Starting phenix.real_space_refine on Sun May 3 00:46:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n2i_48838/05_2026/9n2i_48838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n2i_48838/05_2026/9n2i_48838.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9n2i_48838/05_2026/9n2i_48838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n2i_48838/05_2026/9n2i_48838.map" model { file = "/net/cci-nas-00/data/ceres_data/9n2i_48838/05_2026/9n2i_48838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n2i_48838/05_2026/9n2i_48838.cif" } 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= 0.099 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 56 5.16 5 C 5938 2.51 5 N 1642 2.21 5 O 1717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9353 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3196 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 15, 'TRANS': 379} Chain breaks: 1 Chain: "A" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1909 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} 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: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.40, per 1000 atoms: 0.26 Number of scatterers: 9353 At special positions: 0 Unit cell: (84.288, 100.97, 177.356, 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 56 16.00 O 1717 8.00 N 1642 7.00 C 5938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " 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 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 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: 0.85 Conformation dependent library (CDL) restraints added in 396.2 milliseconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 41.4% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 27 through 49 removed outlier: 3.823A pdb=" N LEU R 49 " --> pdb=" O HIS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 92 removed outlier: 3.873A pdb=" N GLN R 92 " --> pdb=" O HIS R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.925A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU R 129 " --> pdb=" O GLY R 125 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL R 130 " --> pdb=" O GLU R 126 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL R 134 " --> pdb=" O VAL R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 204 removed outlier: 3.511A pdb=" N ARG R 199 " --> pdb=" O ASP R 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN R 204 " --> pdb=" O THR R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 216 Processing helix chain 'R' and resid 223 through 254 removed outlier: 3.501A pdb=" N ALA R 228 " --> pdb=" O CYS R 224 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY R 254 " --> pdb=" O HIS R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 273 removed outlier: 3.651A pdb=" N TYR R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 289 removed outlier: 3.760A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 305 removed outlier: 3.668A pdb=" N TRP R 304 " --> pdb=" O ASN R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 335 removed outlier: 3.520A pdb=" N ILE R 315 " --> pdb=" O VAL R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 359 Proline residue: R 356 - end of helix Processing helix chain 'R' and resid 361 through 366 removed outlier: 3.610A pdb=" N ALA R 366 " --> pdb=" O VAL R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 401 removed outlier: 4.221A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 423 removed outlier: 3.882A pdb=" N LYS R 422 " --> pdb=" O TRP R 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 38 removed outlier: 3.576A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.960A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.699A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.607A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.586A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.634A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.518A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 22 removed outlier: 3.728A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.688A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.010A 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 87 through 91 Processing helix chain 'P' and resid 2 through 28 removed outlier: 3.892A pdb=" N LYS P 12 " --> pdb=" O SER P 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU P 27 " --> pdb=" O ILE P 23 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA P 28 " --> pdb=" O GLU P 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'R' and resid 77 through 80 removed outlier: 3.740A pdb=" N LYS R 98 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.630A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.102A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.632A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.934A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.919A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.999A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.896A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.505A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.889A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.183A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1197 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: 1.63 Time building geometry restraints manager: 1.12 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: 2636 1.33 - 1.45: 1765 1.45 - 1.57: 5082 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 9560 Sorted by residual: bond pdb=" N LYS N 87 " pdb=" CA LYS N 87 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.12e+01 bond pdb=" N PHE R 289 " pdb=" CA PHE R 289 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" N LYS R 344 " pdb=" CA LYS R 344 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.21e-02 6.83e+03 9.98e+00 bond pdb=" N GLN R 113 " pdb=" CA GLN R 113 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.32e+00 bond pdb=" N VAL R 130 " pdb=" CA VAL R 130 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.05e+00 ... (remaining 9555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 12734 2.46 - 4.91: 200 4.91 - 7.37: 10 7.37 - 9.82: 3 9.82 - 12.28: 1 Bond angle restraints: 12948 Sorted by residual: angle pdb=" N HIS R 361 " pdb=" CA HIS R 361 " pdb=" C HIS R 361 " ideal model delta sigma weight residual 114.75 105.94 8.81 1.26e+00 6.30e-01 4.89e+01 angle pdb=" N PHE R 345 " pdb=" CA PHE R 345 " pdb=" C PHE R 345 " ideal model delta sigma weight residual 113.56 104.97 8.59 1.39e+00 5.18e-01 3.82e+01 angle pdb=" N ARG R 346 " pdb=" CA ARG R 346 " pdb=" C ARG R 346 " ideal model delta sigma weight residual 108.79 99.93 8.86 1.53e+00 4.27e-01 3.36e+01 angle pdb=" CA ARG R 346 " pdb=" C ARG R 346 " pdb=" O ARG R 346 " ideal model delta sigma weight residual 121.23 115.27 5.96 1.07e+00 8.73e-01 3.10e+01 angle pdb=" CA ILE A 56 " pdb=" C ILE A 56 " pdb=" O ILE