Starting phenix.real_space_refine on Thu Jul 2 21:26:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pm0_13508/07_2026/7pm0_13508.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm0_13508/07_2026/7pm0_13508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2026/7pm0_13508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2026/7pm0_13508.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2026/7pm0_13508.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2026/7pm0_13508.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2026/7pm0_13508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2026/7pm0_13508.cif" } resolution = 3.6 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= 0.001 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 Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6482 2.51 5 N 1723 2.21 5 O 1897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10169 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6130 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 27, 'TRANS': 723} Chain breaks: 3 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.11, per 1000 atoms: 0.21 Number of scatterers: 10169 At special positions: 0 Unit cell: (104.5, 132, 152.9, 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) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1897 8.00 N 1723 7.00 C 6482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 357.9 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 15 sheets defined 56.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.204A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.482A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.612A pdb=" N ILE A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.670A pdb=" N MET A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.724A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.370A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 6.081A pdb=" N GLU A 273 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.301A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.778A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.675A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.857A pdb=" N MET A 478 " --> pdb=" O GLN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.589A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 4.027A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.777A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.829A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.066A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.584A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.666A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 removed outlier: 3.800A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.899A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.929A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.859A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.643A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.541A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.791A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.286A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.475A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.570A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 375 removed outlier: 4.177A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.653A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 242 removed outlier: 3.988A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 344 removed outlier: 5.539A pdb=" N SER A 342 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 349 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 344 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.589A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.550A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 107 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.524A pdb=" N THR C 66 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.349A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 528 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2916 1.33 - 1.47: 2821 1.47 - 1.60: 4544 1.60 - 1.73: 3 1.73 - 1.87: 102 Bond restraints: 10386 Sorted by residual: bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.05e+00 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.01e+00 bond pdb=" O2 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" O1 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.565 1.507 0.058 2.00e-02 2.50e+03 8.28e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.50e+00 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 13845 2.88 - 5.76: 164 5.76 - 8.65: 12 8.65 - 11.53: 6 11.53 - 14.41: 1 Bond angle restraints: 14028 Sorted by residual: angle pdb=" C20 9UE C 404 " pdb=" C8 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 118.25 103.84 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" CB MET C 82 " pdb=" CG MET C 82 " pdb=" SD MET C 82 " ideal model delta sigma weight residual 112.70 101.23 11.47 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 128.90 117.78 11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CA TYR A 711 " pdb=" CB TYR A 711 " pdb=" CG TYR A 711 " ideal model delta sigma weight residual 113.90 107.26 6.64 1.80e+00 3.09e-01 1.36e+01 angle pdb=" C1' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C3' ADP C 401 " ideal model delta sigma weight residual 111.00 100.01 10.99 3.00e+00 1.11e-01 1.34e+01 ... (remaining 14023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 6139 35.63 - 71.26: 98 71.26 - 106.89: 31 106.89 - 142.52: 6 142.52 - 178.14: 12 Dihedral angle restraints: 6286 sinusoidal: 2602 harmonic: 3684 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 62.63 -122.63 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 178.49 121.51 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 58.88 -118.88 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 6283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1338 0.080 - 0.160: 178 0.160 - 0.241: 7 0.241 - 0.321: 3 0.321 - 0.401: 2 Chirality restraints: 1528 Sorted by residual: chirality pdb=" C3 9UE C 404 " pdb=" O 9UE C 404 " pdb=" C2 9UE C 404 " pdb=" C35 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.21 2.61 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C10 9UE C 404 " pdb=" C18 9UE C 404 " pdb=" C9 9UE C 404 " pdb=" N2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C8 9UE C 404 " pdb=" C20 9UE C 404 " pdb=" C7 9UE C 404 " pdb=" N1 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.15 2.44 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1525 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.137 9.50e-02 1.11e+02 7.89e-02 3.27e+01 pdb=" NE ARG A 248 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " 0.371 9.50e-02 1.11e+02 1.70e-01 3.26e+01 pdb=" NE ARG A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 254 " -0.341 9.50e-02 1.11e+02 1.57e-01 3.07e+01 pdb=" NE ARG C 254 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG C 254 " 0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG C 254 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG C 254 " -0.036 2.00e-02 2.50e+03 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 57 2.58 - 3.16: 8781 3.16 - 3.74: 15049 3.74 - 4.32: 21210 4.32 - 4.90: 35236 Nonbonded interactions: 80333 Sorted by model distance: nonbonded pdb=" O3 PO4 C 402 " pdb="MG MG C 403 " model vdw 2.002 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 403 " model vdw 2.008 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.089 3.040 nonbonded pdb=" O GLU B 118 " pdb=" NH2 ARG A 779 " model vdw 2.207 3.120 nonbonded pdb=" NH2 ARG B 37 " pdb=" O PRO B 43 " model vdw 2.211 3.120 ... (remaining 80328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 10386 Z= 0.251 Angle : 0.868 14.410 14028 Z= 0.494 Chirality : 0.054 0.401 1528 Planarity : 0.010 0.170 1797 Dihedral : 18.285 178.144 3912 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.20), residues: 1242 helix: -1.40 (0.17), residues: 592 sheet: 0.10 (0.37), residues: 157 loop : -0.13 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.011 ARG A 248 TYR 0.036 0.007 TYR A 113 PHE 0.036 0.002 PHE A 707 TRP 0.040 0.003 TRP A 374 HIS 0.014 0.002 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 (10386) covalent geometry : angle 0.86843 / 0.49 (14028) hydrogen bonds : bond 0.15643 / 10.47 ( 526) hydrogen bonds : angle 7.02482 / 5.03 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 PHE cc_start: 0.8549 (m-80) cc_final: 0.8292 (m-10) REVERT: A 359 ILE cc_start: 0.9447 (mt) cc_final: 0.9241 (mm) REVERT: C 195 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 227 MET cc_start: 0.8686 (tpp) cc_final: 0.8479 (tpt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0973 time to fit residues: 23.7521 Evaluate side-chains 101 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 200 ASN A 264 GLN A 410 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 726 GLN C 41 GLN C 111 ASN C 115 ASN C 162 ASN C 296 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058665 restraints weight = 30078.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060895 restraints weight = 14664.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.062373 restraints weight = 9165.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.063411 restraints weight = 6672.