Starting phenix.real_space_refine on Tue Mar 3 12:57:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5h_33620/03_2026/7y5h_33620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5h_33620/03_2026/7y5h_33620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y5h_33620/03_2026/7y5h_33620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5h_33620/03_2026/7y5h_33620.map" model { file = "/net/cci-nas-00/data/ceres_data/7y5h_33620/03_2026/7y5h_33620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5h_33620/03_2026/7y5h_33620.cif" } resolution = 3.72 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= 0.019 sd= 0.082 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 30 5.16 5 C 3066 2.51 5 N 778 2.21 5 O 826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4704 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2350 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 3 Chain: "A" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2350 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 3 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2387 SG CYS A 46 27.718 33.935 76.919 1.00 43.42 S ATOM 4663 SG CYS A 366 55.725 40.607 76.131 1.00 59.27 S ATOM 4688 SG CYS A 369 52.369 42.490 75.334 1.00 55.45 S ATOM 2313 SG CYS B 366 20.829 30.217 75.781 1.00 59.27 S ATOM 2338 SG CYS B 369 24.407 28.745 75.218 1.00 55.45 S ATOM 37 SG CYS B 46 48.769 37.462 77.024 1.00 43.42 S Time building chain proxies: 1.25, per 1000 atoms: 0.27 Number of scatterers: 4704 At special positions: 0 Unit cell: (77.35, 73.1, 102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 30 16.00 O 826 8.00 N 778 7.00 C 3066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 387.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 45 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 47 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 369 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 366 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS A 323 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS A 306 " pdb="ZN ZN A 402 " - pdb=" SG CYS B 46 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 323 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 306 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 46 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS B 45 " pdb="ZN ZN B 402 " - pdb=" ND1 HIS B 47 " pdb="ZN ZN B 402 " - pdb=" SG CYS A 369 " pdb="ZN ZN B 402 " - pdb=" SG CYS A 366 " Number of angles added : 2 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 68.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 51 through 88 removed outlier: 3.830A pdb=" N ALA B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 118 removed outlier: 4.303A pdb=" N HIS B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.628A pdb=" N LEU B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 191 removed outlier: 3.567A pdb=" N LEU B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 229 removed outlier: 4.092A pdb=" N ILE B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 246 removed outlier: 3.509A pdb=" N SER B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 removed outlier: 3.612A pdb=" N ILE B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 264 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 280 removed outlier: 3.558A pdb=" N LEU B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.016A pdb=" N ILE B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 51 through 88 removed outlier: 3.805A pdb=" N ALA A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 118 removed outlier: 3.946A pdb=" N HIS A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.630A pdb=" N LEU A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.557A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.093A pdb=" N ILE A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 246 removed outlier: 3.528A pdb=" N SER A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 267 removed outlier: 3.601A pdb=" N ILE A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N PHE A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.560A pdb=" N LEU A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 298 Processing helix chain 'A' and resid 331 through 345 removed outlier: 4.020A pdb=" N ILE A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing sheet with id=AA1, first strand: chain 'B' and resid 302 through 314 removed outlier: 6.801A pdb=" N ALA B 325 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 305 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N HIS B 323 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER B 307 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER B 321 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N HIS B 309 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 319 " --> pdb=" O HIS B 309 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TRP B 311 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN B 317 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL B 318 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N THR B 353 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 320 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLN B 355 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 322 " --> pdb=" O GLN B 355 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLU B 357 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 324 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 314 removed outlier: 6.803A pdb=" N ALA A 325 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 305 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS A 323 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER A 307 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER A 321 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS A 309 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 319 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP A 311 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLN A 317 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A 318 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N THR A 353 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU A 320 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N GLN A 355 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 322 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLU A 357 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A 324 " --> pdb=" O GLU A 357 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 717 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: 0.61 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1454 1.34 - 1.46: 1054 1.46 - 1.58: 2244 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 4794 Sorted by residual: bond pdb=" CB GLU A 365 " pdb=" CG GLU A 365 " ideal model delta sigma weight residual 1.520 1.538 -0.018 3.00e-02 1.11e+03 3.59e-01 bond pdb=" CG LEU A 308 " pdb=" CD1 LEU A 308 " ideal model delta sigma weight residual 1.521 1.505 0.016 3.30e-02 9.18e+02 2.21e-01 bond pdb=" C ASP A 253 " pdb=" N PRO A 254 " ideal model delta sigma weight residual 1.335 1.342 -0.006 1.36e-02 5.41e+03 2.17e-01 bond pdb=" C ASP B 253 " pdb=" N PRO B 254 " ideal model delta sigma weight residual 1.335 1.342 -0.006 1.36e-02 5.41e+03 2.16e-01 bond pdb=" N GLU B 281 " pdb=" CA GLU B 281 " ideal model delta sigma weight residual 1.460 1.466 -0.006 1.42e-02 4.96e+03 2.09e-01 ... (remaining 4789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 6429 1.30 - 2.61: 57 2.61 - 3.91: 19 3.91 - 5.22: 3 5.22 - 6.52: 2 Bond angle restraints: 6510 Sorted by residual: angle pdb=" C MET A 280 " pdb=" N GLU A 281 " pdb=" CA GLU A 281 " ideal model delta sigma weight residual 122.82 125.84 -3.02 1.42e+00 4.96e-01 4.53e+00 angle pdb=" C MET B 280 " pdb=" N GLU B 281 " pdb=" CA GLU B 281 " ideal model delta sigma weight residual 122.82 125.80 -2.98 1.42e+00 4.96e-01 4.40e+00 angle pdb=" CA LEU B 275 " pdb=" CB LEU B 275 " pdb=" CG LEU B 275 " ideal model delta sigma weight residual 116.30 122.82 -6.52 3.50e+00 8.16e-02 3.47e+00 angle pdb=" CA LEU A 275 " pdb=" CB LEU A 275 " pdb=" CG LEU A 275 " ideal model delta sigma weight residual 116.30 122.61 -6.31 3.50e+00 8.16e-02 3.25e+00 angle pdb=" CA GLU B 281 " pdb=" CB GLU B 281 " pdb=" CG GLU B 281 " ideal model delta sigma weight residual 114.10 117.51 -3.41 2.00e+00 2.50e-01 2.90e+00 ... (remaining 6505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 2531 14.72 - 29.43: 251 29.43 - 44.15: 54 44.15 - 58.86: 4 58.86 - 73.58: 6 Dihedral angle restraints: 2846 sinusoidal: 1082 harmonic: 1764 Sorted by residual: dihedral pdb=" CA PRO A 364 " pdb=" C PRO A 364 " pdb=" N GLU A 365 " pdb=" CA GLU A 365 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB MET A 251 " pdb=" CG MET A 251 " pdb=" SD MET A 251 " pdb=" CE MET A 251 " ideal model delta sinusoidal sigma weight residual 60.00 106.33 -46.33 3 1.50e+01 4.44e-03 8.32e+00 dihedral pdb=" CB MET B 251 " pdb=" CG MET B 251 " pdb=" SD MET B 251 " pdb=" CE MET B 251 " ideal model delta sinusoidal sigma weight residual 60.00 106.19 -46.19 3 1.50e+01 4.44e-03 8.29e+00 ... (remaining 2843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 452 0.024 - 0.049: 208 0.049 - 0.073: 110 0.073 - 0.098: 26 0.098 - 0.122: 10 Chirality restraints: 806 Sorted by residual: chirality pdb=" CA GLU A 281 " pdb=" N GLU A 281 " pdb=" C GLU A 281 " pdb=" CB GLU A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA GLU B 281 " pdb=" N GLU B 281 " pdb=" C GLU B 281 " pdb=" CB GLU B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE B 319 " pdb=" N ILE B 319 " pdb=" C ILE B 319 " pdb=" CB ILE B 319 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 803 not shown) Planarity restraints: 784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 365 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C GLU A 365 " 0.017 2.00e-02 2.50e+03 pdb=" O