Starting phenix.real_space_refine on Thu Jul 2 22:24:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pmi_13535/07_2026/7pmi_13535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmi_13535/07_2026/7pmi_13535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pmi_13535/07_2026/7pmi_13535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmi_13535/07_2026/7pmi_13535.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmi_13535/07_2026/7pmi_13535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmi_13535/07_2026/7pmi_13535.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pmi_13535/07_2026/7pmi_13535.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pmi_13535/07_2026/7pmi_13535.cif" } resolution = 3.3 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6482 2.51 5 N 1730 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 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: 10189 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.60, per 1000 atoms: 0.26 Number of scatterers: 10189 At special positions: 0 Unit cell: (108.9, 130.9, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 5 15.00 Mg 3 11.99 O 1906 8.00 N 1730 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 326.7 milliseconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 14 sheets defined 54.8% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.679A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.521A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.519A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.166A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.560A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 278 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.869A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.125A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.756A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.670A 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 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 504 through 515 removed outlier: 4.009A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.994A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.513A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.150A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.655A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.861A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 683 " --> pdb=" O VAL A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 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 removed outlier: 3.821A pdb=" N THR A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) 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 removed outlier: 3.683A pdb=" N TYR A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.795A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.023A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.758A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.824A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.783A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.541A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.380A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.602A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.006A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.239A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.730A 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 96 removed outlier: 4.160A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 7.302A pdb=" N GLN A 39 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.399A pdb=" N LEU A 107 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 662 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA A 109 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 5.833A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 216 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.594A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.820A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.986A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 504 hydrogen bonds defined for protein. 