Starting phenix.real_space_refine on Thu Jul 2 21:06:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eob_28333/07_2026/8eob_28333.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eob_28333/07_2026/8eob_28333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8eob_28333/07_2026/8eob_28333.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eob_28333/07_2026/8eob_28333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eob_28333/07_2026/8eob_28333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eob_28333/07_2026/8eob_28333.map" model { file = "/net/cci-nas-00/data/ceres_data/8eob_28333/07_2026/8eob_28333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eob_28333/07_2026/8eob_28333.cif" } resolution = 3.1 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= 0.969 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 46 5.16 5 C 6411 2.51 5 N 1701 2.21 5 O 1975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 10141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5053 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 17, 'TRANS': 606} Chain breaks: 2 Chain: "B" Number of atoms: 5024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5024 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 17, 'TRANS': 603} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 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, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.31, per 1000 atoms: 0.23 Number of scatterers: 10141 At special positions: 0 Unit cell: (94.696, 94.696, 130.83, 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 46 16.00 P 6 15.00 Mg 2 11.99 O 1975 8.00 N 1701 7.00 C 6411 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: 0.82 Conformation dependent library (CDL) restraints added in 333.9 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 46.1% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.857A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 60 removed outlier: 4.603A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 189 through 193 removed outlier: 4.132A pdb=" N TYR A 192 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.797A pdb=" N THR A 290 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 397 through 420 removed outlier: 4.146A pdb=" N LEU A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 6.505A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.792A pdb=" N LEU A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.541A pdb=" N LYS A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.338A pdb=" N TYR A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 613 through 620 removed outlier: 3.517A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 648 through 666 Processing helix chain 'A' and resid 672 through 689 removed outlier: 3.882A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 60 removed outlier: 3.548A pdb=" N ILE B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.545A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.614A pdb=" N THR B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 398 through 420 Processing helix chain 'B' and resid 422 through 444 removed outlier: 6.411A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 469 through 476 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.649A pdb=" N VAL B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 525 removed outlier: 4.166A pdb=" N GLU B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 571 removed outlier: 5.482A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.887A pdb=" N MET B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.560A pdb=" N GLY B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 689 removed outlier: 3.739A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.780A pdb=" N HIS B 184 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B 143 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 182 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 145 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS B 180 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 147 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 178 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE B 75 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.745A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215 removed outlier: 3.712A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 219 Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.507A pdb=" N ILE A 335 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 318 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 