GLU A 365 " -0.007 2.00e-02 2.50e+03 pdb=" N CYS A 366 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 363 " 0.016 5.00e-02 4.00e+02 2.35e-02 8.87e-01 pdb=" N PRO A 364 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 253 " 0.009 5.00e-02 4.00e+02 1.36e-02 2.97e-01 pdb=" N PRO B 254 " -0.024 5.00e-02 4.00e+02 pdb=" CA PRO B 254 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO B 254 " 0.008 5.00e-02 4.00e+02 ... (remaining 781 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 21 2.60 - 3.18: 3955 3.18 - 3.75: 6701 3.75 - 4.33: 8672 4.33 - 4.90: 14189 Nonbonded interactions: 33538 Sorted by model distance: nonbonded pdb=" OE2 GLU B 357 " pdb="ZN ZN B 401 " model vdw 2.030 2.230 nonbonded pdb=" OE2 GLU A 357 " pdb="ZN ZN A 402 " model vdw 2.033 2.230 nonbonded pdb=" OG1 THR A 123 " pdb=" O ARG A 125 " model vdw 2.376 3.040 nonbonded pdb=" OG1 THR B 123 " pdb=" O ARG B 125 " model vdw 2.380 3.040 nonbonded pdb=" ND1 HIS B 323 " pdb=" OE2 GLU B 357 " model vdw 2.381 3.120 ... (remaining 33533 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.900 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4808 Z= 0.081 Angle : 0.392 6.520 6512 Z= 0.205 Chirality : 0.036 0.122 806 Planarity : 0.002 0.024 784 Dihedral : 12.510 73.577 1690 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.06 (0.33), residues: 584 helix: 0.37 (0.26), residues: 374 sheet: -1.33 (0.59), residues: 50 loop : 0.13 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 132 TYR 0.008 0.001 TYR A 289 PHE 0.004 0.001 PHE B 63 TRP 0.009 0.001 TRP A 311 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 4794) covalent geometry : angle 0.39193 ( 6510) hydrogen bonds : bond 0.29101 ( 241) hydrogen bonds : angle 6.27662 ( 717) metal coordination : bond 0.00251 ( 14) metal coordination : angle 0.50174 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 LEU cc_start: 0.8354 (tp) cc_final: 0.7922 (tt) REVERT: B 265 LEU cc_start: 0.8372 (mm) cc_final: 0.8023 (mp) REVERT: A 180 LEU cc_start: 0.8406 (tp) cc_final: 0.7997 (tt) REVERT: A 265 LEU cc_start: 0.8387 (mm) cc_final: 0.8040 (mp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1022 time to fit residues: 11.0780 Evaluate side-chains 61 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 0.0570 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN A 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.236507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.222264 restraints weight = 5488.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.207108 restraints weight = 8538.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.205023 restraints weight = 9020.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.204693 restraints weight = 8645.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.205230 restraints weight = 8105.144| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4808 Z= 0.130 Angle : 0.513 5.195 6512 Z= 0.274 Chirality : 0.038 0.119 806 Planarity : 0.003 0.024 784 Dihedral : 3.672 16.843 630 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.89 % Allowed : 9.09 % 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: 0.61 (0.34), residues: 584 helix: 0.92 (0.27), residues: 386 sheet: -0.91 (0.59), residues: 50 loop : -0.21 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.006 0.001 TYR A 289 PHE 0.010 0.001 PHE B 108 TRP 0.007 0.001 TRP A 311 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4794) covalent geometry : angle 0.51306 ( 6510) hydrogen bonds : bond 0.05702 ( 241) hydrogen bonds : angle 3.82682 ( 717) metal coordination : bond 0.00768 ( 14) metal coordination : angle 0.99764 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.173 Fit side-chains REVERT: B 251 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6544 (pmm) REVERT: B 265 LEU cc_start: 0.8466 (mm) cc_final: 0.8055 (mt) REVERT: A 172 MET cc_start: 0.6679 (pmm) cc_final: 0.6428 (pmm) REVERT: A 265 LEU cc_start: 0.8413 (mm) cc_final: 0.7994 (mt) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.0504 time to fit residues: 5.4288 Evaluate side-chains 63 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 245 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.212604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 151)---------------| | r_work = 0.4233 r_free = 0.4233 target = 0.185069 restraints weight = 5553.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.185069 restraints weight = 9503.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 80)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.168728 restraints weight = 9258.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.169398 restraints weight = 8438.