1407 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: 1.94 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1713 1.31 - 1.44: 2744 1.44 - 1.56: 5835 1.56 - 1.69: 9 1.69 - 1.81: 102 Bond restraints: 10403 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.539 0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.436 0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.192 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.585 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 13910 4.22 - 8.43: 133 8.43 - 12.65: 8 12.65 - 16.87: 1 16.87 - 21.08: 1 Bond angle restraints: 14053 Sorted by residual: angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 105.87 21.08 3.00e+00 1.11e-01 4.94e+01 angle pdb=" N CYS H 5 " pdb=" CA CYS H 5 " pdb=" CB CYS H 5 " ideal model delta sigma weight residual 110.50 100.16 10.34 1.70e+00 3.46e-01 3.70e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.89 9.81 1.80e+00 3.09e-01 2.97e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 103.03 8.47 1.70e+00 3.46e-01 2.48e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.86 121.03 -7.17 1.50e+00 4.44e-01 2.29e+01 ... (remaining 14048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 6026 27.26 - 54.52: 181 54.52 - 81.78: 41 81.78 - 109.04: 8 109.04 - 136.30: 5 Dihedral angle restraints: 6261 sinusoidal: 2567 harmonic: 3694 Sorted by residual: 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 300.00 171.94 128.06 1 2.00e+01 2.50e-03 3.88e+01 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 61.86 -121.86 1 2.00e+01 2.50e-03 3.67e+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 57.07 -117.07 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 6258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.044: 1532 1.044 - 2.088: 0 2.088 - 3.132: 0 3.132 - 4.176: 0 4.176 - 5.220: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.67 5.22 2.00e-01 2.50e+01 6.81e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.32 4.84 2.00e-01 2.50e+01 5.86e+02 chirality pdb=" CA MET A 478 " pdb=" N MET A 478 " pdb=" C MET A 478 " pdb=" CB MET A 478 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1531 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 784 " -0.284 9.50e-02 1.11e+02 1.55e-01 1.08e+02 pdb=" NE ARG A 784 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 784 " -0.168 2.00e-02 2.50e+03 pdb=" NH1 ARG A 784 " 0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG A 784 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.044 2.00e-02 2.50e+03 4.36e-02 3.32e+01 pdb=" CG PHE A 564 " 0.101 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 116 " -0.105 9.50e-02 1.11e+02 6.15e-02 2.08e+01 pdb=" NE ARG C 116 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 116 " -0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG C 116 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG C 116 " 0.022 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 21 2.37 - 3.00: 5889 3.00 - 3.63: 14691 3.63 - 4.27: 22860 4.27 - 4.90: 38693 Nonbonded interactions: 82154 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.733 3.620 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.928 2.170 nonbonded pdb=" O2G ANP A1901 " pdb="MG MG A1902 " model vdw 1.940 2.170 nonbonded pdb=" NH1 ARG A 784 " pdb=" O ARG B 37 " model vdw 2.086 3.120 nonbonded pdb=" O LYS B 26 " pdb=" NH2 ARG B 64 " model vdw 2.155 3.120 ... (remaining 82149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.400 Find NCS groups from input model: 0.060 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.014 0.161 10405 Z= 0.607 Angle : 1.175 21.081 14059 Z= 0.660 Chirality : 0.194 5.220 1534 Planarity : 0.010 0.155 1792 Dihedral : 15.299 136.295 3873 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % Cbeta Deviations : 0.17 % 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: -1.50 (0.21), residues: 1235 helix: -1.73 (0.16), residues: 627 sheet: 0.33 (0.37), residues: 167 loop : 0.02 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.171 0.015 ARG A 784 TYR 0.039 0.007 TYR A 477 PHE 0.101 0.004 PHE A 564 TRP 0.076 0.006 TRP A 484 HIS 0.014 0.003 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.01408 / 0.61 (10403) covalent geometry : angle 1.17252 / 0.66 (14053) hydrogen bonds : bond 0.15728 / 10.32 ( 502) hydrogen bonds : angle 6.89197 / 4.74 ( 1407) link_TRANS : bond 0.02380 / 1.19 ( 2) link_TRANS : angle 3.89896 / 2.