Starting phenix.real_space_refine on Wed Aug 5 11:00:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n1q_48821/08_2026/9n1q_48821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n1q_48821/08_2026/9n1q_48821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n1q_48821/08_2026/9n1q_48821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n1q_48821/08_2026/9n1q_48821.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n1q_48821/08_2026/9n1q_48821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n1q_48821/08_2026/9n1q_48821.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.087 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5928 2.51 5 N 1643 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1899 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 249 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3180 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 15, 'TRANS': 377} Chain breaks: 1 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.07, per 1000 atoms: 0.22 Number of scatterers: 9339 At special positions: 0 Unit cell: (81.1164, 102.277, 176.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1713 8.00 N 1643 7.00 C 5928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.04 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 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: 0.96 Conformation dependent library (CDL) restraints added in 361.6 milliseconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 40.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.503A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 4.426A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.530A pdb=" N ASN A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.841A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.692A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.774A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.655A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.738A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'G' and resid 8 through 21 removed outlier: 3.794A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.899A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.843A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.609A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.702A pdb=" N LYS P 12 " --> pdb=" O SER P 8 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP P 15 " --> pdb=" O SER P 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 49 removed outlier: 3.544A pdb=" N LEU R 38 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS R 45 " --> pdb=" O ASP R 41 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU R 49 " --> pdb=" O HIS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 92 removed outlier: 3.954A pdb=" N GLN R 92 " --> pdb=" O HIS R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 165 removed outlier: 3.597A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 202 removed outlier: 3.525A pdb=" N TYR R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 216 Processing helix chain 'R' and resid 217 through 254 removed outlier: 3.621A pdb=" N VAL R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY R 223 " --> pdb=" O GLY R 219 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N CYS R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA R 227 " --> pdb=" O GLY R 223 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY R 246 " --> pdb=" O LEU R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 Processing helix chain 'R' and resid 275 through 287 Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 308 through 336 removed outlier: 3.790A pdb=" N ARG R 336 " --> pdb=" O LYS R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 359 removed outlier: 3.572A pdb=" N ILE R 355 " --> pdb=" O THR R 351 " (cutoff:3.500A) Proline residue: R 356 - end of helix Processing helix chain 'R' and resid 375 through 400 removed outlier: 3.513A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 422 removed outlier: 3.608A pdb=" N LEU R 411 " --> pdb=" O VAL R 407 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.567A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.515A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.655A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.656A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.692A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.762A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.656A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.084A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.899A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.102A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 61 through 62 removed outlier: 3.939A pdb=" N THR R 