333 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS A 320 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA A 331 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER A 322 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 329 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE A 353 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP A 364 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 468 removed outlier: 4.059A pdb=" N HIS A 458 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 577 through 580 Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 323 removed outlier: 6.620A pdb=" N ILE B 335 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL B 318 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 333 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS B 320 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B 331 " --> pdb=" O HIS B 320 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER B 322 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE B 329 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.896A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 577 through 580 482 hydrogen bonds defined for protein. 1335 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: 1.63 Time building geometry restraints manager: 1.03 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: 3319 1.34 - 1.46: 2159 1.46 - 1.58: 4746 1.58 - 1.69: 5 1.69 - 1.81: 80 Bond restraints: 10309 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.566 0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 10304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 13824 3.36 - 6.73: 43 6.73 - 10.09: 6 10.09 - 13.45: 2 13.45 - 16.81: 2 Bond angle restraints: 13877 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.14 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 111.34 15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.37 10.71 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " pdb=" O2G ANP A 801 " ideal model delta sigma weight residual 101.05 110.02 -8.97 3.00e+00 1.11e-01 8.94e+00 ... (remaining 13872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5943 17.72 - 35.44: 326 35.44 - 53.15: 56 53.15 - 70.87: 6 70.87 - 88.59: 2 Dihedral angle restraints: 6333 sinusoidal: 2672 harmonic: 3661 Sorted by residual: dihedral pdb=" N LYS B 481 " pdb=" CA LYS B 481 " pdb=" CB LYS B 481 " pdb=" CG LYS B 481 " ideal model delta sinusoidal sigma weight residual -180.00 -125.36 -54.64 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" N ASN B 150 " pdb=" CA ASN B 150 " pdb=" CB ASN B 150 " pdb=" CG ASN B 150 " ideal model delta sinusoidal sigma weight residual -60.00 -113.44 53.44 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA GLU A 368 " pdb=" CB GLU A 368 " pdb=" CG GLU A 368 " pdb=" CD GLU A 368 " ideal model delta sinusoidal sigma weight residual 60.00 111.90 -51.90 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 6330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1288 0.052 - 0.104: 213 0.104 - 0.156: 42 0.156 - 0.208: 0 0.208 - 0.260: 2 Chirality restraints: 1545 Sorted by residual: chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE B 335 " pdb=" N ILE B 335 " pdb=" C ILE B 335 " pdb=" CB ILE B 335 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1542 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 371 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 370 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 371 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 52 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ASP A 52 " 0.028 2.00e-02 2.50e+03 pdb=" O ASP A 52 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 53 " -0.009 2.00e-02 2.50e+03 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 85 2.54 - 3.13: 7948 3.13 - 3.72: 15479 3.72 - 4.31: 21776 4.31 - 4.90: 37185 Nonbonded interactions: 82473 Sorted by model distance: nonbonded pdb=" O1B ANP B 801 " pdb=" O2G ANP B 801 " model vdw 1.945 3.040 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 1.979 2.170 nonbonded pdb=" O2G ANP B 801 " pdb="MG MG B 802 " model vdw 1.988 2.170 nonbonded pdb=" N3B ANP A 801 " pdb="MG MG A 802 " model vdw 2.062 2.250 nonbonded pdb=" OD1 ASN B 46 " pdb="MG MG B 802 " model vdw 2.081 2.170 ... (remaining 82468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 220 or resid 275 through 345 or resid 351 throu \ gh 802)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.450 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: 0.030 Set