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 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: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9297 (p0) cc_final: 0.8919 (p0) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.1265 time to fit residues: 14.4458 Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 398 ASN A 493 GLN C 162 ASN C 280 ASN C 296 ASN B 75 GLN B 140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.051079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.036424 restraints weight = 53933.548| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 4.09 r_work: 0.2620 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10405 Z= 0.144 Angle : 0.653 7.786 14059 Z= 0.344 Chirality : 0.043 0.160 1534 Planarity : 0.004 0.041 1792 Dihedral : 9.942 148.243 1391 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.28 % Allowed : 3.78 % Favored : 95.94 % Cbeta Deviations : 0.08 % 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: 0.82 (0.23), residues: 1235 helix: 0.58 (0.20), residues: 624 sheet: 0.89 (0.39), residues: 161 loop : 0.64 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 683 TYR 0.014 0.001 TYR A 787 PHE 0.018 0.001 PHE A 564 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 0.00308 / 0.14 (10403) covalent geometry : angle 0.65197 / 0.34 (14053) hydrogen bonds : bond 0.04623 / 2.83 ( 502) hydrogen bonds : angle 4.93068 / 3.38 ( 1407) link_TRANS : bond 0.00216 / 0.10 ( 2) link_TRANS : angle 1.43666 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9001 (tpp) cc_final: 0.8722 (tpp) REVERT: C 47 MET cc_start: 0.8301 (tpp) cc_final: 0.7952 (tpp) REVERT: C 364 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8782 (pp20) REVERT: B 66 ASP cc_start: 0.9527 (p0) cc_final: 0.9207 (t0) REVERT: B 120 MET cc_start: 0.7990 (mtm) cc_final: 0.7307 (ptm) outliers start: 3 outliers final: 0 residues processed: 69 average time/residue: 0.0990 time to fit residues: 9.7502 Evaluate side-chains 56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.035647 restraints weight = 54752.304| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 4.10 r_work: 0.2599 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10405 Z= 0.164 Angle : 0.586 7.901 14059 Z= 0.304 Chirality : 0.041 0.179 1534 Planarity : 0.004 0.037 1792 Dihedral : 9.366 147.096 1390 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.85 % Cbeta Deviations : 0.08 % 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: 1.34 (0.24), residues: 1235 helix: 1.32 (0.21), residues: 614 sheet: 0.68 (0.38), residues: 167 loop : 0.57 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 37 TYR 0.012 0.001 TYR A 787 PHE 0.014 0.001 PHE B 93 TRP 0.031 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (10403) covalent geometry : angle 0.58642 / 0.30 (14053) hydrogen bonds : bond 0.04139 / 2.55 ( 502) hydrogen bonds : angle 4.66909 / 3.19 ( 1407) link_TRANS : bond 0.00267 / 0.14 ( 2) link_TRANS : angle 0.35860 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9015 (mtp) cc_final: 0.8691 (mtp) REVERT: A 323 MET cc_start: 0.9024 (tpp) cc_final: 0.8767 (tpp) REVERT: C 47 MET cc_start: 0.8311 (tpp) cc_final: 0.8062 (tpp) REVERT: B 66 ASP cc_start: 0.9487 (p0) cc_final: 0.9133 (t0) REVERT: B 120 MET cc_start: 0.7958 (mtm) cc_final: 0.7221 (ptm) outliers start: 3 outliers final: 0 residues processed: 56 average time/residue: 0.0977 time to fit residues: 8.0726 Evaluate side-chains 53 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 638 HIS A 775 GLN B 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.050157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.035743 restraints weight = 55079.378| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.99 r_work: 0.2607 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10405 Z= 0.145 Angle : 0.551 6.825 14059 Z= 0.283 Chirality : 0.040 0.173 1534 Planarity : 0.003 0.039 1792 Dihedral : 9.069 148.308 1390 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.74 % Allowed : 4.98 % Favored : 94.29 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1235 