Starting phenix.real_space_refine on Fri Mar 6 00:05:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fwk_3337/03_2026/5fwk_3337.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fwk_3337/03_2026/5fwk_3337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5fwk_3337/03_2026/5fwk_3337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fwk_3337/03_2026/5fwk_3337.map" model { file = "/net/cci-nas-00/data/ceres_data/5fwk_3337/03_2026/5fwk_3337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fwk_3337/03_2026/5fwk_3337.cif" } resolution = 3.9 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 8284 2.51 5 N 2227 2.21 5 O 2530 1.98 5 H 13113 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26225 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 10400 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 10243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 10243 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 17, 'TRANS': 613} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2174 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3344 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 19, 'TRANS': 190} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 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: 4.45, per 1000 atoms: 0.17 Number of scatterers: 26225 At special positions: 0 Unit cell: (99.94, 145.965, 134.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 62 16.00 P 7 15.00 Mg 2 11.99 O 2530 8.00 N 2227 7.00 C 8284 6.00 H 13113 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.0 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3068 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 49.8% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 4.029A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 61 removed outlier: 3.778A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.679A pdb=" N LYS A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 309 removed outlier: 4.824A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 398 through 420 Processing helix chain 'A' and resid 422 through 444 removed outlier: 5.723A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 515 through 522 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 610 removed outlier: 3.633A pdb=" N ALA A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 622 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: 3.573A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 removed outlier: 4.309A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 59 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 117 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 187 through 193 removed outlier: 4.148A pdb=" N THR B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 280 through 284 removed outlier: 4.337A pdb=" N ASN B 283 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 398 through 422 Processing helix chain 'B' and resid 422 through 444 removed outlier: 4.230A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.533A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.582A pdb=" N GLN B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 560 Processing helix chain 'B' and resid 560 through 571 Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 613 through 620 Processing helix chain 'B' and resid 632 through 646 Processing helix chain 'B' and resid 648 through 666 Processing helix chain 'B' and resid 672 through 689 Processing helix chain 'E' and resid 4 through 8 Processing helix chain 'E' and resid 24 through 74 removed outlier: 4.694A pdb=" N ARG E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 112 removed outlier: 3.547A pdb=" N ARG E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 107 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 142 through 144 No H-bonds generated for 'chain 'K' and resid 142 through 144' Processing helix chain 'K' and resid 160 through 164 Processing helix chain 'K' and resid 182 through 187 Processing helix chain 'K' and resid 192 through 210 Processing helix chain 'K' and resid 218 through 230 removed outlier: 4.217A pdb=" N ASP K 228 " --> pdb=" O GLY K 224 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU K 229 " --> pdb=" O LYS K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 261 Processing helix chain 'K' and resid 265 through 277 Processing helix chain 'K' and resid 285 through 291 Processing sheet with id=AA, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.588A pdb=" N GLY B 178 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU B 218 " --> pdb=" O PRO B 77 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AC, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.648A