61 " --> pdb=" O TRP R 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 76 through 80 removed outlier: 3.564A pdb=" N LYS R 98 " --> pdb=" O ALA R 77 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1182 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: 1.69 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1993 1.33 - 1.45: 2287 1.45 - 1.57: 5191 1.57 - 1.69: 0 1.69 - 1.82: 75 Bond restraints: 9546 Sorted by residual: bond pdb=" C LEU P 26 " pdb=" N LEU P 27 " ideal model delta sigma weight residual 1.334 1.288 0.046 1.46e-02 4.69e+03 9.94e+00 bond pdb=" N LYS N 87 " pdb=" CA LYS N 87 " ideal model delta sigma weight residual 1.453 1.479 -0.026 8.30e-03 1.45e+04 9.83e+00 bond pdb=" N VAL R 398 " pdb=" CA VAL R 398 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" C ALA N 101 " pdb=" N PRO N 102 " ideal model delta sigma weight residual 1.329 1.366 -0.037 1.20e-02 6.94e+03 9.43e+00 bond pdb=" N ILE B 18 " pdb=" CA ILE B 18 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.02e+00 ... (remaining 9541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11918 1.28 - 2.57: 753 2.57 - 3.85: 209 3.85 - 5.13: 41 5.13 - 6.42: 7 Bond angle restraints: 12928 Sorted by residual: angle pdb=" CA ASP B 228 " pdb=" C ASP B 228 " pdb=" O ASP B 228 " ideal model delta sigma weight residual 121.87 117.38 4.49 1.16e+00 7.43e-01 1.50e+01 angle pdb=" CA ASP R 195 " pdb=" C ASP R 195 " pdb=" O ASP R 195 " ideal model delta sigma weight residual 120.92 116.66 4.26 1.12e+00 7.97e-01 1.45e+01 angle pdb=" CA PHE N 108 " pdb=" CB PHE N 108 " pdb=" CG PHE N 108 " ideal model delta sigma weight residual 113.80 117.60 -3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 111.57 117.04 -5.47 1.52e+00 4.33e-01 1.30e+01 angle pdb=" CA ASP R 195 " pdb=" CB ASP R 195 " pdb=" CG ASP R 195 " ideal model delta sigma weight residual 112.60 116.19 -3.59 1.00e+00 1.00e+00 1.29e+01 ... (remaining 12923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5109 17.48 - 34.96: 436 34.96 - 52.44: 89 52.44 - 69.92: 13 69.92 - 87.40: 9 Dihedral angle restraints: 5656 sinusoidal: 2254 harmonic: 3402 Sorted by residual: dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 67 " pdb=" CB CYS R 67 " ideal model delta sinusoidal sigma weight residual -86.00 -173.40 87.40 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS R 58 " pdb=" SG CYS R 58 " pdb=" SG CYS R 100 " pdb=" CB CYS R 100 " ideal model delta sinusoidal sigma weight residual -86.00 -126.40 40.40 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " pdb=" SG CYS R 294 " pdb=" CB CYS R 294 " ideal model delta sinusoidal sigma weight residual 93.00 124.33 -31.33 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 5653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1199 0.063 - 0.126: 183 0.126 - 0.189: 32 0.189 - 0.251: 4 0.251 - 0.314: 2 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA LEU P 27 " pdb=" N LEU P 27 " pdb=" C LEU P 27 " pdb=" CB LEU P 27 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA LYS N 87 " pdb=" N LYS N 87 " pdb=" C LYS N 87 " pdb=" CB LYS N 87 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA GLU B 226 " pdb=" N GLU B 226 " pdb=" C GLU B 226 " pdb=" CB GLU B 226 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1417 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 397 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C ALA R 397 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA R 397 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL R 398 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 219 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C PHE A 219 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE A 219 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS A 220 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE N 108 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C PHE N 108 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE N 108 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP N 109 " -0.011 2.00e-02 2.50e+03 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2182 2.79 - 3.32: 8463 3.32 - 3.85: 14271 3.85 - 4.37: 16913 4.37 - 4.90: 29590 Nonbonded interactions: 71419 Sorted by model distance: nonbonded pdb=" OD1 ASP R 63 " pdb=" N LYS R 64 " model vdw 2.265 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.275 3.040 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.282 3.120 nonbonded pdb=" O GLY A 355 " pdb=" NH1 ARG A 389 " model vdw 2.288 3.120 nonbonded pdb=" OD2 ASP A 343 " pdb=" NH2 ARG A 347 " model vdw 2.298 3.120 ... (remaining 71414 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.440 Find NCS groups from input model: 0.050 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9552 