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064108 restraints weight = 5342.083| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10386 Z= 0.163 Angle : 0.704 10.468 14028 Z= 0.362 Chirality : 0.047 0.424 1528 Planarity : 0.004 0.052 1797 Dihedral : 18.382 166.112 1430 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.01 % Allowed : 6.09 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.23), residues: 1242 helix: 0.76 (0.20), residues: 609 sheet: 0.87 (0.41), residues: 156 loop : 0.57 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 110 TYR 0.013 0.002 TYR B 86 PHE 0.018 0.002 PHE A 707 TRP 0.017 0.002 TRP A 374 HIS 0.009 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (10386) covalent geometry : angle 0.70434 / 0.36 (14028) hydrogen bonds : bond 0.04710 / 3.14 ( 526) hydrogen bonds : angle 5.27197 / 3.78 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 PHE cc_start: 0.8588 (m-80) cc_final: 0.8357 (m-10) REVERT: B 105 MET cc_start: 0.9214 (mmp) cc_final: 0.8821 (tpp) REVERT: B 110 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8666 (tpt170) REVERT: A 135 MET cc_start: 0.8694 (mmm) cc_final: 0.8460 (mmm) REVERT: A 305 MET cc_start: 0.8404 (tpt) cc_final: 0.7950 (tpt) REVERT: A 416 VAL cc_start: 0.9217 (t) cc_final: 0.8981 (p) REVERT: C 59 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8151 (tp-100) REVERT: C 123 MET cc_start: 0.9175 (tpp) cc_final: 0.8911 (tpp) REVERT: C 192 ILE cc_start: 0.9122 (tt) cc_final: 0.8840 (tt) REVERT: C 195 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7847 (mt-10) REVERT: C 227 MET cc_start: 0.8616 (tpp) cc_final: 0.8285 (tpt) REVERT: C 236 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7446 (tp) REVERT: C 353 GLN cc_start: 0.8858 (mm110) cc_final: 0.8619 (mm-40) outliers start: 11 outliers final: 3 residues processed: 127 average time/residue: 0.0844 time to fit residues: 15.7058 Evaluate side-chains 94 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 77 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 114 optimal weight: 0.0270 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059174 restraints weight = 30060.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.061417 restraints weight = 14612.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.062946 restraints weight = 9127.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.063972 restraints weight = 6622.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064572 restraints weight = 5293.881| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10386 Z= 0.137 Angle : 0.645 11.945 14028 Z= 0.322 Chirality : 0.044 0.323 1528 Planarity : 0.004 0.056 1797 Dihedral : 17.712 166.298 1430 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.57 % Allowed : 8.03 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1242 helix: 1.28 (0.21), residues: 610 sheet: 0.96 (0.40), residues: 162 loop : 0.67 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 110 TYR 0.010 0.001 TYR A 456 PHE 0.031 0.002 PHE B 19 TRP 0.012 0.002 TRP A 374 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (10386) covalent geometry : angle 0.64459 / 0.32 (14028) hydrogen bonds : bond 0.04104 / 2.74 ( 526) hydrogen bonds : angle 4.93024 / 3.55 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 PHE cc_start: 0.8587 (m-80) cc_final: 0.8369 (m-10) REVERT: B 105 MET cc_start: 0.9213 (mmp) cc_final: 0.8731 (tpp) REVERT: B 110 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8690 (tpt170) REVERT: A 135 MET cc_start: 0.8686 (mmm) cc_final: 0.8288 (mmm) REVERT: A 416 VAL cc_start: 0.9147 (t) cc_final: 0.8904 (p) REVERT: A 441 PHE cc_start: 0.8038 (m-80) cc_final: 0.7660 (t80) REVERT: C 59 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8269 (tp-100) REVERT: C 82 MET cc_start: 0.8252 (ttp) cc_final: 0.7919 (ttp) REVERT: C 195 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7917 (mt-10) REVERT: C 227 MET cc_start: 0.8517 (tpp) cc_final: 0.8176 (tpt) REVERT: C 236 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7355 (tp) REVERT: C 353 GLN cc_start: 0.8851 (mm110) cc_final: 0.8597 (mm-40) outliers start: 17 outliers final: 6 residues processed: 115 average time/residue: 0.0837 time to fit residues: 14.7778 Evaluate side-chains 92 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 6 optimal weight: 0.6980 chunk 89 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 71 optimal weight: 0.0020 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 GLN C 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.081954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059564 restraints weight = 29929.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061784 restraints weight = 14453.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063282 restraints weight = 9013.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.064245 restraints weight = 6535.