pdb=" N GLU A 218 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS A 180 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL A 145 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 182 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 143 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS A 184 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AE, first strand: chain 'A' and resid 317 through 323 removed outlier: 6.708A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 467 through 468 removed outlier: 4.354A pdb=" N HIS A 458 " --> pdb=" O TYR A 512 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'A' and resid 578 through 580 Processing sheet with id=BA, first strand: chain 'B' and resid 360 through 363 removed outlier: 7.039A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 318 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER E 127 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS B 320 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER E 125 " --> pdb=" O HIS B 320 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER B 322 " --> pdb=" O GLY E 123 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 458 through 459 removed outlier: 3.994A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'B' and resid 577 through 580 removed outlier: 3.545A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing sheet with id=KA, first strand: chain 'K' and resid 146 through 148 Processing sheet with id=KB, first strand: chain 'K' and resid 231 through 232 675 hydrogen bonds defined for protein. 1851 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: 6.70 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 13095 1.13 - 1.30: 2264 1.30 - 1.47: 4961 1.47 - 1.64: 6031 1.64 - 1.81: 106 Bond restraints: 26457 Sorted by residual: bond pdb=" CE1 HIS B 632 " pdb=" HE1 HIS B 632 " ideal model delta sigma weight residual 0.930 1.104 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" CD2 HIS B 632 " pdb=" HD2 HIS B 632 " ideal model delta sigma weight residual 0.930 1.098 -0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" N ASP A 311 " pdb=" H ASP A 311 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C4 ATP A 725 " pdb=" C5 ATP A 725 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" CD2 HIS A 632 " pdb=" HD2 HIS A 632 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.89e+01 ... (remaining 26452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.55: 47124 5.55 - 11.09: 815 11.09 - 16.64: 20 16.64 - 22.18: 1 22.18 - 27.73: 3 Bond angle restraints: 47963 Sorted by residual: angle pdb=" PB ATP A 725 " pdb=" O3B ATP A 725 " pdb=" PG ATP A 725 " ideal model delta sigma weight residual 139.87 112.14 27.73 1.00e+00 1.00e+00 7.69e+02 angle pdb=" PB ATP B 725 " pdb=" O3B ATP B 725 " pdb=" PG ATP B 725 " ideal model delta sigma weight residual 139.87 114.43 25.44 1.00e+00 1.00e+00 6.47e+02 angle pdb=" PA ATP B 725 " pdb=" O3A ATP B 725 " pdb=" PB ATP B 725 " ideal model delta sigma weight residual 136.83 112.04 24.79 1.00e+00 1.00e+00 6.15e+02 angle pdb=" PA ATP A 725 " pdb=" O3A ATP A 725 " pdb=" PB ATP A 725 " ideal model delta sigma weight residual 136.83 114.69 22.14 1.00e+00 1.00e+00 4.90e+02 angle pdb=" C ASN B 78 " pdb=" N PRO B 79 " pdb=" CA PRO B 79 " ideal model delta sigma weight residual 119.56 129.61 -10.05 1.02e+00 9.61e-01 9.70e+01 ... (remaining 47958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 11649 17.88 - 35.75: 303 35.75 - 53.63: 137 53.63 - 71.50: 245 71.50 - 89.37: 7 Dihedral angle restraints: 12341 sinusoidal: 6886 harmonic: 5455 Sorted by residual: dihedral pdb=" CD2 HIS A 458 " pdb=" CG HIS A 458 " pdb=" ND1 HIS A 458 " pdb=" HD1 HIS A 458 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CD2 HIS B 315 " pdb=" CG HIS B 315 " pdb=" ND1 HIS B 315 " pdb=" HD1 HIS B 315 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CD2 HIS B 632 " pdb=" CG HIS B 632 " pdb=" ND1 HIS B 632 " pdb=" HD1 HIS B 632 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 12338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1041 0.052 - 0.103: 652 0.103 - 0.155: 227 0.155 - 0.206: 53 0.206 - 0.258: 6 Chirality restraints: 1979 Sorted by residual: chirality pdb=" CA ASN B 425 " pdb=" N ASN B 425 " pdb=" C ASN B 425 " pdb=" CB ASN B 425 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PHE B 659 " pdb=" N PHE B 659 " pdb=" C PHE B 659 " pdb=" CB PHE B 659 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LYS B 36 " pdb=" N LYS B 36 " pdb=" C LYS B 36 " pdb=" CB LYS B 36 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1976 not shown) Planarity restraints: 