Z= 0.336 Angle : 0.756 6.417 12940 Z= 0.499 Chirality : 0.050 0.314 1420 Planarity : 0.004 0.037 1653 Dihedral : 13.688 86.939 3440 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.24), residues: 1155 helix: -0.25 (0.24), residues: 436 sheet: -0.89 (0.34), residues: 222 loop : -1.03 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 108 TYR 0.012 0.001 TYR P 10 PHE 0.023 0.002 PHE B 222 TRP 0.017 0.002 TRP R 106 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.34 ( 9546) covalent geometry : angle 0.75610 / 0.50 (12928) SS BOND : bond 0.00390 / 0.16 ( 6) SS BOND : angle 0.94436 / 0.58 ( 12) hydrogen bonds : bond 0.28976 / 18.53 ( 414) hydrogen bonds : angle 8.01221 / 5.47 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: R 68 TRP cc_start: 0.6261 (m-90) cc_final: 0.5529 (m-10) REVERT: R 344 LYS cc_start: 0.6489 (mmtm) cc_final: 0.5667 (mppt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.5002 time to fit residues: 69.8392 Evaluate side-chains 85 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN B 110 ASN N 31 ASN R 122 GLN R 374 GLN R 392 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.185310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135222 restraints weight = 10538.047| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.48 r_work: 0.3554 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9552 Z= 0.139 Angle : 0.569 9.520 12940 Z= 0.301 Chirality : 0.041 0.152 1420 Planarity : 0.004 0.034 1653 Dihedral : 4.308 34.356 1280 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.90 % Allowed : 10.48 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1155 helix: 1.13 (0.25), residues: 447 sheet: -0.72 (0.31), residues: 249 loop : -1.06 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 94 TYR 0.032 0.001 TYR R 145 PHE 0.025 0.002 PHE R 384 TRP 0.012 0.001 TRP N 47 HIS 0.009 0.001 HIS R 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 9546) covalent geometry : angle 0.56827 / 0.30 (12928) SS BOND : bond 0.00442 / 0.20 ( 6) SS BOND : angle 1.12567 / 0.68 ( 12) hydrogen bonds : bond 0.06495 / 4.27 ( 414) hydrogen bonds : angle 4.71179 / 3.26 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.208 Fit side-chains REVERT: A 209 GLU cc_start: 0.8408 (pt0) cc_final: 0.8007 (tt0) REVERT: B 45 MET cc_start: 0.8502 (mtt) cc_final: 0.8266 (mtt) REVERT: R 43 CYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5065 (m) REVERT: R 66 SER cc_start: 0.7895 (p) cc_final: 0.7271 (t) REVERT: R 195 ASP cc_start: 0.7604 (t0) cc_final: 0.7386 (t0) REVERT: R 344 LYS cc_start: 0.6089 (mmtm) cc_final: 0.5110 (mppt) REVERT: R 419 ARG cc_start: 0.5190 (mmt90) cc_final: 0.4721 (ptm-80) outliers start: 9 outliers final: 1 residues processed: 110 average time/residue: 0.5115 time to fit residues: 60.3807 Evaluate side-chains 84 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain R residue 43 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN ** R 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.182589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132845 restraints weight = 10574.832| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.47 r_work: 0.3524 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9552 Z= 0.142 Angle : 0.541 10.479 12940 Z= 0.285 Chirality : 0.041 0.146 1420 Planarity : 0.004 0.036 1653 Dihedral : 4.233 27.953 1280 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.90 % Allowed : 13.47 % Favored : 84.63 % 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: -0.02 (0.24), residues: 1155 helix: 1.45 (0.25), residues: 452 sheet: -0.63 (0.31), residues: 246 loop : -1.09 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.028 0.001 TYR R 145 PHE 0.024 0.002 PHE N 108 TRP 0.013 0.001 TRP N 47 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9546) covalent geometry : angle 0.53994 / 0.28 (12928) SS BOND : bond 0.00349 / 0.17 ( 6) SS BOND : angle 1.11937 / 0.65 ( 12) hydrogen bonds : bond 0.05888 / 3.86 ( 414) hydrogen bonds : angle 4.36874 / 3.01 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.308 Fit side-chains REVERT: A 209 GLU cc_start: 0.8282 (pt0) cc_final: 0.7933 (mp0) REVERT: B 59 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8138 (t80) REVERT: R 37 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7342 (mttp) REVERT: R 43 CYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5036 (m) REVERT: R 344 LYS cc_start: 0.6139 (mmtm) cc_final: 0.5205 (mppt) REVERT: R 345 PHE cc_start: 0.7291 (t80) cc_final: 0.6743 (m-80) REVERT: R 419 ARG cc_start: 0.5374 (mmt90) cc_final: 0.4870 (ptm-80) outliers start: 19 outliers final: 6 residues processed: 104 average time/residue: 0.5050 time to fit residues: 56.2959 Evaluate side-chains 95 