helix: 1.67 (0.22), residues: 611 sheet: 0.57 (0.38), residues: 167 loop : 0.64 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.010 0.001 TYR A 102 PHE 0.011 0.001 PHE B 93 TRP 0.027 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10403) covalent geometry : angle 0.55073 / 0.28 (14053) hydrogen bonds : bond 0.03785 / 2.31 ( 502) hydrogen bonds : angle 4.51033 / 3.09 ( 1407) link_TRANS : bond 0.00208 / 0.11 ( 2) link_TRANS : angle 0.37555 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9004 (mtp) cc_final: 0.8616 (mtp) REVERT: A 323 MET cc_start: 0.9064 (tpp) cc_final: 0.8824 (tpp) REVERT: C 47 MET cc_start: 0.8268 (tpp) cc_final: 0.8062 (tpp) REVERT: C 299 MET cc_start: 0.9502 (mtp) cc_final: 0.9244 (mtp) REVERT: B 66 ASP cc_start: 0.9503 (p0) cc_final: 0.9152 (t70) REVERT: B 120 MET cc_start: 0.7979 (mtm) cc_final: 0.7151 (ptm) outliers start: 8 outliers final: 2 residues processed: 58 average time/residue: 0.1007 time to fit residues: 8.4904 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 384 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.050186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.035766 restraints weight = 54963.336| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.12 r_work: 0.2609 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10405 Z= 0.132 Angle : 0.536 7.364 14059 Z= 0.272 Chirality : 0.040 0.170 1534 Planarity : 0.003 0.043 1792 Dihedral : 8.777 149.434 1390 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.55 % Allowed : 5.99 % Favored : 93.46 % Cbeta Deviations : 0.08 % 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: 1.76 (0.24), residues: 1235 helix: 1.88 (0.22), residues: 609 sheet: 0.44 (0.40), residues: 157 loop : 0.62 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 789 TYR 0.010 0.001 TYR A 102 PHE 0.011 0.001 PHE B 93 TRP 0.018 0.002 TRP A 781 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10403) covalent geometry : angle 0.53607 / 0.27 (14053) hydrogen bonds : bond 0.03564 / 2.17 ( 502) hydrogen bonds : angle 4.38013 / 3.00 ( 1407) link_TRANS : bond 0.00164 / 0.08 ( 2) link_TRANS : angle 0.24565 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9004 (mtp) cc_final: 0.8712 (mtp) REVERT: A 323 MET cc_start: 0.9106 (tpp) cc_final: 0.8876 (tpp) REVERT: C 292 ASP cc_start: 0.9238 (t0) cc_final: 0.8985 (t0) REVERT: C 299 MET cc_start: 0.9513 (mtp) cc_final: 0.9201 (mtp) REVERT: B 66 ASP cc_start: 0.9483 (p0) cc_final: 0.9146 (t70) outliers start: 6 outliers final: 1 residues processed: 65 average time/residue: 0.0887 time to fit residues: 8.8033 Evaluate side-chains 54 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** 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 = 0.3326 r_free = 0.3326 target = 0.050289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.035841 restraints weight = 55504.541| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 4.03 r_work: 0.2620 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10405 Z= 0.125 Angle : 0.560 10.877 14059 Z= 0.279 Chirality : 0.040 0.216 1534 Planarity : 0.003 0.044 1792 Dihedral : 8.619 149.422 1390 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.55 % Allowed : 7.47 % Favored : 91.98 % Cbeta Deviations : 0.08 % 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: 1.81 (0.24), residues: 1235 helix: 1.95 (0.22), residues: 610 sheet: 0.49 (0.40), residues: 155 loop : 0.59 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.009 0.001 TYR A 102 PHE 0.009 0.001 PHE B 93 TRP 0.016 0.001 TRP A 781 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10403) covalent geometry : angle 0.56038 / 0.28 (14053) hydrogen bonds : bond 0.03410 / 2.09 ( 502) hydrogen bonds : angle 4.32204 / 2.97 ( 1407) link_TRANS : bond 0.00142 / 0.07 ( 2) link_TRANS : angle 0.20879 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8990 (mtp) cc_final: 0.8726 (mtp) REVERT: A 305 MET cc_start: 0.9282 (tpp) cc_final: 0.9017 (mtt) REVERT: A 323 MET cc_start: 0.9105 (tpp) cc_final: 0.8879 (tpp) REVERT: C 292 ASP cc_start: 0.9246 (t0) cc_final: 0.8987 (t0) REVERT: C 299 MET cc_start: 0.9497 (mtp) cc_final: 0.9174 (mtp) REVERT: B 66 ASP cc_start: 