3848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 46 " -0.293 2.00e-02 2.50e+03 3.71e-01 2.07e+03 pdb=" CG ASN B 46 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN B 46 " 0.363 2.00e-02 2.50e+03 pdb=" ND2 ASN B 46 " -0.083 2.00e-02 2.50e+03 pdb="HD21 ASN B 46 " 0.579 2.00e-02 2.50e+03 pdb="HD22 ASN B 46 " -0.513 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 46 " -0.231 2.00e-02 2.50e+03 2.27e-01 7.74e+02 pdb=" CG ASN A 46 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 46 " 0.218 2.00e-02 2.50e+03 pdb=" ND2 ASN A 46 " -0.007 2.00e-02 2.50e+03 pdb="HD21 ASN A 46 " 0.321 2.00e-02 2.50e+03 pdb="HD22 ASN A 46 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 458 " -0.072 2.00e-02 2.50e+03 7.58e-02 1.29e+02 pdb=" CG HIS A 458 " -0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS A 458 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 HIS A 458 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS A 458 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 458 " 0.024 2.00e-02 2.50e+03 pdb=" HD1 HIS A 458 " 0.175 2.00e-02 2.50e+03 pdb=" HD2 HIS A 458 " 0.060 2.00e-02 2.50e+03 pdb=" HE1 HIS A 458 " -0.058 2.00e-02 2.50e+03 ... (remaining 3845 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.86: 356 1.86 - 2.54: 25305 2.54 - 3.23: 84419 3.23 - 3.91: 105558 3.91 - 4.60: 166662 Nonbonded interactions: 382300 Sorted by model distance: nonbonded pdb=" OD1 ASN A 46 " pdb="MG MG A 726 " model vdw 1.173 2.050 nonbonded pdb=" HB2 GLN B 609 " pdb=" HG3 ARG B 612 " model vdw 1.204 2.440 nonbonded pdb=" OD1 ASN B 46 " pdb="MG MG B 726 " model vdw 1.316 2.050 nonbonded pdb=" OE1 GLN A 80 " pdb=" H GLN A 80 " model vdw 1.471 2.450 nonbonded pdb=" OE1 GLU B 299 " pdb=" H GLU B 299 " model vdw 1.483 2.450 ... (remaining 382295 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 10 through 220 or resid 273 through 726)) selection = (chain 'B' and (resid 10 through 690 or (resid 691 and (name N )) or resid 725 t \ hrough 726)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.810 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:1.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.016 0.113 13344 Z= 0.990 Angle : 1.315 27.726 17970 Z= 0.951 Chirality : 0.071 0.258 1979 Planarity : 0.011 0.153 2301 Dihedral : 10.313 89.375 5213 Min Nonbonded Distance : 1.173 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.95 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: -0.44 (0.20), residues: 1593 helix: -0.21 (0.17), residues: 675 sheet: 0.04 (0.36), residues: 208 loop : -0.29 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 82 TYR 0.044 0.007 TYR A 192 PHE 0.039 0.006 PHE A 329 TRP 0.043 0.009 TRP E 31 HIS 0.008 0.002 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.01571 (13344) covalent geometry : angle 1.31496 (17970) hydrogen bonds : bond 0.16227 ( 675) hydrogen bonds : angle 7.27892 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7045 (t0) cc_final: 0.6321 (m-30) REVERT: A 275 LYS cc_start: 0.9189 (mttt) cc_final: 0.8560 (mmmt) REVERT: A 276 TYR cc_start: 0.7713 (m-80) cc_final: 0.7221 (p90) REVERT: A 563 LEU cc_start: 0.7795 (tp) cc_final: 0.7338 (tp) REVERT: A 567 MET cc_start: 0.8793 (mtp) cc_final: 0.8086 (mtp) REVERT: A 606 MET cc_start: 0.8266 (mmm) cc_final: 0.7787 (mmm) REVERT: A 609 GLN cc_start: 0.7934 (tt0) cc_final: 0.6663 (tm-30) REVERT: A 683 MET cc_start: 0.9004 (mmm) cc_final: 0.8752 (mmm) REVERT: B 305 TYR cc_start: 0.8130 (t80) cc_final: 0.7656 (t80) REVERT: B 323 VAL cc_start: 0.9163 (m) cc_final: 0.8764 (m) REVERT: B 363 MET cc_start: 0.7230 (ptp) cc_final: 0.6828 (ptp) REVERT: B 565 LYS cc_start: 0.8864 (mttt) cc_final: 0.8603 (ttpt) REVERT: B 593 THR cc_start: 0.8259 (m) cc_final: 0.7772 (p) REVERT: B 602 MET cc_start: 0.8125 (tpp) cc_final: 0.7829 (tpp) REVERT: B 621 MET cc_start: 0.8505 (mmp) cc_final: 0.8269 (mmp) REVERT: E 14 ASP cc_start: 0.8259 (p0) cc_final: 0.7944 (p0) REVERT: E 34 GLN cc_start: 0.8251 (tp40) cc_final: 0.7897 (tp40) REVERT: E 51 ASP cc_start: 0.7290 (t70) cc_final: 0.7040 (t0) REVERT: K 210 ARG cc_start: 0.6642 (ttp-170) cc_final: 0.6259 (ttp80) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.2972 time to fit residues: 179.0621 Evaluate side-chains 265 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 310 ASN B 396 GLN B 397 GLN B 523 GLN K 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.123901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.095286 restraints weight = 94519.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099406 restraints weight = 43034.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.101992 restraints weight = 25681.