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 13 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.0301 > 50:) overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN R 93 HIS R 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.181894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133719 restraints weight = 10693.984| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.72 r_work: 0.3527 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9552 Z= 0.139 Angle : 0.531 9.451 12940 Z= 0.280 Chirality : 0.041 0.150 1420 Planarity : 0.004 0.033 1653 Dihedral : 4.217 28.762 1280 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.30 % Allowed : 14.37 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1155 helix: 1.65 (0.25), residues: 453 sheet: -0.58 (0.31), residues: 245 loop : -1.16 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.028 0.001 TYR R 145 PHE 0.022 0.002 PHE N 108 TRP 0.013 0.001 TRP N 47 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9546) covalent geometry : angle 0.52982 / 0.28 (12928) SS BOND : bond 0.00329 / 0.17 ( 6) SS BOND : angle 1.12013 / 0.65 ( 12) hydrogen bonds : bond 0.05332 / 3.52 ( 414) hydrogen bonds : angle 4.19455 / 2.89 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.292 Fit side-chains REVERT: A 209 GLU cc_start: 0.8218 (pt0) cc_final: 0.7820 (tt0) REVERT: B 45 MET cc_start: 0.8745 (mtt) cc_final: 0.8140 (mtt) REVERT: B 59 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8108 (t80) REVERT: R 43 CYS cc_start: 0.5976 (OUTLIER) cc_final: 0.5010 (m) REVERT: R 344 LYS cc_start: 0.6040 (mmtm) cc_final: 0.5151 (mppt) REVERT: R 345 PHE cc_start: 0.7278 (t80) cc_final: 0.6754 (m-80) REVERT: R 412 ARG cc_start: 0.5547 (mmt180) cc_final: 0.5185 (mpt-90) REVERT: R 419 ARG cc_start: 0.5259 (mmt90) cc_final: 0.4653 (ptm-80) outliers start: 23 outliers final: 7 residues processed: 111 average time/residue: 0.4910 time to fit residues: 58.6897 Evaluate side-chains 95 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN R 318 ASN R 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.183365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132389 restraints weight = 10341.795| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.57 r_work: 0.3492 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9552 Z= 0.129 Angle : 0.519 10.656 12940 Z= 0.273 Chirality : 0.040 0.145 1420 Planarity : 0.003 0.034 1653 Dihedral : 4.137 28.150 1280 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.40 % Allowed : 15.67 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1155 helix: 1.83 (0.25), residues: 453 sheet: -0.53 (0.31), residues: 245 loop : -1.14 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.025 0.001 TYR R 145 PHE 0.020 0.001 PHE N 108 TRP 0.012 0.001 TRP N 47 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9546) covalent geometry : angle 0.51674 / 0.27 (12928) SS BOND : bond 0.00296 / 0.16 ( 6) SS BOND : angle 1.79464 / 1.10 ( 12) hydrogen bonds : bond 0.05018 / 3.32 ( 414) hydrogen bonds : angle 4.06166 / 2.80 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.279 Fit side-chains REVERT: B 59 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7853 (t80) REVERT: P 11 SER cc_start: 0.8317 (m) cc_final: 0.8052 (p) REVERT: R 43 CYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5035 (m) REVERT: R 344 LYS cc_start: 0.5982 (mmtm) cc_final: 0.5139 (mppt) REVERT: R 345 PHE cc_start: 0.7186 (t80) cc_final: 0.6732 (m-80) REVERT: R 419 ARG cc_start: 0.5129 (mmt90) cc_final: 0.4544 (ptm-80) outliers start: 24 outliers final: 10 residues processed: 113 average time/residue: 0.4814 time to fit residues: 58.5914 Evaluate side-chains 100 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 77 optimal weight: 0.0060 chunk 102 optimal weight: 0.0370 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.9676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN R 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.184178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133160 restraints weight = 10355.348| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.58 r_work: 0.3502 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9552 Z= 0.116 Angle : 0.512 9.992 12940 Z= 0.267 Chirality : 0.040 0.143 1420 Planarity : 0.003 0.035 1653 Dihedral : 4.043 28.138 1280 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.40 % Allowed : 16.77 % Favored : 80.84 % 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: 0.40 (0.25), residues: 1155 helix: 2.10 (0.25), residues: 444 sheet: -0.46 (0.31), residues: 247 loop : -1.14 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.022 0.001 TYR R 145 PHE 0.015 0.001 PHE N 108 TRP 0.011 0.001 TRP N 47 HIS 0.006 0.001 HIS R 