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.169568 restraints weight = 6969.047| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4808 Z= 0.123 Angle : 0.485 5.612 6512 Z= 0.256 Chirality : 0.038 0.136 806 Planarity : 0.003 0.025 784 Dihedral : 3.537 15.520 630 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.08 % Allowed : 14.02 % Favored : 83.90 % 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: 0.88 (0.35), residues: 584 helix: 1.20 (0.28), residues: 386 sheet: -0.90 (0.62), residues: 50 loop : -0.31 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.011 0.001 TYR B 289 PHE 0.007 0.001 PHE B 128 TRP 0.009 0.001 TRP A 130 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4794) covalent geometry : angle 0.48474 ( 6510) hydrogen bonds : bond 0.05163 ( 241) hydrogen bonds : angle 3.33304 ( 717) metal coordination : bond 0.00695 ( 14) metal coordination : angle 0.78706 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.172 Fit side-chains REVERT: B 265 LEU cc_start: 0.8394 (mm) cc_final: 0.8056 (mt) REVERT: B 315 MET cc_start: 0.7397 (tpp) cc_final: 0.6917 (tpp) REVERT: A 172 MET cc_start: 0.6588 (pmm) cc_final: 0.6299 (pmm) REVERT: A 265 LEU cc_start: 0.8365 (mm) cc_final: 0.8022 (mt) outliers start: 11 outliers final: 10 residues processed: 67 average time/residue: 0.0506 time to fit residues: 4.9333 Evaluate side-chains 64 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 353 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.210690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.184854 restraints weight = 5682.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.169955 restraints weight = 8900.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167397 restraints weight = 6854.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168745 restraints weight = 8026.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168829 restraints weight = 6908.040| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4808 Z= 0.121 Angle : 0.503 6.974 6512 Z= 0.267 Chirality : 0.037 0.136 806 Planarity : 0.003 0.024 784 Dihedral : 3.479 14.407 630 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.60 % Allowed : 14.20 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.35), residues: 584 helix: 1.35 (0.28), residues: 386 sheet: -0.85 (0.64), residues: 50 loop : -0.15 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 57 TYR 0.011 0.001 TYR B 289 PHE 0.018 0.001 PHE A 63 TRP 0.008 0.001 TRP A 130 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4794) covalent geometry : angle 0.50329 ( 6510) hydrogen bonds : bond 0.04569 ( 241) hydrogen bonds : angle 3.15216 ( 717) metal coordination : bond 0.00619 ( 14) metal coordination : angle 0.75646 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.182 Fit side-chains REVERT: A 172 MET cc_start: 0.6459 (pmm) cc_final: 0.6185 (pmm) outliers start: 19 outliers final: 13 residues processed: 66 average time/residue: 0.0530 time to fit residues: 5.0648 Evaluate side-chains 64 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 353 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.206264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3951 r_free = 0.3951 target = 0.162398 restraints weight = 5596.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162687 restraints weight = 5663.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.163017 restraints weight = 5546.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.163017 restraints weight = 5380.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.163017 restraints weight = 5380.110| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4808 Z= 0.119 Angle : 0.512 6.173 6512 Z= 0.273 Chirality : 0.037 0.147 806 Planarity : 0.003 0.022 784 Dihedral : 3.465 14.037 630 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.84 % Allowed : 15.34 % Favored : 81.82 % 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: 1.34 (0.35), residues: 584 helix: 1.54 (0.28), residues: 382 sheet: -0.70 (0.65), residues: 50 loop : -0.04 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 57 TYR 0.010 0.001 TYR B 289 PHE 0.018 0.001 PHE B 63 TRP 0.008 0.001 TRP B 311 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4794) covalent geometry : angle 0.51233 ( 6510) hydrogen bonds : bond 0.04347 ( 241) hydrogen bonds : angle 3.05823 ( 717) metal coordination : bond 0.00573 ( 14) metal coordination : angle 0.62757 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.178 Fit side-chains REVERT: A 172 MET cc_start: 0.6440 (pmm) cc_final: 0.6205 (pmm) REVERT: A 315 MET cc_start: 0.7449 (tpp) cc_final: 0.7183 (tpp) outliers start: 15 outliers final: 13 residues processed: 64 average time/residue: 0.0506 time to fit residues: 4.7033 Evaluate side-chains 63 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 353 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 0.0470 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.205885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 168)---------------| | r_work = 0.4135 r_free = 0.4135 target = 0.174722 restraints weight = 5711.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.168587 restraints weight = 6355.