0.9482 (p0) cc_final: 0.9141 (t70) outliers start: 6 outliers final: 2 residues processed: 58 average time/residue: 0.1000 time to fit residues: 8.7122 Evaluate side-chains 54 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 106 optimal weight: 0.0980 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.034768 restraints weight = 55155.870| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.97 r_work: 0.2578 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10405 Z= 0.215 Angle : 0.596 12.692 14059 Z= 0.298 Chirality : 0.042 0.171 1534 Planarity : 0.003 0.045 1792 Dihedral : 8.571 146.806 1390 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.83 % Allowed : 7.83 % Favored : 91.34 % Cbeta Deviations : 0.08 % 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: 1235 helix: 1.99 (0.22), residues: 605 sheet: 0.43 (0.38), residues: 170 loop : 0.56 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.012 0.001 TYR A 263 PHE 0.010 0.001 PHE A 564 TRP 0.014 0.002 TRP A 781 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (10403) covalent geometry : angle 0.59657 / 0.30 (14053) hydrogen bonds : bond 0.03808 / 2.34 ( 502) hydrogen bonds : angle 4.42028 / 3.04 ( 1407) link_TRANS : bond 0.00379 / 0.19 ( 2) link_TRANS : angle 0.36435 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8932 (mtp) cc_final: 0.8652 (mtm) REVERT: A 305 MET cc_start: 0.9344 (tpp) cc_final: 0.9041 (mtt) REVERT: A 323 MET cc_start: 0.9136 (tpp) cc_final: 0.8921 (tpp) REVERT: C 283 MET cc_start: 0.8783 (mmm) cc_final: 0.8542 (mmm) REVERT: C 299 MET cc_start: 0.9531 (mtp) cc_final: 0.9182 (mtp) REVERT: B 66 ASP cc_start: 0.9469 (p0) cc_final: 0.9099 (t70) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.0813 time to fit residues: 7.4045 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** 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 = 0.3302 r_free = 0.3302 target = 0.049388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.034977 restraints weight = 55243.230| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.99 r_work: 0.2591 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10405 Z= 0.169 Angle : 0.598 12.064 14059 Z= 0.299 Chirality : 0.041 0.205 1534 Planarity : 0.003 0.045 1792 Dihedral : 8.504 146.843 1390 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.55 % Allowed : 7.93 % Favored : 91.52 % Cbeta Deviations : 0.08 % 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: 1.79 (0.24), residues: 1235 helix: 1.98 (0.22), residues: 607 sheet: 0.42 (0.38), residues: 168 loop : 0.55 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 779 TYR 0.011 0.001 TYR A 787 PHE 0.009 0.001 PHE C 255 TRP 0.015 0.001 TRP A 781 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (10403) covalent geometry : angle 0.59843 / 0.30 (14053) hydrogen bonds : bond 0.03702 / 2.26 ( 502) hydrogen bonds : angle 4.38232 / 3.01 ( 1407) link_TRANS : bond 0.00268 / 0.13 ( 2) link_TRANS : angle 0.29097 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8925 (mtp) cc_final: 0.8635 (mtm) REVERT: A 305 MET cc_start: 0.9358 (tpp) cc_final: 0.9045 (mtt) REVERT: A 323 MET cc_start: 0.9122 (tpp) cc_final: 0.8902 (tpp) REVERT: C 283 MET cc_start: 0.8736 (mmm) cc_final: 0.8493 (mmm) REVERT: C 299 MET cc_start: 0.9530 (mtp) cc_final: 0.9160 (mtp) REVERT: B 65 VAL cc_start: 0.7929 (OUTLIER) cc_final: 0.7672 (m) REVERT: B 66 ASP cc_start: 0.9475 (p0) cc_final: 0.9123 (t0) REVERT: B 120 MET cc_start: 0.8467 (mmm) cc_final: 0.8261 (mmm) outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 0.0831 time to fit residues: 7.6589 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.049250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.034795 restraints weight = 55386.584| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 4.09 r_work: 0.2582 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10405 Z= 0.172 Angle : 0.603 11.942 14059 Z= 0.302 Chirality : 0.041 0.183 1534 Planarity : 0.003 0.043 1792 Dihedral : 8.460 145.534 1390 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.65 % Allowed : 8.48 % Favored : 90.88 % Cbeta Deviations : 0.08 % 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: 1235 helix: 