scattering table: 0.040 Process input model: 9.650 Find NCS groups from input model: 0.120 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 10309 Z= 0.236 Angle : 0.607 16.814 13877 Z= 0.296 Chirality : 0.041 0.260 1545 Planarity : 0.003 0.043 1765 Dihedral : 11.238 88.591 3959 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.78 % Allowed : 6.41 % Favored : 91.81 % 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: 0.42 (0.24), residues: 1233 helix: 1.34 (0.24), residues: 509 sheet: 0.36 (0.35), residues: 227 loop : -0.83 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 82 TYR 0.015 0.002 TYR A 134 PHE 0.009 0.001 PHE B 334 TRP 0.012 0.002 TRP A 157 HIS 0.002 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (10309) covalent geometry : angle 0.60676 / 0.30 (13877) hydrogen bonds : bond 0.13827 / 8.88 ( 482) hydrogen bonds : angle 6.26189 / 4.28 ( 1335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLN cc_start: 0.8811 (pm20) cc_final: 0.8582 (pm20) REVERT: A 374 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8840 (mp) REVERT: A 553 MET cc_start: 0.7275 (tpp) cc_final: 0.6984 (tpp) REVERT: A 606 MET cc_start: 0.8016 (ptp) cc_final: 0.7686 (ptp) REVERT: A 607 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8389 (mttt) REVERT: A 629 ASN cc_start: 0.9296 (t0) cc_final: 0.8731 (t0) REVERT: A 636 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7378 (tm-30) REVERT: A 660 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8128 (mt-10) REVERT: B 70 GLU cc_start: 0.8044 (tt0) cc_final: 0.7730 (tt0) REVERT: B 118 GLN cc_start: 0.9042 (pp30) cc_final: 0.8560 (pp30) REVERT: B 196 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.8206 (tpp80) REVERT: B 312 TRP cc_start: 0.8050 (p90) cc_final: 0.7792 (p90) REVERT: B 377 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8810 (mt) REVERT: B 490 SER cc_start: 0.8974 (t) cc_final: 0.8638 (t) REVERT: B 494 VAL cc_start: 0.9299 (t) cc_final: 0.8920 (m) REVERT: B 526 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8912 (mmtm) REVERT: B 553 MET cc_start: 0.6635 (tpp) cc_final: 0.6204 (tpp) REVERT: B 581 SER cc_start: 0.8392 (t) cc_final: 0.7873 (t) REVERT: B 584 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8718 (mm) REVERT: B 599 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 602 MET cc_start: 0.8438 (tpp) cc_final: 0.7973 (tpp) REVERT: B 607 LYS cc_start: 0.8692 (tppt) cc_final: 0.8360 (mmtp) outliers start: 20 outliers final: 7 residues processed: 182 average time/residue: 0.1002 time to fit residues: 25.4456 Evaluate side-chains 123 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS A 678 ASN B 46 ASN B 80 GLN B 447 ASN B 493 GLN B 674 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.078604 restraints weight = 18170.151| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.01 r_work: 0.2849 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10309 Z= 0.106 Angle : 0.457 5.570 13877 Z= 0.244 Chirality : 0.040 0.153 1545 Planarity : 0.003 0.040 1765 Dihedral : 5.266 47.954 1374 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.78 % Allowed : 9.88 % Favored : 88.33 % 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: 1.11 (0.25), residues: 1233 helix: 1.99 (0.24), residues: 507 sheet: 0.57 (0.36), residues: 221 loop : -0.45 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 682 TYR 0.011 0.001 TYR B 373 PHE 0.009 0.001 PHE B 15 TRP 0.014 0.001 TRP A 157 HIS 0.002 0.000 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10309) covalent geometry : angle 0.45678 / 0.24 (13877) hydrogen bonds : bond 0.03488 / 2.27 ( 482) hydrogen bonds : angle 4.45029 / 3.12 ( 1335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8711 (p90) cc_final: 0.8368 (p90) REVERT: A 465 GLU cc_start: 0.8045 (pp20) cc_final: 0.7688 (pp20) REVERT: A 553 MET cc_start: 0.7356 (tpp) cc_final: 0.7016 (tpp) REVERT: A 602 MET cc_start: 0.8114 (tpp) cc_final: 0.7497 (tpt) REVERT: A 619 TYR cc_start: 0.8484 (m-80) cc_final: 0.8095 (m-80) REVERT: A 621 MET cc_start: 0.8598 (mmm) cc_final: 0.8349 (mmm) REVERT: A 629 ASN cc_start: 0.9295 (t0) cc_final: 0.8825 (t0) REVERT: A 636 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7442 (tm-30) REVERT: A 660 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8758 (mm-30) REVERT: A 678 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7635 (m110) REVERT: B 70 GLU cc_start: 0.8080 (tt0) cc_final: 0.7800 (tt0) REVERT: B 114 MET cc_start: 0.8890 (tpp) cc_final: 0.8668 (mmm) REVERT: B 118 GLN cc_start: 0.9103 (pp30) cc_final: 0.8696 (pp30) REVERT: B 312 TRP cc_start: 0.8072 (p90) cc_final: 0.7858 (p90) REVERT: B 368 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6831 (pm20) REVERT: B 372 GLU cc_start: 0.8115 (tp30) cc_final: 0.7879 (tp30) REVERT: B 375 ASN cc_start: 0.8611 (p0) cc_final: 0.8306 (p0) REVERT: B 405 ARG cc_start: 0.8714 (ttm-80) cc_final: 0.8427 (ttm-80) REVERT: B 490 SER cc_start: 0.8493 (t) cc_final: 0.7632 (p) REVERT: B 494 VAL cc_start: 0.9224 (t) cc_final: 0.8837 (m) REVERT: B 526 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8882 (mmtm) REVERT: B 553 MET cc_start: 0.6821 (tpp) cc_final: 0.6360 (tpp) REVERT: B 599 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8626 (p) REVERT: B 602 MET cc_start: 0.8602 (tpp) cc_final: 0.8095 (tpp) REVERT: B 607 LYS cc_start: 0.8658 (tppt) cc_final: 0.8435 (mttm) REVERT: B 612 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7783 (mtp180) outliers start: 20 outliers final: 6 residues processed: 145 average time/residue: 0.0913 time to fit residues: 19.1763 Evaluate side-chains 120 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.096095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.073137 restraints weight = 18638.161| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.94 r_work: 0.2743 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 10309 Z= 0.295 Angle : 0.577 7.468 13877 Z= 0.301 Chirality : 0.044 0.159 1545 Planarity : 0.004 0.040 1765 Dihedral : 5.225 49.029 1362 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.03 % Allowed : 10.86 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.24), residues: 1233 helix: 1.72 (0.23), residues: 501 sheet: 0.21 (0.35), residues: 232 loop : -0.63 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 41 TYR 0.019 0.002 TYR A 426 PHE 0.014 0.002 PHE B 15 TRP 0.014 0.002 TRP A 157 HIS 0.005 0.001 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.30 (10309) covalent geometry : angle 0.57683 / 0.30 (13877) hydrogen bonds : bond 0.04051 / 2.65 ( 482) hydrogen bonds : angle 4.55440 / 3.21 ( 1335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8690 (p90) cc_final: 0.8358 (p90) REVERT: A 368 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: A 465 GLU cc_start: 0.8145 (pp20) cc_final: 0.7751 (pp20) REVERT: A 553 MET cc_start: 0.7495 (tpp) cc_final: 0.7214 (tpp) REVERT: A 602 MET cc_start: 0.8163 (tpp) cc_final: 0.7945 (tpt) REVERT: A 629 ASN cc_start: 0.9347 (t0) cc_final: 0.8870 (t0) REVERT: A 636 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7623 (tm-30) REVERT: A 660 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8703 (mm-30) REVERT: B 70 GLU cc_start: 0.8177 (tt0) cc_final: 0.7905 (tt0) REVERT: B 118 GLN cc_start: 0.9101 (pp30) cc_final: 0.8697 (pp30) REVERT: B 368 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7022 (pm20) REVERT: B 490 SER cc_start: 0.8694 (t) cc_final: 0.7997 (p) REVERT: B 553 MET cc_start: 0.6863 (tpp) cc_final: 0.6354 (tpp) REVERT: B 584 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8644 (mm) REVERT: B 599 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8679 (p) REVERT: B 601 ASN cc_start: 0.7821 (t0) cc_final: 0.6745 (t0) REVERT: B 602 MET cc_start: 0.8536 (tpp) cc_final: 0.8033 (tpp) REVERT: B 607 LYS cc_start: 0.8643 (tppt) cc_final: 0.8418 (mttm) REVERT: B 627 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7890 (mt-10) outliers start: 34 outliers final: 17 residues processed: 129 average time/residue: 0.0841 time to fit residues: 16.3887 Evaluate side-chains 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 683 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.098987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.077620 restraints weight = 18421.909| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.81 r_work: 0.2820 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 0.050 10309 Z= 0.111 Angle : 0.436 5.818 13877 Z= 0.233 Chirality : 0.040 0.151 1545 Planarity : 0.003 0.039 1765 Dihedral : 4.669 39.116 1362 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.14 % Allowed : 11.67 % Favored : 86.20 % 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: 1.02 (0.25), residues: 1233 helix: 2.01 (0.23), residues: 498 sheet: 0.30 (0.35), residues: 231 loop : -0.46 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 450 TYR 0.011 0.001 TYR B 373 PHE 0.007 0.001 PHE B 15 TRP 0.016 0.002 TRP A 157 HIS 0.002 0.000 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10309) covalent geometry : angle 0.43623 / 0.23 (13877) hydrogen bonds : bond 0.03072 / 2.00 ( 