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.166876 restraints weight = 6355.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.166872 restraints weight = 6663.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.166872 restraints weight = 6656.730| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4808 Z= 0.120 Angle : 0.512 6.372 6512 Z= 0.269 Chirality : 0.037 0.147 806 Planarity : 0.003 0.021 784 Dihedral : 3.492 14.213 630 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.65 % Allowed : 16.10 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.35), residues: 584 helix: 1.63 (0.28), residues: 382 sheet: -0.69 (0.65), residues: 50 loop : 0.07 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 57 TYR 0.011 0.001 TYR B 289 PHE 0.026 0.001 PHE B 109 TRP 0.008 0.001 TRP A 311 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4794) covalent geometry : angle 0.51211 ( 6510) hydrogen bonds : bond 0.04087 ( 241) hydrogen bonds : angle 2.99217 ( 717) metal coordination : bond 0.00565 ( 14) metal coordination : angle 0.62580 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.165 Fit side-chains REVERT: A 172 MET cc_start: 0.6613 (pmm) cc_final: 0.6349 (pmm) REVERT: A 315 MET cc_start: 0.7622 (tpp) cc_final: 0.7280 (tpp) outliers start: 14 outliers final: 14 residues processed: 64 average time/residue: 0.0445 time to fit residues: 4.1694 Evaluate side-chains 63 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 353 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.203557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 156)---------------| | r_work = 0.4125 r_free = 0.4125 target = 0.173796 restraints weight = 5750.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 81)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.160877 restraints weight = 9989.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160411 restraints weight = 8058.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.160366 restraints weight = 8011.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161039 restraints weight = 6120.629| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4808 Z= 0.209 Angle : 0.636 6.877 6512 Z= 0.336 Chirality : 0.041 0.168 806 Planarity : 0.003 0.023 784 Dihedral : 4.212 17.360 630 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.98 % Allowed : 16.67 % Favored : 79.36 % 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: 1.03 (0.35), residues: 584 helix: 1.28 (0.28), residues: 382 sheet: -1.30 (0.64), residues: 50 loop : 0.11 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.021 0.001 TYR B 289 PHE 0.020 0.002 PHE A 63 TRP 0.013 0.002 TRP A 130 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 4794) covalent geometry : angle 0.63544 ( 6510) hydrogen bonds : bond 0.05072 ( 241) hydrogen bonds : angle 3.30683 ( 717) metal coordination : bond 0.01077 ( 14) metal coordination : angle 1.41937 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.175 Fit side-chains REVERT: A 172 MET cc_start: 0.6656 (pmm) cc_final: 0.6370 (pmm) outliers start: 21 outliers final: 15 residues processed: 72 average time/residue: 0.0474 time to fit residues: 4.9660 Evaluate side-chains 70 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 353 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.209147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 130)---------------| | r_work = 0.4190 r_free = 0.4190 target = 0.180803 restraints weight = 5770.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164248 restraints weight = 8395.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.163931 restraints weight = 9450.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.164321 restraints weight = 7806.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.164286 restraints weight = 7455.902| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4808 Z= 0.130 Angle : 0.590 9.298 6512 Z= 0.301 Chirality : 0.038 0.154 806 Planarity : 0.003 0.021 784 Dihedral : 3.742 15.062 630 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.60 % Allowed : 17.99 % Favored : 78.41 % 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: 1.13 (0.35), residues: 584 helix: 1.42 (0.27), residues: 382 sheet: -1.31 (0.63), residues: 50 loop : -0.01 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 57 TYR 0.011 0.001 TYR B 289 PHE 0.025 0.001 PHE A 109 TRP 0.008 0.001 TRP B 311 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4794) covalent geometry : angle 0.58983 ( 6510) hydrogen bonds : bond 0.04256 ( 241) hydrogen bonds : angle 3.07542 ( 717) metal coordination : bond 0.00560 ( 14) metal coordination : angle 0.81650 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.131 Fit side-chains REVERT: A 172 MET cc_start: 0.6679 (pmm) cc_final: 0.6435 (pmm) REVERT: A 315 MET cc_start: 0.7652 (tpp) cc_final: 0.7380 (tpp) outliers start: 19 outliers final: 18 residues processed: 65 average time/residue: 0.0508 time to fit residues: 4.7142 Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.211305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.4017 r_free = 0.4017 target = 0.168178 restraints weight = 5583.