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064978 restraints weight = 5255.192| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10386 Z= 0.121 Angle : 0.595 9.987 14028 Z= 0.297 Chirality : 0.043 0.287 1528 Planarity : 0.004 0.056 1797 Dihedral : 17.078 166.087 1430 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.20 % Allowed : 9.78 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.24), residues: 1242 helix: 1.53 (0.21), residues: 616 sheet: 0.90 (0.40), residues: 165 loop : 0.68 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 110 TYR 0.011 0.001 TYR A 456 PHE 0.026 0.001 PHE B 19 TRP 0.012 0.002 TRP C 86 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10386) covalent geometry : angle 0.59508 / 0.30 (14028) hydrogen bonds : bond 0.03750 / 2.49 ( 526) hydrogen bonds : angle 4.68585 / 3.38 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.321 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: B 105 MET cc_start: 0.9182 (mmp) cc_final: 0.8636 (tpp) REVERT: B 110 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8693 (tpt170) REVERT: A 135 MET cc_start: 0.8627 (mmm) cc_final: 0.8270 (mmm) REVERT: A 416 VAL cc_start: 0.9132 (t) cc_final: 0.8862 (p) REVERT: A 441 PHE cc_start: 0.8053 (m-80) cc_final: 0.7720 (t80) REVERT: A 507 ASP cc_start: 0.7747 (m-30) cc_final: 0.7190 (m-30) REVERT: C 227 MET cc_start: 0.8417 (tpp) cc_final: 0.8099 (tpt) REVERT: C 236 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7752 (mm) REVERT: C 283 MET cc_start: 0.8827 (mmm) cc_final: 0.8626 (mmm) outliers start: 13 outliers final: 6 residues processed: 105 average time/residue: 0.0749 time to fit residues: 12.0886 Evaluate side-chains 96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 121 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.081994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059591 restraints weight = 29770.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061805 restraints weight = 14539.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.063316 restraints weight = 9106.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.064352 restraints weight = 6605.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065070 restraints weight = 5267.885| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10386 Z= 0.119 Angle : 0.585 9.877 14028 Z= 0.288 Chirality : 0.043 0.328 1528 Planarity : 0.004 0.054 1797 Dihedral : 16.218 165.938 1430 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.01 % Allowed : 10.70 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.24), residues: 1242 helix: 1.69 (0.21), residues: 616 sheet: 1.00 (0.40), residues: 163 loop : 0.77 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 784 TYR 0.011 0.001 TYR A 456 PHE 0.017 0.001 PHE B 19 TRP 0.011 0.001 TRP C 79 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10386) covalent geometry : angle 0.58525 / 0.29 (14028) hydrogen bonds : bond 0.03570 / 2.38 ( 526) hydrogen bonds : angle 4.52553 / 3.26 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.404 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: B 105 MET cc_start: 0.9212 (mmp) cc_final: 0.8684 (tpp) REVERT: B 110 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8656 (tpt170) REVERT: A 135 MET cc_start: 0.8629 (mmm) cc_final: 0.8260 (mmm) REVERT: A 416 VAL cc_start: 0.9068 (t) cc_final: 0.8826 (p) REVERT: A 441 PHE cc_start: 0.8027 (m-80) cc_final: 0.7758 (t80) REVERT: A 507 ASP cc_start: 0.7742 (m-30) cc_final: 0.7178 (m-30) REVERT: C 123 MET cc_start: 0.8870 (tpp) cc_final: 0.8655 (tpp) REVERT: C 195 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7731 (mt-10) REVERT: C 227 MET cc_start: 0.8463 (tpp) cc_final: 0.8196 (tpt) REVERT: C 236 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7834 (mm) outliers start: 11 outliers final: 6 residues processed: 107 average time/residue: 0.0846 time to fit residues: 13.9526 Evaluate side-chains 101 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.081232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.058510 restraints weight = 30166.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.060706 restraints weight = 14797.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.062193 restraints weight = 9324.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063190 restraints weight = 6807.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063864 restraints weight = 5476.023| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10386 Z= 0.145 Angle : 0.596 10.781 14028 Z= 0.293 Chirality : 0.043 0.337 1528 Planarity : 0.004 0.056 1797 Dihedral : 15.753 166.279 1430 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.48 % Allowed : 10.79 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1242 helix: 1.73 (0.21), residues: 614 sheet: 0.91 (0.41), residues: 161 loop : 0.71 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 110 TYR 0.012 0.001 TYR A 456 PHE 0.011 0.001 PHE B 19 TRP 0.011 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10386) covalent geometry : angle 0.59589 / 0.29 (14028) hydrogen bonds : bond 0.03637 / 2.41 ( 526) hydrogen bonds : angle 4.45857 / 3.22 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 VAL cc_start: 0.9105 (t) cc_final: 0.8858 (p) REVERT: A 441 PHE cc_start: 0.7945 (m-80) cc_final: 0.7738 (t80) REVERT: A 507 ASP cc_start: 0.7835 (m-30) cc_final: 0.7291 (m-30) REVERT: C 123 MET cc_start: 0.8847 (tpp) cc_final: 0.8639 (tpp) REVERT: C 195 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 227 MET cc_start: 0.8486 (tpp) cc_final: 0.8227 (tpt) REVERT: C 236 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7887 (mm) outliers start: 16 outliers final: 6 residues processed: 104 average time/residue: 0.0918 time to fit residues: 14.3874 Evaluate side-chains 97 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 115 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.081048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058692 restraints weight = 29610.