS B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Proline residue: B 295 - end of helix removed outlier: 3.902A pdb=" N GLN B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 316 " --> pdb=" O CYS B 312 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 389 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 464 removed outlier: 3.568A pdb=" N ILE B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 removed outlier: 3.680A pdb=" N ALA B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.934A pdb=" N ILE B 492 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 removed outlier: 4.006A pdb=" N LEU B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.277A pdb=" N ASN B 542 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 568 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 353 removed outlier: 5.595A pdb=" N GLN A 351 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE A 340 " --> pdb=" O GLN A 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 353 removed outlier: 5.595A pdb=" N GLN A 351 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE A 340 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE A 335 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR A 392 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS A 337 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER A 390 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.527A pdb=" N ASP A 496 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A 493 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 495 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 363 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY A 364 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU A 542 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 366 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 549 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP A 543 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA5, first strand: chain 'B' and resid 358 through 365 removed outlier: 6.790A pdb=" N LYS B 359 " --> pdb=" O GLN B 348 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN B 348 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU B 361 " --> pdb=" O HIS B 346 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL B 347 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS B 396 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 418 through 421 removed outlier: 3.589A pdb=" N ILE B 501 " --> pdb=" O GLY B 419 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B 500 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 371 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 556 " --> pdb=" O VAL B 548 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1791 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: 1.21 Time building geometry restraints manager: 1.12 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: 2927 1.34 - 1.46: 1454 1.46 - 1.57: 4780 1.57 - 1.69: 10 1.69 - 1.81: 77 Bond restraints: 9248 Sorted by residual: bond pdb=" CB CYS B 312 " pdb=" SG CYS B 312 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CA THR B 172 " pdb=" C THR B 172 " ideal model delta sigma weight residual 1.522 1.535 -0.014 1.26e-02 6.30e+03 1.15e+00 bond pdb=" CA VAL B 496 " pdb=" CB VAL B 496 " ideal model delta sigma weight residual 1.537 1.526 0.011 1.29e-02 6.01e+03 7.88e-01 bond pdb=" CA ASN A 178 " pdb=" C ASN A 178 " ideal model delta sigma weight residual 1.521 1.532 -0.010 1.17e-02 7.31e+03 7.70e-01 bond pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.05e-02 9.07e+03 6.67e-01 ... (remaining 9243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 12306 1.29 - 2.58: 178 2.58 - 3.87: 39 3.87 - 5.16: 15 5.16 - 6.45: 4 Bond angle restraints: 12542 Sorted by residual: angle pdb=" CA MET B 55 " pdb=" CB MET B 55 " pdb=" CG MET B 55 " ideal model delta sigma weight residual 114.10 119.40 -5.30 2.00e+00 2.50e-01 7.03e+00 angle pdb=" C ASP B 334 " pdb=" N GLU B 335 " pdb=" CA GLU B 335 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.70e+00 angle pdb=" CB MET B 55 " pdb=" CG MET B 55 " pdb=" SD MET B 55 " ideal model delta sigma weight residual 112.70 119.15 -6.45 3.00e+00 1.11e-01 4.62e+00 angle pdb=" N VAL A 32 " pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 