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.103573 restraints weight = 18541.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.104548 restraints weight = 15212.003| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13344 Z= 0.160 Angle : 0.588 5.383 17970 Z= 0.330 Chirality : 0.041 0.182 1979 Planarity : 0.006 0.059 2301 Dihedral : 7.656 86.247 1815 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.24 % Allowed : 7.94 % Favored : 90.81 % 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: 0.28 (0.21), residues: 1593 helix: 0.87 (0.19), residues: 687 sheet: -0.11 (0.34), residues: 214 loop : -0.30 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 506 TYR 0.018 0.002 TYR A 426 PHE 0.020 0.002 PHE B 39 TRP 0.030 0.002 TRP E 31 HIS 0.009 0.001 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00343 (13344) covalent geometry : angle 0.58840 (17970) hydrogen bonds : bond 0.05792 ( 675) hydrogen bonds : angle 5.78310 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7177 (t0) cc_final: 0.6667 (m-30) REVERT: A 275 LYS cc_start: 0.8188 (mttt) cc_final: 0.7839 (mmtt) REVERT: A 457 TYR cc_start: 0.8826 (m-80) cc_final: 0.8595 (m-80) REVERT: A 563 LEU cc_start: 0.7562 (tp) cc_final: 0.7044 (tp) REVERT: A 567 MET cc_start: 0.8383 (mtp) cc_final: 0.7682 (mtp) REVERT: A 592 VAL cc_start: 0.9055 (m) cc_final: 0.8424 (p) REVERT: A 606 MET cc_start: 0.7562 (mmm) cc_final: 0.7207 (mmm) REVERT: A 609 GLN cc_start: 0.7467 (tt0) cc_final: 0.6575 (pp30) REVERT: A 683 MET cc_start: 0.8842 (mmm) cc_final: 0.8501 (mmm) REVERT: B 49 ASP cc_start: 0.7832 (m-30) cc_final: 0.7401 (m-30) REVERT: B 200 GLU cc_start: 0.8069 (tt0) cc_final: 0.7843 (tt0) REVERT: B 305 TYR cc_start: 0.8028 (t80) cc_final: 0.7510 (t80) REVERT: B 363 MET cc_start: 0.7010 (ptp) cc_final: 0.6561 (ptp) REVERT: B 425 ASN cc_start: 0.8334 (m-40) cc_final: 0.7835 (m110) REVERT: B 512 TYR cc_start: 0.8026 (m-80) cc_final: 0.7591 (m-80) REVERT: B 593 THR cc_start: 0.8429 (m) cc_final: 0.7861 (p) REVERT: B 602 MET cc_start: 0.7713 (tpp) cc_final: 0.7238 (tpp) REVERT: E 28 LEU cc_start: 0.8250 (tt) cc_final: 0.7976 (tt) REVERT: E 31 TRP cc_start: 0.6962 (t60) cc_final: 0.6593 (t60) REVERT: E 46 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7360 (tm-30) REVERT: K 144 GLU cc_start: 0.7479 (mp0) cc_final: 0.7083 (tm-30) outliers start: 18 outliers final: 10 residues processed: 302 average time/residue: 0.2390 time to fit residues: 104.8877 Evaluate side-chains 244 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 234 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain E residue 3 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.116433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.087720 restraints weight = 97715.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.091408 restraints weight = 45998.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.093763 restraints weight = 28442.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095223 restraints weight = 21036.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095919 restraints weight = 17535.840| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13344 Z= 0.285 Angle : 0.679 6.202 17970 Z= 0.377 Chirality : 0.042 0.214 1979 Planarity : 0.005 0.051 2301 Dihedral : 7.689 89.354 1815 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.93 % Allowed : 9.88 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.05 (0.20), residues: 1593 helix: 0.75 (0.19), residues: 686 sheet: -0.30 (0.33), residues: 206 loop : -0.65 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 168 TYR 0.021 0.003 TYR A 426 PHE 0.027 0.002 PHE K 124 TRP 0.023 0.002 TRP E 31 HIS 0.007 0.002 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00630 (13344) covalent geometry : angle 0.67870 (17970) hydrogen bonds : bond 0.05553 ( 675) hydrogen bonds : angle 5.64607 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.8982 (tttt) cc_final: 0.8731 (tttp) REVERT: A 385 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.6697 (m-30) REVERT: A 503 VAL cc_start: 0.9081 (t) cc_final: 0.8863 (p) REVERT: A 563 LEU cc_start: 0.7816 (tp) cc_final: 0.7273 (tp) REVERT: A 567 MET cc_start: 0.8296 (mtp) cc_final: 0.7694 (mtp) REVERT: A 606 MET cc_start: 0.7735 (mmm) cc_final: 0.7201 (mmm) REVERT: A 609 GLN cc_start: 0.7205 (tt0) cc_final: 0.6858 (tm-30) REVERT: A 620 MET cc_start: 0.5677 (mtp) cc_final: 0.5122 (mtp) REVERT: A 625 HIS cc_start: 0.7453 (m-70) cc_final: 0.6999 (m-70) REVERT: B 126 ILE cc_start: 0.6701 (pt) cc_final: 0.6460 (pt) REVERT: B 602 MET cc_start: 0.8073 (tpp) cc_final: 0.7365 (tpp) REVERT: B 605 ILE cc_start: 0.9048 (mt) cc_final: 0.8747 (tp) REVERT: B 