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060867 restraints weight = 14544.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062344 restraints weight = 9136.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.063316 restraints weight = 6650.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.064019 restraints weight = 5363.420| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10386 Z= 0.154 Angle : 0.627 10.299 14028 Z= 0.309 Chirality : 0.044 0.338 1528 Planarity : 0.004 0.055 1797 Dihedral : 15.583 166.131 1430 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.92 % Allowed : 11.35 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1242 helix: 1.72 (0.21), residues: 614 sheet: 0.99 (0.41), residues: 159 loop : 0.60 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.014 0.001 TYR A 658 PHE 0.010 0.001 PHE B 19 TRP 0.028 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (10386) covalent geometry : angle 0.62656 / 0.31 (14028) hydrogen bonds : bond 0.03676 / 2.43 ( 526) hydrogen bonds : angle 4.49461 / 3.24 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.475 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: B 105 MET cc_start: 0.9116 (mmp) cc_final: 0.8739 (tpp) REVERT: B 110 ARG cc_start: 0.9132 (mmt180) cc_final: 0.8909 (tpt170) REVERT: A 507 ASP cc_start: 0.7844 (m-30) cc_final: 0.7295 (m-30) REVERT: C 123 MET cc_start: 0.8868 (tpp) cc_final: 0.8666 (tpp) REVERT: C 195 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7766 (mt-10) REVERT: C 227 MET cc_start: 0.8486 (tpp) cc_final: 0.8193 (tpt) REVERT: C 236 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7902 (mm) outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 0.1021 time to fit residues: 15.0145 Evaluate side-chains 91 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 80 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 102 optimal weight: 0.3980 chunk 105 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.082167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059440 restraints weight = 29922.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.061682 restraints weight = 14751.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063194 restraints weight = 9308.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.064208 restraints weight = 6792.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.064922 restraints weight = 5471.558| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10386 Z= 0.116 Angle : 0.609 12.961 14028 Z= 0.298 Chirality : 0.042 0.311 1528 Planarity : 0.004 0.054 1797 Dihedral : 15.540 167.115 1430 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.65 % Allowed : 11.90 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.24), residues: 1242 helix: 1.75 (0.21), residues: 613 sheet: 0.57 (0.43), residues: 147 loop : 0.59 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.012 0.001 TYR A 658 PHE 0.008 0.001 PHE B 19 TRP 0.033 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10386) covalent geometry : angle 0.60873 / 0.30 (14028) hydrogen bonds : bond 0.03446 / 2.26 ( 526) hydrogen bonds : angle 4.40812 / 3.18 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.415 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: B 105 MET cc_start: 0.9106 (mmp) cc_final: 0.8718 (tpp) REVERT: B 110 ARG cc_start: 0.9116 (mmt180) cc_final: 0.8876 (tpt170) REVERT: A 135 MET cc_start: 0.8257 (mmm) cc_final: 0.8039 (mmm) REVERT: A 416 VAL cc_start: 0.9046 (t) cc_final: 0.8795 (p) REVERT: A 507 ASP cc_start: 0.7844 (m-30) cc_final: 0.7188 (m-30) REVERT: C 195 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7752 (mt-10) REVERT: C 227 MET cc_start: 0.8478 (tpp) cc_final: 0.8242 (tpt) REVERT: C 236 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7938 (mm) outliers start: 7 outliers final: 4 residues processed: 93 average time/residue: 0.0938 time to fit residues: 12.9692 Evaluate side-chains 92 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 111 optimal weight: 0.4980 chunk 64 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.081969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059158 restraints weight = 30315.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061380 restraints weight = 15010.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062862 restraints weight = 9489.