108.88 113.40 -4.52 2.16e+00 2.14e-01 4.37e+00 angle pdb=" CA LEU B 400 " pdb=" CB LEU B 400 " pdb=" CG LEU B 400 " ideal model delta sigma weight residual 116.30 122.26 -5.96 3.50e+00 8.16e-02 2.90e+00 ... (remaining 12537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5068 17.65 - 35.29: 442 35.29 - 52.94: 86 52.94 - 70.58: 10 70.58 - 88.23: 8 Dihedral angle restraints: 5614 sinusoidal: 2289 harmonic: 3325 Sorted by residual: dihedral pdb=" CB GLU B 305 " pdb=" CG GLU B 305 " pdb=" CD GLU B 305 " pdb=" OE1 GLU B 305 " ideal model delta sinusoidal sigma weight residual 0.00 88.23 -88.23 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA PHE A 134 " pdb=" C PHE A 134 " pdb=" N LEU A 135 " pdb=" CA LEU A 135 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CG ARG A 305 " pdb=" CD ARG A 305 " pdb=" NE ARG A 305 " pdb=" CZ ARG A 305 " ideal model delta sinusoidal sigma weight residual -180.00 -138.67 -41.33 2 1.50e+01 4.44e-03 9.30e+00 ... (remaining 5611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1079 0.037 - 0.073: 308 0.073 - 0.110: 72 0.110 - 0.147: 18 0.147 - 0.184: 2 Chirality restraints: 1479 Sorted by residual: chirality pdb=" CG LEU A 23 " pdb=" CB LEU A 23 " pdb=" CD1 LEU A 23 " pdb=" CD2 LEU A 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.43e-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 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE B 325 " pdb=" N ILE B 325 " pdb=" C ILE B 325 " pdb=" CB ILE B 325 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 1476 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 18 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 19 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 172 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO B 173 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 151 " -0.008 2.00e-02 2.50e+03 9.99e-03 1.75e+00 pdb=" CG PHE B 151 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 151 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 151 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 151 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 151 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 151 " 0.001 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 77 2.61 - 3.18: 8093 3.18 - 3.76: 14270 3.76 - 4.33: 18920 4.33 - 4.90: 32249 Nonbonded interactions: 73609 Sorted by model distance: nonbonded pdb=" OE1 GLN A 415 " pdb="MG MG A 702 " model vdw 2.040 2.170 nonbonded pdb=" O1G ATP A 701 " pdb="MG MG A 702 " model vdw 2.065 2.170 nonbonded pdb=" OE1 GLN B 423 " pdb="MG MG B 602 " model vdw 2.079 2.170 nonbonded pdb=" O1G ATP B 601 " pdb="MG MG B 602 " model vdw 2.082 2.170 nonbonded pdb=" OG SER A 374 " pdb="MG MG A 702 " model vdw 2.086 2.170 ... (remaining 73604 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: 2.370 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 0.002 0.036 9248 Z= 0.108 Angle : 0.451 6.450 12542 Z= 0.237 Chirality : 0.038 0.184 1479 Planarity : 0.003 0.037 1569 Dihedral : 13.700 88.227 3464 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 2.15 (0.25), residues: 1136 helix: 2.42 (0.19), residues: 773 sheet: -0.11 (0.64), residues: 65 loop : -0.94 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 411 TYR 0.008 0.001 TYR B 292 PHE 0.023 0.001 PHE B 151 TRP 0.010 0.001 TRP B 196 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 9248) covalent geometry : angle 0.45087 / 0.24 (12542) hydrogen bonds : bond 0.14549 / 10.01 ( 608) hydrogen bonds : angle 4.94871 / 3.60 ( 1791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 77 SER cc_start: 0.8102 (t) cc_final: 0.7893 (p) REVERT: A 105 ASP cc_start: 0.7621 (m-30) cc_final: 0.7087 (m-30) REVERT: A 150 ARG cc_start: 0.6999 (mtp180) cc_final: 0.6669 (ptm-80) REVERT: A 324 LYS cc_start: 0.7943 (tttt) cc_final: 0.7699 (mtpp) REVERT: A 439 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6819 (pt0) REVERT: A 525 ILE cc_start: 0.7638 (mm) cc_final: 0.7385 (tp) REVERT: A 544 LYS cc_start: 0.7994 (mttt) cc_final: 0.7711 (mtmt) REVERT: A 561 LYS cc_start: 0.8249 (tmmt) cc_final: 0.7715 (tmmt) REVERT: B 28 THR cc_start: 0.7046 (t) cc_final: 0.6785 (t) REVERT: B 121 MET cc_start: 0.7224 (mpp) cc_final: 0.6919 (mpp) REVERT: B 283 THR cc_start: 