482) hydrogen bonds : angle 4.15926 / 2.94 ( 1335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8740 (p90) cc_final: 0.8432 (p90) REVERT: A 374 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8682 (mp) REVERT: A 406 LYS cc_start: 0.8126 (mttm) cc_final: 0.7920 (mtmt) REVERT: A 465 GLU cc_start: 0.7993 (pp20) cc_final: 0.7603 (pp20) REVERT: A 553 MET cc_start: 0.7522 (tpp) cc_final: 0.7176 (tpp) REVERT: A 606 MET cc_start: 0.8305 (ptp) cc_final: 0.7999 (ptm) REVERT: A 629 ASN cc_start: 0.9264 (t0) cc_final: 0.8804 (t0) REVERT: A 636 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7531 (tm-30) REVERT: B 70 GLU cc_start: 0.8081 (tt0) cc_final: 0.7841 (tt0) REVERT: B 118 GLN cc_start: 0.9087 (pp30) cc_final: 0.8642 (pp30) REVERT: B 366 CYS cc_start: 0.8115 (t) cc_final: 0.7731 (m) REVERT: B 368 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: B 372 GLU cc_start: 0.8122 (tp30) cc_final: 0.7897 (tp30) REVERT: B 375 ASN cc_start: 0.8546 (p0) cc_final: 0.8288 (p0) REVERT: B 490 SER cc_start: 0.8428 (t) cc_final: 0.7557 (p) REVERT: B 494 VAL cc_start: 0.9191 (t) cc_final: 0.8790 (m) REVERT: B 553 MET cc_start: 0.6947 (tpp) cc_final: 0.6466 (tpp) REVERT: B 601 ASN cc_start: 0.7497 (t0) cc_final: 0.7296 (t0) REVERT: B 602 MET cc_start: 0.8441 (tpp) cc_final: 0.8241 (tpp) REVERT: B 607 LYS cc_start: 0.8640 (tppt) cc_final: 0.8401 (mttm) REVERT: B 627 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 629 ASN cc_start: 0.9055 (t0) cc_final: 0.8832 (t0) REVERT: B 654 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8777 (tp) REVERT: B 663 LEU cc_start: 0.8879 (tp) cc_final: 0.8580 (mp) REVERT: B 683 MET cc_start: 0.8301 (ptm) cc_final: 0.7883 (ptp) outliers start: 24 outliers final: 10 residues processed: 126 average time/residue: 0.0962 time to fit residues: 18.0678 Evaluate side-chains 116 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 654 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 108 optimal weight: 0.0050 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.099272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.076657 restraints weight = 18310.633| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.93 r_work: 0.2808 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10309 Z= 0.125 Angle : 0.439 5.800 13877 Z= 0.234 Chirality : 0.039 0.154 1545 Planarity : 0.003 0.038 1765 Dihedral : 4.483 39.069 1359 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.05 % Allowed : 12.38 % Favored : 85.57 % 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: 1.07 (0.25), residues: 1233 helix: 2.02 (0.23), residues: 501 sheet: 0.31 (0.35), residues: 231 loop : -0.41 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.012 0.001 TYR B 134 PHE 0.007 0.001 PHE B 15 TRP 0.014 0.001 TRP A 157 HIS 0.002 0.000 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (10309) covalent geometry : angle 0.43903 / 0.23 (13877) hydrogen bonds : bond 0.03041 / 2.00 ( 482) hydrogen bonds : angle 4.07940 / 2.87 ( 1335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8678 (p90) cc_final: 0.8384 (p90) REVERT: A 374 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8585 (mp) REVERT: A 406 LYS cc_start: 0.8175 (mttm) cc_final: 0.7973 (mtmt) REVERT: A 465 GLU cc_start: 0.7977 (pp20) cc_final: 0.7578 (pp20) REVERT: A 553 MET cc_start: 0.7461 (tpp) cc_final: 0.7114 (tpp) REVERT: A 606 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7890 (ptm) REVERT: A 629 ASN cc_start: 0.9274 (t0) cc_final: 0.8980 (t0) REVERT: A 636 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7572 (tm-30) REVERT: B 70 GLU cc_start: 0.8117 (tt0) cc_final: 0.7868 (tt0) REVERT: B 118 GLN cc_start: 0.9090 (pp30) cc_final: 0.8652 (pp30) REVERT: B 366 CYS cc_start: 0.8136 (t) cc_final: 0.7778 (m) REVERT: B 368 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7086 (pm20) REVERT: B 372 GLU cc_start: 0.8180 (tp30) cc_final: 0.7916 (tp30) REVERT: B 375 ASN cc_start: 0.8564 (p0) cc_final: 0.8282 (p0) REVERT: B 490 SER cc_start: 0.8464 (t) cc_final: 0.7802 (p) REVERT: B 515 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8129 (mm-30) REVERT: B 553 MET cc_start: 0.6966 (tpp) cc_final: 0.6479 (tpp) REVERT: B 564 CYS cc_start: 0.8767 (m) cc_final: 0.8414 (m) REVERT: B 601 ASN cc_start: 0.7487 (t0) cc_final: 0.7173 (t0) REVERT: B 602 MET cc_start: 0.8556 (tpp) cc_final: 0.7940 (tpp) REVERT: B 607 LYS cc_start: 0.8667 (tppt) cc_final: 0.8409 (mttm) REVERT: B 617 MET cc_start: 0.7164 (mmt) cc_final: 0.6936 (mmt) REVERT: B 629 ASN cc_start: 0.9098 (t0) cc_final: 0.8816 (t0) outliers start: 23 outliers final: 15 residues processed: 119 average time/residue: 0.0899 time to fit residues: 15.8420 Evaluate side-chains 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.097572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.075004 restraints weight = 18667.421| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.92 r_work: 0.2777 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10309 Z= 0.188 Angle : 0.484 6.145 13877 Z= 0.255 Chirality : 0.041 0.159 1545 Planarity : 0.003 0.039 1765 Dihedral : 4.649 42.336 1359 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.14 % Allowed : 12.82 % Favored : 85.04 % 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: 0.96 (0.24), residues: 1233 helix: 1.95 (0.23), residues: 500 sheet: 0.26 (0.35), residues: 231 loop : -0.49 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.016 0.002 TYR A 426 PHE 0.010 0.001 PHE B 15 TRP 0.012 0.001 TRP A 157 HIS 0.003 0.001 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (10309) covalent geometry : angle 0.48364 / 0.26 (13877) hydrogen bonds : bond 0.03330 / 2.19 ( 482) hydrogen bonds : angle 4.20020 / 2.96 ( 1335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8686 (p90) cc_final: 0.8396 (p90) REVERT: A 374 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8628 (mp) REVERT: A 406 LYS cc_start: 0.8209 (mttm) cc_final: 0.8003 (mtmt) REVERT: A 465 GLU cc_start: 0.8084 (pp20) cc_final: 0.7674 (pp20) REVERT: A 553 MET cc_start: 0.7477 (tpp) cc_final: 0.7170 (tpp) REVERT: A 573 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8283 (pttm) REVERT: A 606 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.8027 (ptm) REVERT: A 629 ASN cc_start: 0.9294 (t0) cc_final: 0.9005 (t0) REVERT: A 636 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7594 (tm-30) REVERT: B 70 GLU cc_start: 0.8077 (tt0) cc_final: 0.7827 (tt0) REVERT: B 118 GLN cc_start: 0.9112 (pp30) cc_final: 0.8681 (pp30) REVERT: B 366 CYS cc_start: 0.8149 (t) cc_final: 0.7785 (m) REVERT: B 368 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: B 490 SER cc_start: 0.8515 (t) cc_final: 0.7878 (p) REVERT: B 515 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8205 (mm-30) REVERT: B 519 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7794 (mm-30) REVERT: B 553 MET cc_start: 0.7004 (tpp) cc_final: 0.6507 (tpp) REVERT: B 601 ASN cc_start: 0.7673 (t0) cc_final: 0.7384 (t0) REVERT: B 602 MET cc_start: 0.8565 (tpp) cc_final: 0.7917 (tpp) REVERT: B 607 LYS cc_start: 0.8674 (tppt) cc_final: 0.8410 (mttm) REVERT: B 629 ASN cc_start: 0.9131 (t0) cc_final: 0.8798 (t0) outliers start: 24 outliers final: 13 residues processed: 121 average time/residue: 0.0967 time to fit residues: 17.4545 Evaluate side-chains 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.098437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.075800 restraints weight = 18438.669| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.94 r_work: 0.2791 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10309 Z= 0.154 Angle : 0.477 6.842 13877 Z= 0.251 Chirality : 0.040 0.157 1545 Planarity : 0.003 0.039 1765 Dihedral : 4.580 40.157 1359 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.23 % Allowed : 13.54 % Favored : 84.24 % 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: 0.99 (0.24), residues: 1233 helix: 1.97 (0.23), residues: 500 sheet: 0.26 (0.35), residues: 231 loop : -0.46 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 450 TYR 0.012 0.001 TYR B 134 PHE 0.008 0.001 PHE B 15 TRP 0.014 0.001 TRP A 157 HIS 0.002 0.001 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (10309) covalent geometry : angle 0.47748 / 0.25 (13877) hydrogen bonds : bond 0.03205 / 2.11 ( 482) hydrogen bonds : angle 4.15715 / 2.93 ( 1335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8689 (p90) cc_final: 0.8413 (p90) REVERT: A 343 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 374 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8631 (mp) REVERT: A 465 GLU cc_start: 0.8022 (pp20) cc_final: 0.7599 (pp20) REVERT: A 553 MET cc_start: 0.7389 (tpp) cc_final: 0.7038 (tpp) REVERT: A 629 ASN cc_start: 0.9274 (t0) cc_final: 0.8996 (t0) REVERT: A 636 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7587 (tm-30) REVERT: B 70 GLU cc_start: 0.8070 (tt0) cc_final: 0.7823 (tt0) REVERT: B 118 GLN cc_start: 0.9092 (pp30) cc_final: 0.8750 (pp30) REVERT: B 366 CYS cc_start: 0.8134 (t) cc_final: 0.7783 (m) REVERT: B 368 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: B 490 SER cc_start: 0.8484 (t) cc_final: 0.7847 (p) REVERT: B 515 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8038 (mm-30) REVERT: B 519 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7348 (mm-30) REVERT: B 553 MET cc_start: 0.7123 (tpp) cc_final: 0.6645 (tpp) REVERT: B 601 ASN cc_start: 0.7710 (t0) cc_final: 0.7424 (t0) REVERT: B 602 MET cc_start: 0.8590 (tpp) cc_final: 0.8110 (tpp) REVERT: B 607 LYS cc_start: 0.8661 (tppt) cc_final: 0.8385 (mttm) REVERT: B 627 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7031 (tt0) REVERT: B 629 ASN cc_start: 0.9160 (t0) cc_final: 0.8847 (t0) outliers start: 25 outliers final: 16 residues processed: 122 average time/residue: 0.0934 time to fit residues: 17.0832 Evaluate side-chains 121 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 635 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.098113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.075477 restraints weight = 18439.838| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.94 r_work: 0.2780 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10309 Z= 0.179 Angle : 0.500 7.106 13877 Z= 0.261 Chirality : 0.041 0.159 1545 Planarity : 0.003 0.039 1765 Dihedral : 4.642 41.643 1359 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.78 % Allowed : 13.80 % Favored : 84.42 % 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: 0.90 (0.24), residues: 1233 helix: 1.90 (0.23), residues: 506 sheet: 0.24 (0.35), residues: 231 loop : -0.56 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.014 0.002 TYR A 426 PHE 0.009 0.001 PHE B 15 TRP 0.013 0.001 TRP A 157 HIS 0.003 0.001 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (10309) covalent geometry : angle 0.50025 / 0.26 (13877) hydrogen bonds : bond 0.03331 / 2.19 ( 482) hydrogen bonds : angle 4.19622 / 2.96 ( 1335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8672 (p90) cc_final: 0.8395 (p90) REVERT: A 343 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8094 (tt) REVERT: A 374 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8628 (mp) REVERT: A 465 GLU cc_start: 0.8042 (pp20) cc_final: 0.7614 (pp20) REVERT: A 553 MET cc_start: 0.7476 (tpp) cc_final: 0.7165 (tpp) REVERT: A 629 ASN cc_start: 0.9284 (t0) cc_final: 0.9001 (t0) REVERT: A 636 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7598 (tm-30) REVERT: B 70 GLU cc_start: 0.8087 (tt0) cc_final: 0.7842 (tt0) REVERT: B 118 GLN cc_start: 0.9088 (pp30) cc_final: 0.8751 (pp30) REVERT: B 366 CYS cc_start: 0.8107 (t) cc_final: 0.7680 (m) REVERT: B 368 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: B 372 GLU cc_start: 0.8282 (tp30) cc_final: 0.8078 (tp30) REVERT: B 490 SER cc_start: 0.8501 (t) cc_final: 0.7871 (p) REVERT: B 515 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: B 519 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 553 MET cc_start: 0.7047 (tpp) cc_final: 0.6577 (tpp) REVERT: B 601 ASN cc_start: 0.7765 (t0) cc_final: 0.7548 (t0) REVERT: B 602 MET cc_start: 0.8623 (tpp) cc_final: 0.7912 (tpp) REVERT: B 607 LYS cc_start: 0.8668 (tppt) cc_final: 0.8391 (mttm) REVERT: B 627 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7198 (tt0) outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 0.0963 time to fit residues: 16.4227 Evaluate side-chains 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.100828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.078358 restraints weight = 18334.716| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.95 r_work: 0.2828 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10309 Z= 0.101 Angle : 0.454 7.789 13877 Z= 0.239 Chirality : 0.039 0.150 1545 Planarity : 0.003 0.039 1765 Dihedral : 4.323 35.282 1359 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.34 % Allowed : 13.98 % Favored : 84.68 % 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: 1.10 (0.25), residues: 1233 helix: 2.06 (0.24), residues: 507 sheet: 0.35 (0.35), residues: 236 loop : -0.46 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 450 TYR 0.009 0.001 TYR B 373 PHE 0.007 0.001 PHE A 165 TRP 0.018 0.002 TRP A 157 HIS 0.002 0.000 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (10309) covalent geometry : angle 0.45366 / 0.24 (13877) hydrogen bonds : bond 0.02858 / 1.88 ( 482) hydrogen bonds : angle 4.00592 / 2.82 ( 1335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 TYR cc_start: 0.8434 (m-80) cc_final: 0.8149 (m-80) REVERT: A 312 TRP cc_start: 0.8670 (p90) cc_final: 0.8418 (p90) REVERT: A 343 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 465 GLU cc_start: 0.8033 (pp20) cc_final: 0.7609 (pp20) REVERT: A 553 MET cc_start: 0.7564 (tpp) cc_final: 0.7231 (tpp) REVERT: A 629 ASN cc_start: 0.9267 (t0) cc_final: 0.9034 (t0) REVERT: B 70 GLU cc_start: 0.8061 (tt0) cc_final: 0.7841 (tt0) REVERT: B 118 GLN cc_start: 0.9101 (pp30) cc_final: 0.8707 (pp30) REVERT: B 366 CYS cc_start: 0.8092 (t) cc_final: 0.7737 (m) REVERT: B 368 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6848 (pm20) REVERT: B 405 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.8278 (ttm-80) REVERT: B 490 SER cc_start: 0.8391 (t) cc_final: 0.7480 (p) REVERT: B 494 VAL cc_start: 0.9213 (t) cc_final: 0.8823 (m) REVERT: B 515 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7983 (mm-30) REVERT: B 519 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 553 MET cc_start: 0.7059 (tpp) cc_final: 0.6612 (tpp) REVERT: B 602 MET cc_start: 0.8604 (tpp) cc_final: 0.8128 (tpp) REVERT: B 607 LYS cc_start: 0.8671 (tppt) cc_final: 0.8397 (mttm) REVERT: B 617 MET cc_start: 0.7309 (mmt) cc_final: 0.6929 (mmt) REVERT: B 627 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7113 (tt0) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 0.0951 time to fit residues: 17.4749 Evaluate side-chains 122 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.077911 restraints weight = 18133.751| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.80 r_work: 0.2831 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10309 Z= 0.126 Angle : 0.478 8.680 13877 Z= 0.249 Chirality : 0.040 0.154 1545 Planarity : 0.003 0.040 1765 Dihedral : 4.363 36.992 1359 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.25 % Allowed : 14.51 % Favored : 84.24 % 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: 1.05 (0.25), residues: 1233 helix: 1.99 (0.23), residues: 513 sheet: 0.36 (0.35), residues: 236 loop : -0.51 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 450 TYR 0.010 0.001 TYR B 134 PHE 0.008 0.001 PHE B 560 TRP 0.014 0.002 TRP A 157 HIS 0.003 0.000 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10309) covalent geometry : angle 0.47833 / 0.25 (13877) hydrogen bonds : bond 0.02974 / 1.96 ( 482) hydrogen bonds : angle 4.02240 / 2.83 ( 1335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8665 (p90) cc_final: 0.8420 (p90) REVERT: A 343 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8089 (tt) REVERT: A 465 GLU cc_start: 0.7967 (pp20) cc_final: 0.7535 (pp20) REVERT: A 553 MET cc_start: 0.7526 (tpp) cc_final: 0.7211 (tpp) REVERT: A 629 ASN cc_start: 0.9290 (t0) cc_final: 0.9062 (t0) REVERT: B 70 GLU cc_start: 0.8059 (tt0) cc_final: 0.7843 (tt0) REVERT: B 118 GLN cc_start: 0.9088 (pp30) cc_final: 0.8702 (pp30) REVERT: B 366 CYS cc_start: 0.8088 (t) cc_final: 0.7776 (m) REVERT: B 368 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: B 405 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8273 (ttm-80) REVERT: B 490 SER cc_start: 0.8417 (t) cc_final: 0.7739 (p) REVERT: B 553 MET cc_start: 0.7049 (tpp) cc_final: 0.6591 (tpp) REVERT: B 602 MET cc_start: 0.8619 (tpp) cc_final: 0.8119 (tpt) REVERT: B 607 LYS cc_start: 0.8685 (tppt) cc_final: 0.8416 (mttm) REVERT: B 617 MET cc_start: 0.7356 (mmt) cc_final: 0.7013 (mmt) REVERT: B 627 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7112 (tt0) outliers start: 14 outliers final: 12 residues processed: 114 average time/residue: 0.0953 time to fit residues: 16.2548 Evaluate side-chains 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.096775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.075332 restraints weight = 18439.723| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.84 r_work: 0.2781 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10309 Z= 0.204 Angle : 0.537 6.961 13877 Z= 0.278 Chirality : 0.041 0.163 1545 Planarity : 0.003 0.041 1765 Dihedral : 4.661 43.662 1359 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.42 % Allowed : 14.51 % Favored : 84.06 % 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: 0.90 (0.24), residues: 1233 helix: 1.87 (0.23), residues: 512 sheet: 0.32 (0.35), residues: 231 loop : -0.59 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.018 0.002 TYR A 426 PHE 0.009 0.001 PHE B 15 TRP 0.011 0.002 TRP A 157 HIS 0.004 0.001 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (10309) covalent geometry : angle 0.53742 / 0.28 (13877) hydrogen bonds : bond 0.03402 / 2.25 ( 482) hydrogen bonds : angle 4.21731 / 2.97 ( 1335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1991.12 seconds wall clock time: 35 minutes 15.60 seconds (2115.60 seconds total)