1.93 (0.22), residues: 607 sheet: 0.35 (0.38), residues: 167 loop : 0.54 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 231 TYR 0.012 0.001 TYR A 232 PHE 0.008 0.001 PHE C 255 TRP 0.017 0.002 TRP A 781 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (10403) covalent geometry : angle 0.60341 / 0.30 (14053) hydrogen bonds : bond 0.03639 / 2.23 ( 502) hydrogen bonds : angle 4.39085 / 3.02 ( 1407) link_TRANS : bond 0.00262 / 0.13 ( 2) link_TRANS : angle 0.30697 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8940 (mtp) cc_final: 0.8633 (mtm) REVERT: A 305 MET cc_start: 0.9354 (tpp) cc_final: 0.8971 (mtt) REVERT: A 323 MET cc_start: 0.9138 (tpp) cc_final: 0.8921 (tpp) REVERT: C 283 MET cc_start: 0.8763 (mmm) cc_final: 0.8517 (mmm) REVERT: C 299 MET cc_start: 0.9547 (mtp) cc_final: 0.9161 (mtp) REVERT: B 66 ASP cc_start: 0.9478 (p0) cc_final: 0.9185 (p0) REVERT: B 120 MET cc_start: 0.8483 (mmm) cc_final: 0.8270 (mmm) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.0888 time to fit residues: 7.9633 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** 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 = 0.3317 r_free = 0.3317 target = 0.049884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035517 restraints weight = 54077.370| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.06 r_work: 0.2609 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10405 Z= 0.123 Angle : 0.592 10.437 14059 Z= 0.294 Chirality : 0.040 0.177 1534 Planarity : 0.003 0.042 1792 Dihedral : 8.324 145.610 1390 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.55 % Allowed : 8.66 % Favored : 90.78 % Cbeta Deviations : 0.08 % 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: 1235 helix: 1.90 (0.22), residues: 616 sheet: 0.32 (0.40), residues: 155 loop : 0.45 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 231 TYR 0.010 0.001 TYR A 102 PHE 0.008 0.001 PHE C 255 TRP 0.019 0.002 TRP A 781 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10403) covalent geometry : angle 0.59165 / 0.29 (14053) hydrogen bonds : bond 0.03392 / 2.05 ( 502) hydrogen bonds : angle 4.29434 / 2.97 ( 1407) link_TRANS : bond 0.00135 / 0.07 ( 2) link_TRANS : angle 0.19466 / 0.10 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8939 (mtp) cc_final: 0.8624 (mtm) REVERT: A 305 MET cc_start: 0.9349 (tpp) cc_final: 0.9051 (mtt) REVERT: A 323 MET cc_start: 0.9146 (tpp) cc_final: 0.8933 (tpp) REVERT: C 184 ASP cc_start: 0.9146 (m-30) cc_final: 0.8937 (m-30) REVERT: C 269 MET cc_start: 0.8844 (mtm) cc_final: 0.8110 (ptp) REVERT: C 283 MET cc_start: 0.8732 (mmm) cc_final: 0.8503 (mmm) REVERT: C 299 MET cc_start: 0.9521 (mtp) cc_final: 0.9149 (mtp) REVERT: B 66 ASP cc_start: 0.9502 (p0) cc_final: 0.9203 (p0) REVERT: B 120 MET cc_start: 0.8501 (mmm) cc_final: 0.8246 (mmm) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.0881 time to fit residues: 8.1487 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** 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 = 0.3317 r_free = 0.3317 target = 0.049861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.035514 restraints weight = 54656.948| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.98 r_work: 0.2615 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10405 Z= 0.131 Angle : 0.597 9.808 14059 Z= 0.296 Chirality : 0.041 0.205 1534 Planarity : 0.003 0.043 1792 Dihedral : 8.257 144.077 1390 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.37 % Allowed : 9.12 % Favored : 90.51 % Cbeta Deviations : 0.08 % 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: 1235 helix: 1.90 (0.22), residues: 616 sheet: 0.30 (0.40), residues: 155 loop : 0.47 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.009 0.001 TYR A 102 PHE 0.021 0.001 PHE B 70 TRP 0.019 0.002 TRP A 781 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10403) covalent geometry : angle 0.59666 / 0.30 (14053) hydrogen bonds : bond 0.03409 / 2.08 ( 502) hydrogen bonds : angle 4.30001 / 2.97 ( 1407) link_TRANS : bond 0.00157 / 0.08 ( 2) link_TRANS : angle 0.20297 / 0.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2123.29 seconds wall clock time: 37 minutes 24.20 seconds (2244.20 seconds total)