0.7601 (m) cc_final: 0.7192 (p) REVERT: B 335 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8104 (tm-30) REVERT: B 526 LYS cc_start: 0.7647 (tppt) cc_final: 0.7412 (mmtt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0775 time to fit residues: 20.2211 Evaluate side-chains 110 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105535 restraints weight = 12819.381| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.84 r_work: 0.3125 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9248 Z= 0.182 Angle : 0.528 5.627 12542 Z= 0.277 Chirality : 0.040 0.146 1479 Planarity : 0.004 0.039 1569 Dihedral : 7.787 75.645 1299 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.72 % Allowed : 7.87 % Favored : 90.41 % 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: 1.96 (0.25), residues: 1136 helix: 2.29 (0.18), residues: 783 sheet: -0.70 (0.63), residues: 60 loop : -1.03 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 445 TYR 0.011 0.001 TYR B 93 PHE 0.012 0.001 PHE B 285 TRP 0.009 0.001 TRP B 196 HIS 0.004 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 ( 9248) covalent geometry : angle 0.52800 / 0.28 (12542) hydrogen bonds : bond 0.05150 / 3.32 ( 608) hydrogen bonds : angle 4.17088 / 3.01 ( 1791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.236 Fit side-chains REVERT: A 105 ASP cc_start: 0.7579 (m-30) cc_final: 0.7153 (m-30) REVERT: A 150 ARG cc_start: 0.7109 (mtp180) cc_final: 0.6661 (mtp85) REVERT: A 249 MET cc_start: 0.8512 (mmt) cc_final: 0.8298 (mmt) REVERT: A 278 TYR cc_start: 0.5554 (m-10) cc_final: 0.5139 (m-10) REVERT: A 403 LEU cc_start: 0.8638 (mm) cc_final: 0.8362 (mt) REVERT: A 439 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7579 (pt0) REVERT: A 561 LYS cc_start: 0.8012 (tmmt) cc_final: 0.7735 (tmmt) REVERT: A 565 ASP cc_start: 0.8499 (m-30) cc_final: 0.8243 (m-30) REVERT: B 151 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7388 (t80) REVERT: B 335 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8519 (tm-30) REVERT: B 525 MET cc_start: 0.8289 (mtm) cc_final: 0.8025 (mtt) REVERT: B 526 LYS cc_start: 0.7882 (tppt) cc_final: 0.7651 (mmtt) outliers start: 17 outliers final: 13 residues processed: 124 average time/residue: 0.0637 time to fit residues: 11.6084 Evaluate side-chains 112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN A 397 GLN B 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105418 restraints weight = 12624.852| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.95 r_work: 0.3131 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9248 Z= 0.131 Angle : 0.467 5.617 12542 Z= 0.247 Chirality : 0.038 0.142 1479 Planarity : 0.003 0.039 1569 Dihedral : 7.494 75.693 1299 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.51 % Allowed : 10.49 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.06 (0.25), residues: 1136 helix: 2.38 (0.18), residues: 782 sheet: -0.80 (0.63), residues: 60 loop : -1.04 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 270 TYR 0.008 0.001 TYR B 93 PHE 0.011 0.001 PHE A 453 TRP 0.011 0.001 TRP B 196 HIS 0.003 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9248) covalent geometry : angle 0.46678 / 0.25 (12542) hydrogen bonds : bond 0.04628 / 2.97 ( 608) hydrogen bonds : angle 3.94655 / 2.85 ( 1791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.269 Fit side-chains REVERT: A 77 SER cc_start: 0.9013 (t) cc_final: 0.8807 (p) REVERT: A 105 ASP cc_start: 0.7624 (m-30) cc_final: 0.7174 (m-30) REVERT: A 150 ARG cc_start: 0.7052 (mtp180) cc_final: 0.6791 (mtp85) REVERT: A 278 TYR cc_start: 0.5540 (m-10) cc_final: 0.5197 (m-10) REVERT: A 439 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7454 (pt0) REVERT: A 487 MET cc_start: 0.9173 (mmm) cc_final: 0.8839 (mmm) REVERT: B 151 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7339 (t80) REVERT: B 335 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8458 (tm-30) REVERT: B 525 MET cc_start: 0.8100 (mtm) cc_final: 0.7569 (mtt) REVERT: B 526 LYS cc_start: 0.7875 (tppt) cc_final: 0.7621 (mmtt) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 0.0547 time to fit residues: 10.0277 Evaluate side-chains 112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105842 restraints weight = 