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.063889 restraints weight = 6961.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064583 restraints weight = 5599.440| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10386 Z= 0.128 Angle : 0.600 9.586 14028 Z= 0.298 Chirality : 0.043 0.307 1528 Planarity : 0.004 0.053 1797 Dihedral : 15.712 168.947 1430 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.83 % Allowed : 11.44 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1242 helix: 1.76 (0.21), residues: 619 sheet: 0.63 (0.43), residues: 143 loop : 0.57 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.012 0.001 TYR A 456 PHE 0.008 0.001 PHE A 707 TRP 0.032 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10386) covalent geometry : angle 0.60003 / 0.30 (14028) hydrogen bonds : bond 0.03463 / 2.27 ( 526) hydrogen bonds : angle 4.43554 / 3.20 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.425 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: B 105 MET cc_start: 0.9087 (mmp) cc_final: 0.8631 (tpp) REVERT: A 135 MET cc_start: 0.8225 (mmm) cc_final: 0.7993 (mmm) REVERT: A 416 VAL cc_start: 0.9047 (t) cc_final: 0.8793 (p) REVERT: A 507 ASP cc_start: 0.7867 (m-30) cc_final: 0.7210 (m-30) REVERT: C 195 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7784 (mt-10) REVERT: C 227 MET cc_start: 0.8461 (tpp) cc_final: 0.8225 (tpt) REVERT: C 236 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7955 (mm) outliers start: 9 outliers final: 5 residues processed: 96 average time/residue: 0.0914 time to fit residues: 13.2763 Evaluate side-chains 94 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 15 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.081362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058569 restraints weight = 29971.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060771 restraints weight = 14967.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062285 restraints weight = 9516.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063327 restraints weight = 6955.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063926 restraints weight = 5581.037| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10386 Z= 0.148 Angle : 0.634 12.175 14028 Z= 0.314 Chirality : 0.043 0.294 1528 Planarity : 0.004 0.053 1797 Dihedral : 15.834 170.476 1430 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.65 % Allowed : 11.99 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1242 helix: 1.73 (0.21), residues: 619 sheet: 0.60 (0.43), residues: 143 loop : 0.57 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 789 TYR 0.014 0.001 TYR A 456 PHE 0.008 0.001 PHE C 255 TRP 0.039 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (10386) covalent geometry : angle 0.63443 / 0.31 (14028) hydrogen bonds : bond 0.03580 / 2.35 ( 526) hydrogen bonds : angle 4.51222 / 3.25 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9125 (mmp) cc_final: 0.8591 (tpp) REVERT: B 110 ARG cc_start: 0.9100 (tpt170) cc_final: 0.8613 (mmt180) REVERT: A 135 MET cc_start: 0.8251 (mmm) cc_final: 0.8022 (mmm) REVERT: A 507 ASP cc_start: 0.7882 (m-30) cc_final: 0.7227 (m-30) REVERT: C 195 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 227 MET cc_start: 0.8460 (tpp) cc_final: 0.8209 (tpt) REVERT: C 236 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7950 (mm) REVERT: C 355 MET cc_start: 0.8501 (mmt) cc_final: 0.8260 (mmp) outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 0.0899 time to fit residues: 12.5184 Evaluate side-chains 87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 102 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.081153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.058801 restraints weight = 29820.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.060988 restraints weight = 14731.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062467 restraints weight = 9277.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063467 restraints weight = 6767.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064090 restraints weight = 5436.279| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10386 Z= 0.147 Angle : 0.635 15.168 14028 Z= 0.314 Chirality : 0.043 0.280 1528 Planarity : 0.004 0.052 1797 Dihedral : 15.921 170.902 1430 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.55 % Allowed : 12.36 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1242 helix: 1.74 (0.21), residues: 621 sheet: 0.70 (0.42), residues: 152 loop : 0.56 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.013 0.001 TYR A 456 PHE 0.023 0.001 PHE B 12 TRP 0.033 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10386) covalent geometry : angle 0.63466 / 0.31 (14028) hydrogen bonds : bond 0.03629 / 2.38 ( 526) hydrogen bonds : angle 4.53462 / 3.27 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.41 seconds wall clock time: 33 minutes 50.34 seconds (2030.34 seconds total)