606 MET cc_start: 0.8397 (mmm) cc_final: 0.7932 (mmt) REVERT: B 621 MET cc_start: 0.8077 (mmp) cc_final: 0.7857 (mmp) REVERT: E 46 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7966 (tm-30) REVERT: K 144 GLU cc_start: 0.7590 (mp0) cc_final: 0.7355 (tm-30) REVERT: K 210 ARG cc_start: 0.6420 (ttp-170) cc_final: 0.5305 (tpt90) outliers start: 28 outliers final: 19 residues processed: 250 average time/residue: 0.2259 time to fit residues: 84.1593 Evaluate side-chains 225 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain E residue 3 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 123 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.118016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089265 restraints weight = 96202.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093054 restraints weight = 45259.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095454 restraints weight = 27809.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096934 restraints weight = 20537.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097830 restraints weight = 17069.985| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13344 Z= 0.150 Angle : 0.535 5.888 17970 Z= 0.292 Chirality : 0.039 0.165 1979 Planarity : 0.004 0.042 2301 Dihedral : 7.321 86.893 1815 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.31 % Allowed : 11.46 % Favored : 87.22 % 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: 0.24 (0.21), residues: 1593 helix: 1.18 (0.19), residues: 690 sheet: -0.50 (0.33), residues: 213 loop : -0.60 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.016 0.002 TYR A 137 PHE 0.015 0.002 PHE A 429 TRP 0.017 0.002 TRP E 31 HIS 0.005 0.001 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00328 (13344) covalent geometry : angle 0.53474 (17970) hydrogen bonds : bond 0.04565 ( 675) hydrogen bonds : angle 5.20033 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 TYR cc_start: 0.6241 (t80) cc_final: 0.5988 (t80) REVERT: A 563 LEU cc_start: 0.7727 (tp) cc_final: 0.7073 (tp) REVERT: A 567 MET cc_start: 0.8245 (mtp) cc_final: 0.7651 (mtp) REVERT: A 606 MET cc_start: 0.7611 (mmm) cc_final: 0.7085 (mmm) REVERT: A 609 GLN cc_start: 0.7111 (tt0) cc_final: 0.6769 (tm-30) REVERT: B 422 ASP cc_start: 0.6031 (t0) cc_final: 0.5630 (t0) REVERT: B 425 ASN cc_start: 0.8173 (m-40) cc_final: 0.7771 (m110) REVERT: B 602 MET cc_start: 0.8068 (tpp) cc_final: 0.7445 (tpp) REVERT: E 46 GLU cc_start: 0.8592 (tm-30) cc_final: 0.7960 (tm-30) REVERT: K 259 SER cc_start: 0.5500 (p) cc_final: 0.5218 (t) outliers start: 19 outliers final: 14 residues processed: 230 average time/residue: 0.1991 time to fit residues: 70.3594 Evaluate side-chains 212 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain E residue 3 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 137 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 0.0030 chunk 68 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.119603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091157 restraints weight = 95314.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094883 restraints weight = 44870.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.097255 restraints weight = 27668.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098707 restraints weight = 20468.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099607 restraints weight = 17058.709| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13344 Z= 0.114 Angle : 0.505 6.540 17970 Z= 0.271 Chirality : 0.039 0.166 1979 Planarity : 0.004 0.042 2301 Dihedral : 7.059 89.477 1815 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.24 % Allowed : 12.15 % Favored : 86.60 % 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: 0.48 (0.21), residues: 1593 helix: 1.47 (0.20), residues: 692 sheet: -0.54 (0.33), residues: 208 loop : -0.52 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.015 0.001 TYR A 457 PHE 0.015 0.001 PHE A 429 TRP 0.014 0.001 TRP E 31 HIS 0.004 0.001 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00249 (13344) covalent geometry : angle 0.50520 (17970) hydrogen bonds : bond 0.04027 ( 675) hydrogen bonds : angle 4.90859 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 LEU cc_start: 0.7763 (tp) cc_final: 0.7095 (tp) REVERT: A 567 MET cc_start: 0.8248 (mtp) cc_final: 0.7638 (mtp) REVERT: A 606 MET cc_start: 0.7603 (mmm) cc_final: 0.7033 (mmm) REVERT: A 609 GLN cc_start: 0.7024 (tt0) cc_final: 0.6664 (tm-30) REVERT: B 54 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8433 (tp) REVERT: B 422 ASP cc_start: 0.6292 (t0) cc_final: 0.5874 (t0) REVERT: B 425 ASN cc_start: 0.8123 (m-40) cc_final: 0.7712 (m110) REVERT: B 602 MET cc_start: 0.8012 (tpp) cc_final: 0.7610 (tpp) REVERT: E 46 GLU cc_start: 0.8641 (tm-30) cc_final: 0.7977 (tm-30) REVERT: K 210 ARG cc_start: 0.6374 (ttp-170) cc_final: 0.4920 (tpt90) outliers start: 18 outliers final: 13 residues processed: 229 average time/residue: 0.2064 time to fit residues: 72.0575 Evaluate side-chains 211 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 73 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 130 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 396 GLN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.118163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089770 restraints weight = 96004.