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9546) covalent geometry : angle 0.50990 / 0.27 (12928) SS BOND : bond 0.00429 / 0.23 ( 6) SS BOND : angle 1.62417 / 0.92 ( 12) hydrogen bonds : bond 0.04668 / 3.09 ( 414) hydrogen bonds : angle 3.96164 / 2.73 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.314 Fit side-chains REVERT: B 45 MET cc_start: 0.8610 (mtt) cc_final: 0.8017 (mtt) REVERT: B 59 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7832 (t80) REVERT: B 217 MET cc_start: 0.7974 (pmm) cc_final: 0.7582 (pmt) REVERT: B 234 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: P 26 LEU cc_start: 0.7555 (tp) cc_final: 0.7249 (tt) REVERT: R 43 CYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5096 (m) REVERT: R 344 LYS cc_start: 0.5981 (mmtm) cc_final: 0.5132 (mppt) REVERT: R 345 PHE cc_start: 0.7235 (t80) cc_final: 0.6809 (m-80) REVERT: R 419 ARG cc_start: 0.5328 (mmt90) cc_final: 0.4677 (ptm-80) outliers start: 24 outliers final: 13 residues processed: 109 average time/residue: 0.4785 time to fit residues: 56.2669 Evaluate side-chains 98 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN R 174 ASN R 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.177837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131134 restraints weight = 10669.506| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.60 r_work: 0.3454 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9552 Z= 0.196 Angle : 0.604 11.414 12940 Z= 0.316 Chirality : 0.043 0.171 1420 Planarity : 0.004 0.035 1653 Dihedral : 4.428 25.506 1280 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.79 % Allowed : 16.67 % Favored : 80.54 % 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: 0.04 (0.25), residues: 1155 helix: 1.74 (0.25), residues: 451 sheet: -0.53 (0.32), residues: 241 loop : -1.40 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.034 0.002 TYR R 145 PHE 0.032 0.002 PHE N 108 TRP 0.014 0.002 TRP N 47 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 9546) covalent geometry : angle 0.60277 / 0.31 (12928) SS BOND : bond 0.00507 / 0.27 ( 6) SS BOND : angle 1.45650 / 0.84 ( 12) hydrogen bonds : bond 0.05871 / 3.91 ( 414) hydrogen bonds : angle 4.25963 / 2.95 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.320 Fit side-chains REVERT: B 59 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: P 26 LEU cc_start: 0.7749 (tp) cc_final: 0.7432 (tt) REVERT: R 43 CYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5061 (m) REVERT: R 344 LYS cc_start: 0.6159 (mmtm) cc_final: 0.5317 (mppt) REVERT: R 345 PHE cc_start: 0.7394 (t80) cc_final: 0.6998 (m-80) REVERT: R 419 ARG cc_start: 0.5400 (mmt90) cc_final: 0.4603 (ptm-80) outliers start: 28 outliers final: 15 residues processed: 108 average time/residue: 0.5444 time to fit residues: 63.1004 Evaluate side-chains 99 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 174 ASN R 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.184336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.133580 restraints weight = 10303.601| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.57 r_work: 0.3502 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9552 Z= 0.106 Angle : 0.506 10.877 12940 Z= 0.264 Chirality : 0.039 0.164 1420 Planarity : 0.003 0.036 1653 Dihedral : 4.052 29.258 1280 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.70 % Allowed : 18.36 % Favored : 79.94 % 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: 0.41 (0.25), residues: 1155 helix: 2.11 (0.25), residues: 444 sheet: -0.37 (0.32), residues: 243 loop : -1.20 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.023 0.001 TYR R 84 PHE 0.012 0.001 PHE R 384 TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS R 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 9546) covalent geometry : angle 0.50490 / 0.26 (12928) SS BOND : bond 0.00217 / 0.13 ( 6) SS BOND : angle 1.35374 / 0.76 ( 12) hydrogen bonds : bond 0.04452 / 2.94 ( 414) hydrogen bonds : angle 3.90603 / 2.70 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.343 Fit side-chains REVERT: B 45 MET cc_start: 0.8569 (mtt) cc_final: 0.8038 (mtt) REVERT: B 59 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: P 26 LEU cc_start: 0.7490 (tp) cc_final: 0.7272 (tt) REVERT: R 43 CYS cc_start: 0.5890 (OUTLIER) cc_final: 0.5036 (m) REVERT: R 344 LYS cc_start: 0.5986 (mmtm) cc_final: 0.5136 (mppt) REVERT: R 345 PHE cc_start: 0.7356 (t80) cc_final: 0.6992 (m-80) REVERT: R 412 ARG cc_start: 0.5540 (mmt180) cc_final: 0.5140 (mpt-90) REVERT: R 419 ARG cc_start: 0.5316 (mmt90) cc_final: 0.4531 (ptm-80) outliers start: 17 outliers final: 10 residues processed: 103 average time/residue: 0.6016 time to fit residues: 66.0162 Evaluate side-chains 96 