12159.503| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.88 r_work: 0.3129 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.004 0.045 9248 Z= 0.157 Angle : 0.487 5.661 12542 Z= 0.257 Chirality : 0.039 0.150 1479 Planarity : 0.003 0.040 1569 Dihedral : 7.360 80.047 1299 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.83 % Allowed : 11.91 % Favored : 85.27 % 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: 1.93 (0.25), residues: 1136 helix: 2.31 (0.18), residues: 782 sheet: -1.00 (0.62), residues: 60 loop : -1.12 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.011 0.001 TYR B 93 PHE 0.012 0.001 PHE A 453 TRP 0.010 0.001 TRP B 196 HIS 0.003 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 9248) covalent geometry : angle 0.48746 / 0.26 (12542) hydrogen bonds : bond 0.04812 / 3.08 ( 608) hydrogen bonds : angle 3.92129 / 2.84 ( 1791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.217 Fit side-chains REVERT: A 105 ASP cc_start: 0.7716 (m-30) cc_final: 0.7249 (m-30) REVERT: A 150 ARG cc_start: 0.6960 (mtp180) cc_final: 0.6719 (ptm-80) REVERT: A 278 TYR cc_start: 0.5750 (m-10) cc_final: 0.5441 (m-10) REVERT: A 439 GLN cc_start: 0.7513 (tm-30) cc_final: 0.7124 (pt0) REVERT: A 565 ASP cc_start: 0.8371 (m-30) cc_final: 0.8163 (m-30) REVERT: B 151 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7087 (t80) REVERT: B 335 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 442 LYS cc_start: 0.8526 (mmtt) cc_final: 0.7965 (mtpt) REVERT: B 525 MET cc_start: 0.7963 (mtm) cc_final: 0.7609 (mtt) outliers start: 28 outliers final: 16 residues processed: 128 average time/residue: 0.0559 time to fit residues: 11.0617 Evaluate side-chains 122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.128523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107232 restraints weight = 12080.457| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.80 r_work: 0.3141 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9248 Z= 0.139 Angle : 0.476 7.001 12542 Z= 0.250 Chirality : 0.039 0.139 1479 Planarity : 0.003 0.041 1569 Dihedral : 7.157 79.075 1299 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.52 % Allowed : 13.32 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1136 helix: 2.37 (0.18), residues: 782 sheet: -1.01 (0.63), residues: 60 loop : -1.17 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.010 0.001 TYR B 292 PHE 0.012 0.001 PHE A 453 TRP 0.010 0.001 TRP B 196 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9248) covalent geometry : angle 0.47576 / 0.25 (12542) hydrogen bonds : bond 0.04611 / 2.94 ( 608) hydrogen bonds : angle 3.83410 / 2.77 ( 1791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.394 Fit side-chains REVERT: A 105 ASP cc_start: 0.7733 (m-30) cc_final: 0.7261 (m-30) REVERT: A 278 TYR cc_start: 0.5879 (m-10) cc_final: 0.5636 (m-10) REVERT: A 439 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7309 (pt0) REVERT: A 487 MET cc_start: 0.9068 (mmm) cc_final: 0.8695 (mmm) REVERT: A 565 ASP cc_start: 0.8462 (m-30) cc_final: 0.8215 (m-30) REVERT: B 151 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7212 (t80) REVERT: B 335 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8349 (tm-30) REVERT: B 456 ASN cc_start: 0.8716 (t0) cc_final: 0.8281 (t0) REVERT: B 533 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8267 (mt) outliers start: 25 outliers final: 19 residues processed: 130 average time/residue: 0.0719 time to fit residues: 14.4801 Evaluate side-chains 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106101 restraints weight = 12492.251| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.78 r_work: 0.3124 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9248 Z= 0.149 Angle : 0.485 6.072 12542 Z= 0.255 Chirality : 0.039 0.138 1479 Planarity : 0.003 0.042 1569 Dihedral : 7.098 79.994 1299 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.62 % Allowed : 14.33 % Favored : 83.05 % 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: 1136 helix: 2.30 (0.18), residues: 786 sheet: -1.07 (0.63), residues: 60 loop : -1.30 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 150 TYR 0.016 0.001 TYR B 288 PHE 0.012 0.001 PHE A 149 TRP 0.010 0.001 TRP B 196 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9248) covalent geometry : angle 0.48512 / 0.25 (12542) hydrogen bonds : bond 0.04684 / 3.00 ( 608) hydrogen bonds : angle 3.83876 / 2.78 ( 1791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.348 Fit side-chains REVERT: A 105 ASP cc_start: 0.7665 (m-30) cc_final: 0.7285 (m-30) REVERT: A 150 ARG cc_start: 0.7677 (ptm-80) cc_final: 0.7288 (ptp-110) REVERT: A 278 TYR cc_start: 0.6215 (m-10) cc_final: 0.5860 (m-10) REVERT: A 561 LYS cc_start: 0.8018 (tmmt) cc_final: 0.7687 (mtmm) REVERT: B 151 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7498 (t80) REVERT: B 398 GLN cc_start: 0.8044 (pt0) cc_final: 0.7835 (pt0) REVERT: B 456 ASN cc_start: 0.8840 (t0) cc_final: 0.8489 (t0) REVERT: B 526 LYS cc_start: 0.8122 (tppt) cc_final: 0.7663 (mmtt) REVERT: B 533 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8391 (mt) outliers start: 26 outliers final: 22 residues processed: 125 average time/residue: 0.0740 time to fit residues: 14.0236 Evaluate side-chains 125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 417 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105471 restraints weight = 12662.342| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.86 r_work: 0.3133 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9248 Z= 0.119 Angle : 0.457 5.973 12542 Z= 0.242 Chirality : 0.038 0.138 1479 Planarity : 0.003 0.041 1569 Dihedral : 6.884 81.430 1299 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.52 % Allowed : 14.23 % Favored : 83.25 % 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: 2.06 (0.25), residues: 1136 helix: 2.45 (0.18), residues: 782 sheet: -1.01 (0.63), residues: 60 loop : -1.20 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 150 TYR 0.011 0.001 TYR B 288 PHE 0.013 0.001 PHE A 388 TRP 0.012 0.001 TRP B 196 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9248) covalent geometry : angle 0.45706 / 0.24 (12542) hydrogen bonds : bond 0.04345 / 2.78 ( 608) hydrogen bonds : angle 3.72420 / 2.70 ( 1791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.352 Fit side-chains REVERT: A 105 ASP cc_start: 0.7750 (m-30) cc_final: 0.7334 (m-30) REVERT: A 150 ARG cc_start: 0.7690 (ptm-80) cc_final: 0.7157 (ptp-110) REVERT: A 278 TYR cc_start: 0.6156 (m-10) cc_final: 0.5815 (m-10) REVERT: A 487 MET cc_start: 0.9158 (mmm) cc_final: 0.8758 (mmm) REVERT: B 151 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7425 (t80) REVERT: B 456 ASN cc_start: 0.8776 (t0) cc_final: 0.8431 (t0) REVERT: B 525 MET cc_start: 0.8100 (mtm) cc_final: 0.7858 (mtm) REVERT: B 526 LYS cc_start: 0.8039 (tppt) cc_final: 0.7617 (mmtt) outliers start: 25 outliers final: 19 residues processed: 121 average time/residue: 0.0725 time to fit residues: 13.6096 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106071 restraints weight = 12669.064| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.81 r_work: 0.3134 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9248 Z= 0.130 Angle : 0.470 7.711 12542 Z= 0.246 Chirality : 0.038 0.138 1479 Planarity : 0.003 0.041 1569 Dihedral : 6.850 80.895 1299 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.72 % Allowed : 14.53 % Favored : 82.74 % 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: 1136 helix: 2.40 (0.18), residues: 786 sheet: -1.05 (0.63), residues: 60 loop : -1.30 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.011 0.001 TYR B 288 PHE 0.011 0.001 PHE A 453 TRP 0.011 0.001 TRP B 196 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9248) covalent geometry : angle 0.46980 / 0.25 (12542) hydrogen bonds : bond 0.04432 / 2.84 ( 608) hydrogen bonds : angle 3.72873 / 2.71 ( 1791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.352 Fit side-chains REVERT: A 105 ASP cc_start: 0.7744 (m-30) cc_final: 0.7342 (m-30) REVERT: A 150 ARG cc_start: 0.7692 (ptm-80) cc_final: 0.7170 (ptp-110) REVERT: A 278 TYR cc_start: 0.6197 (m-10) cc_final: 0.5917 (m-10) REVERT: B 151 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7464 (t80) REVERT: B 456 ASN cc_start: 0.8774 (t0) cc_final: 0.8429 (t0) REVERT: B 525 MET cc_start: 0.8136 (mtm) cc_final: 0.7920 (mtm) REVERT: B 533 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8342 (mt) outliers start: 27 outliers final: 23 residues processed: 122 average time/residue: 0.0748 time to fit residues: 