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093527 restraints weight = 44099.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095931 restraints weight = 26726.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097413 restraints weight = 19432.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098244 restraints weight = 16022.678| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13344 Z= 0.120 Angle : 0.509 6.895 17970 Z= 0.270 Chirality : 0.039 0.161 1979 Planarity : 0.003 0.040 2301 Dihedral : 6.967 88.141 1815 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.10 % Allowed : 13.19 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1593 helix: 1.59 (0.20), residues: 691 sheet: -0.48 (0.33), residues: 206 loop : -0.48 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 240 TYR 0.013 0.001 TYR A 457 PHE 0.013 0.001 PHE A 429 TRP 0.012 0.001 TRP E 31 HIS 0.004 0.001 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00265 (13344) covalent geometry : angle 0.50930 (17970) hydrogen bonds : bond 0.03897 ( 675) hydrogen bonds : angle 4.81714 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 LEU cc_start: 0.8003 (tp) cc_final: 0.7473 (tp) REVERT: A 567 MET cc_start: 0.8270 (mtp) cc_final: 0.7655 (mtp) REVERT: A 606 MET cc_start: 0.7609 (mmm) cc_final: 0.7023 (mmm) REVERT: A 609 GLN cc_start: 0.7010 (tt0) cc_final: 0.6635 (tm-30) REVERT: B 54 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8435 (tp) REVERT: B 422 ASP cc_start: 0.6343 (t0) cc_final: 0.5854 (t0) REVERT: B 425 ASN cc_start: 0.8011 (m-40) cc_final: 0.7616 (m110) REVERT: B 602 MET cc_start: 0.8051 (tpp) cc_final: 0.7620 (tpp) REVERT: E 46 GLU cc_start: 0.8594 (tm-30) cc_final: 0.7956 (tm-30) REVERT: K 141 LEU cc_start: 0.6722 (tp) cc_final: 0.6447 (tt) REVERT: K 210 ARG cc_start: 0.6397 (ttp-170) cc_final: 0.5197 (tpt90) outliers start: 16 outliers final: 11 residues processed: 218 average time/residue: 0.2103 time to fit residues: 70.0646 Evaluate side-chains 206 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain K residue 282 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 42 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 279 GLN B 320 HIS ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.116588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.088393 restraints weight = 96617.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092123 restraints weight = 44639.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.094484 restraints weight = 27044.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095969 restraints weight = 19691.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096798 restraints weight = 16219.806| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13344 Z= 0.162 Angle : 0.529 6.581 17970 Z= 0.283 Chirality : 0.039 0.158 1979 Planarity : 0.004 0.040 2301 Dihedral : 7.141 88.019 1815 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.24 % Allowed : 13.54 % Favored : 85.22 % 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: 0.47 (0.21), residues: 1593 helix: 1.52 (0.20), residues: 694 sheet: -0.52 (0.33), residues: 206 loop : -0.61 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 504 TYR 0.014 0.002 TYR A 457 PHE 0.018 0.002 PHE B 433 TRP 0.013 0.001 TRP E 31 HIS 0.004 0.001 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00358 (13344) covalent geometry : angle 0.52884 (17970) hydrogen bonds : bond 0.04013 ( 675) hydrogen bonds : angle 4.88402 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 LEU cc_start: 0.8068 (tp) cc_final: 0.7520 (tp) REVERT: A 567 MET cc_start: 0.8275 (mtp) cc_final: 0.7701 (mtp) REVERT: A 606 MET cc_start: 0.7614 (mmm) cc_final: 0.7022 (mmm) REVERT: A 609 GLN cc_start: 0.7013 (tt0) cc_final: 0.6639 (tm-30) REVERT: A 683 MET cc_start: 0.8973 (mmm) cc_final: 0.8490 (mmm) REVERT: B 54 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8489 (tp) REVERT: B 422 ASP cc_start: 0.6334 (t0) cc_final: 0.5835 (t0) REVERT: B 425 ASN cc_start: 0.8120 (m-40) cc_final: 0.7763 (m110) REVERT: B 602 MET cc_start: 0.8082 (tpp) cc_final: 0.7675 (tpp) REVERT: E 46 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8009 (tm-30) REVERT: K 210 ARG cc_start: 0.6404 (ttp-170) cc_final: 0.5236 (tpt90) outliers start: 18 outliers final: 11 residues processed: 214 average time/residue: 0.2145 time to fit residues: 70.4321 Evaluate side-chains 202 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain K residue 282 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 436 ASN ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.116393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.088090 restraints weight = 97075.