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165820 restraints weight = 5623.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165820 restraints weight = 5447.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165820 restraints weight = 5447.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165820 restraints weight = 5447.263| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4808 Z= 0.119 Angle : 0.587 8.953 6512 Z= 0.299 Chirality : 0.037 0.145 806 Planarity : 0.002 0.021 784 Dihedral : 3.423 14.966 630 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.22 % Allowed : 18.37 % Favored : 78.41 % 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: 1.43 (0.35), residues: 584 helix: 1.69 (0.27), residues: 382 sheet: -1.09 (0.65), residues: 50 loop : -0.08 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.008 0.001 TYR B 289 PHE 0.024 0.001 PHE B 109 TRP 0.006 0.001 TRP B 116 HIS 0.002 0.000 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4794) covalent geometry : angle 0.58696 ( 6510) hydrogen bonds : bond 0.03576 ( 241) hydrogen bonds : angle 2.87409 ( 717) metal coordination : bond 0.00477 ( 14) metal coordination : angle 0.90818 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.171 Fit side-chains REVERT: B 275 LEU cc_start: 0.8416 (tt) cc_final: 0.8167 (tt) REVERT: A 172 MET cc_start: 0.6733 (pmm) cc_final: 0.6486 (pmm) REVERT: A 275 LEU cc_start: 0.8429 (tt) cc_final: 0.8139 (tt) outliers start: 17 outliers final: 15 residues processed: 65 average time/residue: 0.0512 time to fit residues: 4.8230 Evaluate side-chains 63 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.203598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 157)---------------| | r_work = 0.4140 r_free = 0.4140 target = 0.175270 restraints weight = 5834.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.158963 restraints weight = 8870.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.158475 restraints weight = 8349.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158517 restraints weight = 6944.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.158563 restraints weight = 6934.690| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4808 Z= 0.126 Angle : 0.594 8.964 6512 Z= 0.300 Chirality : 0.037 0.149 806 Planarity : 0.002 0.021 784 Dihedral : 3.495 15.488 630 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.65 % Allowed : 18.94 % Favored : 78.41 % 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: 1.60 (0.35), residues: 584 helix: 1.80 (0.27), residues: 376 sheet: -0.99 (0.65), residues: 50 loop : 0.11 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.010 0.001 TYR B 289 PHE 0.021 0.001 PHE A 63 TRP 0.007 0.001 TRP A 311 HIS 0.002 0.000 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4794) covalent geometry : angle 0.59354 ( 6510) hydrogen bonds : bond 0.03643 ( 241) hydrogen bonds : angle 2.93752 ( 717) metal coordination : bond 0.00501 ( 14) metal coordination : angle 0.85186 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.173 Fit side-chains REVERT: A 172 MET cc_start: 0.6482 (pmm) cc_final: 0.6271 (pmm) outliers start: 14 outliers final: 12 residues processed: 60 average time/residue: 0.0513 time to fit residues: 4.4531 Evaluate side-chains 58 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.0870 chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.202713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 150)---------------| | r_work = 0.3944 r_free = 0.3944 target = 0.159332 restraints weight = 5819.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156695 restraints weight = 8272.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156693 restraints weight = 8024.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156693 restraints weight = 7952.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156693 restraints weight = 7952.850| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4808 Z= 0.129 Angle : 0.612 9.056 6512 Z= 0.312 Chirality : 0.037 0.149 806 Planarity : 0.003 0.020 784 Dihedral : 3.515 16.371 630 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.84 % Allowed : 18.94 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.35), residues: 584 helix: 1.80 (0.27), residues: 378 sheet: -0.95 (0.65), residues: 50 loop : -0.03 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.010 0.001 TYR B 289 PHE 0.027 0.001 PHE B 109 TRP 0.007 0.001 TRP A 311 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4794) covalent geometry : angle 0.61221 ( 6510) hydrogen bonds : bond 0.03650 ( 241) hydrogen bonds : angle 2.91083 ( 717) metal coordination : bond 0.00520 ( 14) metal coordination : angle 1.05134 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1009.54 seconds wall clock time: 18 minutes 1.93 seconds (1081.93 seconds total)