13.7696 Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 89 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.128232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106375 restraints weight = 12728.467| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.02 r_work: 0.3165 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9248 Z= 0.174 Angle : 0.511 6.433 12542 Z= 0.267 Chirality : 0.040 0.141 1479 Planarity : 0.004 0.041 1569 Dihedral : 7.014 86.209 1299 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.62 % Allowed : 15.04 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.78 (0.25), residues: 1136 helix: 2.24 (0.18), residues: 786 sheet: -1.19 (0.62), residues: 60 loop : -1.32 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.012 0.001 TYR A 278 PHE 0.012 0.001 PHE A 453 TRP 0.008 0.001 TRP B 196 HIS 0.003 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 9248) covalent geometry : angle 0.51085 / 0.27 (12542) hydrogen bonds : bond 0.04905 / 3.15 ( 608) hydrogen bonds : angle 3.84444 / 2.80 ( 1791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.344 Fit side-chains REVERT: A 105 ASP cc_start: 0.7803 (m-30) cc_final: 0.7350 (m-30) REVERT: A 150 ARG cc_start: 0.7514 (ptm-80) cc_final: 0.7109 (ptp-110) REVERT: A 278 TYR cc_start: 0.6497 (m-10) cc_final: 0.6259 (m-10) REVERT: B 151 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7498 (t80) REVERT: B 456 ASN cc_start: 0.8835 (t0) cc_final: 0.8507 (t0) REVERT: B 533 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8473 (mt) outliers start: 26 outliers final: 21 residues processed: 117 average time/residue: 0.0750 time to fit residues: 13.2580 Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 0.6980 chunk 100 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107058 restraints weight = 12670.761| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.81 r_work: 0.3150 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9248 Z= 0.112 Angle : 0.461 6.024 12542 Z= 0.242 Chirality : 0.038 0.138 1479 Planarity : 0.003 0.041 1569 Dihedral : 6.733 83.467 1299 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.92 % Allowed : 15.74 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.10 (0.25), residues: 1136 helix: 2.48 (0.18), residues: 782 sheet: -1.01 (0.63), residues: 60 loop : -1.20 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.011 0.001 TYR B 292 PHE 0.013 0.001 PHE A 149 TRP 0.013 0.001 TRP B 196 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9248) covalent geometry : angle 0.46108 / 0.24 (12542) hydrogen bonds : bond 0.04246 / 2.71 ( 608) hydrogen bonds : angle 3.70061 / 2.68 ( 1791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.355 Fit side-chains REVERT: A 105 ASP cc_start: 0.7823 (m-30) cc_final: 0.7404 (m-30) REVERT: A 150 ARG cc_start: 0.7672 (ptm-80) cc_final: 0.7247 (ptp-110) REVERT: B 151 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7463 (t80) REVERT: B 456 ASN cc_start: 0.8758 (t0) cc_final: 0.8474 (t0) REVERT: B 533 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8246 (mt) outliers start: 19 outliers final: 16 residues processed: 111 average time/residue: 0.0703 time to fit residues: 12.3138 Evaluate side-chains 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107032 restraints weight = 12560.083| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.78 r_work: 0.3143 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9248 Z= 0.122 Angle : 0.474 6.548 12542 Z= 0.247 Chirality : 0.038 0.140 1479 Planarity : 0.003 0.040 1569 Dihedral : 6.711 83.078 1299 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.92 % Allowed : 15.84 % Favored : 82.24 % 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: 1136 helix: 2.44 (0.18), residues: 786 sheet: -0.95 (0.64), residues: 60 loop : -1.24 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 104 TYR 0.010 0.001 TYR B 292 PHE 0.013 0.001 PHE A 149 TRP 0.011 0.001 TRP B 196 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9248) covalent geometry : angle 0.47419 / 0.25 (12542) hydrogen bonds : bond 0.04320 / 2.76 ( 608) hydrogen bonds : angle 3.70963 / 2.70 ( 1791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1954.73 seconds wall clock time: 34 minutes 18.43 seconds (2058.43 seconds total)