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.091823 restraints weight = 44950.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094162 restraints weight = 27231.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095617 restraints weight = 19875.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.096338 restraints weight = 16428.095| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13344 Z= 0.158 Angle : 0.529 7.155 17970 Z= 0.283 Chirality : 0.039 0.161 1979 Planarity : 0.004 0.039 2301 Dihedral : 7.146 87.740 1815 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.45 % Allowed : 13.81 % Favored : 84.74 % 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: 0.48 (0.21), residues: 1593 helix: 1.61 (0.20), residues: 694 sheet: -0.52 (0.34), residues: 208 loop : -0.71 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 30 TYR 0.017 0.001 TYR A 56 PHE 0.021 0.002 PHE A 321 TRP 0.016 0.001 TRP A 157 HIS 0.004 0.001 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00348 (13344) covalent geometry : angle 0.52879 (17970) hydrogen bonds : bond 0.03941 ( 675) hydrogen bonds : angle 4.83370 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8497 (t0) cc_final: 0.6500 (t0) REVERT: A 37 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7010 (mt-10) REVERT: A 563 LEU cc_start: 0.8071 (tp) cc_final: 0.7514 (tp) REVERT: A 567 MET cc_start: 0.8289 (mtp) cc_final: 0.7685 (mtp) REVERT: A 606 MET cc_start: 0.7589 (mmm) cc_final: 0.6986 (mmm) REVERT: A 609 GLN cc_start: 0.7016 (tt0) cc_final: 0.6656 (tm-30) REVERT: A 683 MET cc_start: 0.8984 (mmm) cc_final: 0.8468 (mmm) REVERT: B 54 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8466 (tp) REVERT: B 422 ASP cc_start: 0.6355 (t0) cc_final: 0.5842 (t0) REVERT: B 425 ASN cc_start: 0.8144 (m-40) cc_final: 0.7800 (m110) REVERT: B 602 MET cc_start: 0.8099 (tpp) cc_final: 0.7658 (tpp) REVERT: E 46 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8018 (tm-30) REVERT: K 141 LEU cc_start: 0.6456 (tp) cc_final: 0.5989 (pt) REVERT: K 210 ARG cc_start: 0.6384 (ttp-170) cc_final: 0.5240 (tpt90) outliers start: 21 outliers final: 19 residues processed: 211 average time/residue: 0.2053 time to fit residues: 66.3694 Evaluate side-chains 207 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain K residue 282 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 16 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.117294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.089008 restraints weight = 96196.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.092716 restraints weight = 44399.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095072 restraints weight = 26883.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.096510 restraints weight = 19595.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.097149 restraints weight = 16206.255| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13344 Z= 0.117 Angle : 0.508 7.699 17970 Z= 0.269 Chirality : 0.039 0.165 1979 Planarity : 0.003 0.038 2301 Dihedral : 6.970 85.498 1815 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.10 % Allowed : 14.57 % Favored : 84.32 % 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: 0.58 (0.21), residues: 1593 helix: 1.69 (0.20), residues: 698 sheet: -0.52 (0.33), residues: 214 loop : -0.66 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 30 TYR 0.012 0.001 TYR A 457 PHE 0.021 0.001 PHE A 321 TRP 0.013 0.001 TRP A 157 HIS 0.003 0.001 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00262 (13344) covalent geometry : angle 0.50830 (17970) hydrogen bonds : bond 0.03698 ( 675) hydrogen bonds : angle 4.71450 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8434 (t0) cc_final: 0.6733 (t0) REVERT: A 37 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7024 (mt-10) REVERT: A 563 LEU cc_start: 0.7960 (tp) cc_final: 0.7123 (tp) REVERT: A 567 MET cc_start: 0.8276 (mtp) cc_final: 0.7532 (mtp) REVERT: A 606 MET cc_start: 0.7582 (mmm) cc_final: 