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 368 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN N 31 ASN R 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.179901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133717 restraints weight = 10532.146| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.57 r_work: 0.3483 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9552 Z= 0.148 Angle : 0.547 10.836 12940 Z= 0.286 Chirality : 0.041 0.153 1420 Planarity : 0.003 0.035 1653 Dihedral : 4.198 26.078 1280 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.60 % Allowed : 18.36 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1155 helix: 2.02 (0.25), residues: 444 sheet: -0.38 (0.33), residues: 230 loop : -1.26 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.026 0.002 TYR R 145 PHE 0.022 0.002 PHE N 108 TRP 0.012 0.001 TRP R 68 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9546) covalent geometry : angle 0.54522 / 0.29 (12928) SS BOND : bond 0.00522 / 0.26 ( 6) SS BOND : angle 1.34685 / 0.76 ( 12) hydrogen bonds : bond 0.05044 / 3.35 ( 414) hydrogen bonds : angle 4.01614 / 2.78 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.365 Fit side-chains REVERT: B 45 MET cc_start: 0.8591 (mtt) cc_final: 0.8102 (mtt) REVERT: B 59 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: P 26 LEU cc_start: 0.7632 (tp) cc_final: 0.7398 (tt) REVERT: R 43 CYS cc_start: 0.5888 (OUTLIER) cc_final: 0.5149 (m) REVERT: R 344 LYS cc_start: 0.6171 (mmtm) cc_final: 0.5326 (mppt) REVERT: R 345 PHE cc_start: 0.7360 (t80) cc_final: 0.6978 (m-80) REVERT: R 412 ARG cc_start: 0.5662 (mmt180) cc_final: 0.5330 (mpt-90) REVERT: R 419 ARG cc_start: 0.5389 (mmt90) cc_final: 0.4505 (ptm-80) outliers start: 16 outliers final: 11 residues processed: 103 average time/residue: 0.5948 time to fit residues: 65.5936 Evaluate side-chains 97 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 368 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135417 restraints weight = 10581.397| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.69 r_work: 0.3504 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9552 Z= 0.112 Angle : 0.519 11.620 12940 Z= 0.268 Chirality : 0.040 0.177 1420 Planarity : 0.003 0.035 1653 Dihedral : 4.038 27.637 1280 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.30 % Allowed : 18.76 % Favored : 79.94 % 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: 0.49 (0.25), residues: 1155 helix: 2.18 (0.25), residues: 444 sheet: -0.26 (0.33), residues: 230 loop : -1.17 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.025 0.001 TYR R 84 PHE 0.016 0.001 PHE N 108 TRP 0.013 0.001 TRP R 68 HIS 0.006 0.001 HIS R 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9546) covalent geometry : angle 0.51785 / 0.27 (12928) SS BOND : bond 0.00490 / 0.24 ( 6) SS BOND : angle 1.29904 / 0.72 ( 12) hydrogen bonds : bond 0.04464 / 2.95 ( 414) hydrogen bonds : angle 3.86946 / 2.68 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.367 Fit side-chains REVERT: B 45 MET cc_start: 0.8563 (mtt) cc_final: 0.8019 (mtt) REVERT: B 59 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: R 43 CYS cc_start: 0.5837 (OUTLIER) cc_final: 0.5058 (m) REVERT: R 344 LYS cc_start: 0.6182 (mmtm) cc_final: 0.5291 (mppt) REVERT: R 345 PHE cc_start: 0.7436 (t80) cc_final: 0.7051 (m-80) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.5724 time to fit residues: 61.4286 Evaluate side-chains 98 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 102 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN R 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.183394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135751 restraints weight = 10430.157| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.77 r_work: 0.3537 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9552 Z= 0.104 Angle : 0.500 11.366 12940 Z= 0.261 Chirality : 0.039 0.160 1420 Planarity : 0.003 0.036 1653 Dihedral : 3.930 26.915 1280 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.40 % Allowed : 18.86 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1155 helix: 2.24 (0.25), residues: 446 sheet: -0.30 (0.33), residues: 233 loop : -1.06 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.023 0.001 TYR R 84 PHE 0.012 0.001 PHE R 384 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS R 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9546) covalent geometry : angle 0.49850 / 0.26 (12928) SS BOND : bond 0.00416 / 0.21 ( 6) SS BOND : angle 1.24092 / 0.69 ( 12) hydrogen bonds : bond 0.04099 / 2.70 ( 414) hydrogen bonds : angle 3.75921 / 2.60 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.43 seconds wall clock time: 49 minutes 43.29 seconds (2983.29 seconds total)