0.6980 (mmm) REVERT: A 609 GLN cc_start: 0.6868 (tt0) cc_final: 0.6519 (tm-30) REVERT: A 683 MET cc_start: 0.8978 (mmm) cc_final: 0.8463 (mmm) REVERT: B 54 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8403 (tp) REVERT: B 125 MET cc_start: 0.7545 (mmt) cc_final: 0.7223 (mmp) REVERT: B 422 ASP cc_start: 0.6301 (t0) cc_final: 0.5761 (t0) REVERT: B 425 ASN cc_start: 0.8013 (m-40) cc_final: 0.7691 (m110) REVERT: B 602 MET cc_start: 0.8021 (tpp) cc_final: 0.7584 (tpp) REVERT: E 46 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8119 (tm-30) REVERT: K 141 LEU cc_start: 0.6585 (tp) cc_final: 0.5974 (pt) REVERT: K 210 ARG cc_start: 0.6355 (ttp-170) cc_final: 0.5203 (tpt90) outliers start: 16 outliers final: 14 residues processed: 208 average time/residue: 0.2021 time to fit residues: 64.5740 Evaluate side-chains 208 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 142 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.117086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.088691 restraints weight = 96690.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092425 restraints weight = 45081.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094789 restraints weight = 27436.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096260 restraints weight = 20032.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096967 restraints weight = 16567.782| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13344 Z= 0.128 Angle : 0.520 9.147 17970 Z= 0.275 Chirality : 0.039 0.163 1979 Planarity : 0.004 0.045 2301 Dihedral : 6.942 84.388 1815 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.10 % Allowed : 14.78 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.56 (0.21), residues: 1593 helix: 1.67 (0.20), residues: 699 sheet: -0.44 (0.34), residues: 208 loop : -0.69 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 612 TYR 0.011 0.001 TYR A 457 PHE 0.023 0.001 PHE A 321 TRP 0.014 0.001 TRP A 157 HIS 0.004 0.001 HIS B 632 Details of bonding type rmsd covalent geometry : bond 0.00284 (13344) covalent geometry : angle 0.52040 (17970) hydrogen bonds : bond 0.03683 ( 675) hydrogen bonds : angle 4.70180 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8442 (t0) cc_final: 0.6992 (t0) REVERT: A 37 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7113 (mt-10) REVERT: A 563 LEU cc_start: 0.8052 (tp) cc_final: 0.7530 (tp) REVERT: A 567 MET cc_start: 0.8213 (mtp) cc_final: 0.7674 (mtp) REVERT: A 570 ILE cc_start: 0.9253 (mm) cc_final: 0.8773 (tp) REVERT: A 606 MET cc_start: 0.7580 (mmm) cc_final: 0.6991 (mmm) REVERT: A 609 GLN cc_start: 0.6862 (tt0) cc_final: 0.6528 (tm-30) REVERT: A 683 MET cc_start: 0.8937 (mmm) cc_final: 0.8399 (mmm) REVERT: B 54 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8411 (tp) REVERT: B 422 ASP cc_start: 0.6287 (t0) cc_final: 0.5742 (t0) REVERT: B 425 ASN cc_start: 0.8072 (m-40) cc_final: 0.7748 (m110) REVERT: B 602 MET cc_start: 0.8045 (tpp) cc_final: 0.7589 (tpp) REVERT: E 46 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8126 (tm-30) REVERT: K 141 LEU cc_start: 0.6332 (tp) cc_final: 0.5940 (pt) outliers start: 16 outliers final: 14 residues processed: 211 average time/residue: 0.2058 time to fit residues: 66.7342 Evaluate side-chains 210 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.116734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.088635 restraints weight = 96145.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.092305 restraints weight = 44442.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094644 restraints weight = 26951.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096103 restraints weight = 19648.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096810 restraints weight = 16195.312| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13344 Z= 0.135 Angle : 0.514 7.814 17970 Z= 0.273 Chirality : 0.039 0.165 1979 Planarity : 0.004 0.044 2301 Dihedral : 6.946 83.868 1815 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.10 % Allowed : 14.99 % Favored : 83.91 % 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: 0.56 (0.21), residues: 1593 helix: 1.69 (0.20), residues: 699 sheet: -0.46 (0.34), residues: 205 loop : -0.72 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 612 TYR 0.011 0.001 TYR A 457 PHE 0.029 0.001 PHE A 321 TRP 0.013 0.001 TRP A 157 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00302 (13344) covalent geometry : angle 0.51365 (17970) hydrogen bonds : bond 0.03681 ( 675) hydrogen bonds : angle 4.71323 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4322.05 seconds wall clock time: 74 minutes 20.52 seconds (4460.52 seconds total)