A 56 " ideal model delta sigma weight residual 122.63 118.00 4.63 8.70e-01 1.32e+00 2.84e+01 ... (remaining 12943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5109 17.89 - 35.78: 445 35.78 - 53.67: 86 53.67 - 71.56: 16 71.56 - 89.45: 7 Dihedral angle restraints: 5663 sinusoidal: 2254 harmonic: 3409 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 -155.82 69.82 1 1.00e+01 1.00e-02 6.29e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+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 93.00 124.80 -31.80 1 1.00e+01 1.00e-02 1.44e+01 ... (remaining 5660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1183 0.056 - 0.112: 190 0.112 - 0.168: 40 0.168 - 0.223: 8 0.223 - 0.279: 2 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CA ARG R 346 " pdb=" N ARG R 346 " pdb=" C ARG R 346 " pdb=" CB ARG R 346 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ASP B 246 " pdb=" N ASP B 246 " pdb=" C ASP B 246 " pdb=" CB ASP B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LEU R 49 " pdb=" N LEU R 49 " pdb=" C LEU R 49 " pdb=" CB LEU R 49 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1420 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 287 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C CYS R 287 " 0.060 2.00e-02 2.50e+03 pdb=" O CYS R 287 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU R 288 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 400 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C TYR R 400 " -0.054 2.00e-02 2.50e+03 pdb=" O TYR R 400 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS R 401 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 294 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C CYS R 294 " 0.042 2.00e-02 2.50e+03 pdb=" O CYS R 294 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP R 295 " -0.014 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1422 2.76 - 3.30: 8673 3.30 - 3.83: 14362 3.83 - 4.37: 17603 4.37 - 4.90: 30500 Nonbonded interactions: 72560 Sorted by model distance: nonbonded pdb=" O TYR R 65 " pdb=" OH TYR R 84 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR A 263 " pdb=" OE2 GLU N 46 " model vdw 2.232 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.280 3.040 nonbonded pdb=" ND2 ASN R 74 " pdb=" O THR R 76 " model vdw 2.284 3.120 ... (remaining 72555 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: 1.910 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.540 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: 0.000 Load rotamer database and sin/cos tables:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.004 0.041 9565 Z= 0.286 Angle : 0.666 12.275 12958 Z= 0.443 Chirality : 0.046 0.279 1423 Planarity : 0.004 0.034 1656 Dihedral : 13.955 89.450 3446 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.98 (0.23), residues: 1157 helix: -0.42 (0.23), residues: 447 sheet: 0.03 (0.36), residues: 206 loop : -1.03 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 108 TYR 0.012 0.001 TYR R 145 PHE 0.014 0.001 PHE B 234 TRP 0.013 0.001 TRP R 304 HIS 0.004 0.001 HIS P 1 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9560) covalent geometry : angle 0.66525 (12948) SS BOND : bond 0.00265 ( 5) SS BOND : angle 1.38514 ( 10) hydrogen bonds : bond 0.28543 ( 419) hydrogen bonds : angle 7.68974 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 90 LYS cc_start: 0.7606 (mttp) cc_final: 0.7354 (ttmp) REVERT: R 117 ASP cc_start: 0.6666 (t70) cc_final: 0.6185 (m-30) REVERT: R 334 ARG cc_start: 0.7135 (ttm170) cc_final: 0.6130 (ttm-80) REVERT: N 34 MET cc_start: 0.7730 (mtp) cc_final: 0.7429 (mtp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.5928 time to fit residues: 72.5465 Evaluate side-chains 92 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 0.0170 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 142 GLN A 35 GLN A 54 ASN B 237 ASN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.213237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171311 restraints weight = 9636.599| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.66 r_work: 0.3704 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9565 Z= 0.138 Angle : 0.558 6.677 12958 Z= 0.298 Chirality : 0.042 0.152 1423 Planarity : 0.004 0.030 1656 Dihedral : 4.090 24.663 1283 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.39 % Allowed : 8.27 % Favored : 90.34 % 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 (0.24), residues: 1157 helix: 1.23 (0.24), residues: 450 sheet: 0.23 (0.37), residues: 200 loop : -1.12 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 414 TYR 0.032 0.001 TYR R 145 PHE 0.016 0.002 PHE N 108 TRP 0.011 0.001 TRP P 25 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9560) covalent geometry : angle 0.55530 (12948) SS BOND : bond 0.00289 ( 5) SS BOND : angle 1.91175 ( 10) hydrogen bonds : bond 0.07048 ( 419) hydrogen bonds : angle 4.45856 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.390 Fit side-chains REVERT: R 334 ARG cc_start: 0.6999 (ttm170) cc_final: 0.6083 (ttm170) REVERT: A 229 ASP cc_start: 0.7197 (p0) cc_final: 0.6621 (m-30) REVERT: A 386 MET cc_start: 0.8754 (tmm) cc_final: 0.8478 (ttm) REVERT: A 390 GLN cc_start: 0.7312 (mt0) cc_final: 0.7029 (mt0) REVERT: B 65 THR cc_start: 0.7807 (m) cc_final: 0.7582 (p) REVERT: B 226 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8085 (mt-10) outliers start: 14 outliers final: 3 residues processed: 94 average time/residue: 0.5751 time to fit residues: 58.3221 Evaluate side-chains 83 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 255 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 0.0170 chunk 31 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 52 optimal weight: 0.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN B 155 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.215154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174367 restraints weight = 9630.166| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.68 r_work: 0.3723 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9565 Z= 0.106 Angle : 0.471 6.190 12958 Z= 0.252 Chirality : 0.040 0.142 1423 Planarity : 0.003 0.032 1656 Dihedral : 3.881 22.885 1283 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.39 % Allowed : 12.05 % Favored : 86.55 % 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 (0.25), residues: 1157 helix: 1.93 (0.25), residues: 451 sheet: 0.35 (0.35), residues: 226 loop : -1.08 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 414 TYR 0.022 0.001 TYR R 145 PHE 0.012 0.001 PHE B 292 TRP 0.011 0.001 TRP R 241 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 9560) covalent geometry : angle 0.46883 (12948) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.82351 ( 10) hydrogen bonds : bond 0.05091 ( 419) hydrogen bonds : angle 3.86404 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.372 Fit side-chains REVERT: R 334 ARG cc_start: 0.6810 (ttm170) cc_final: 0.5936 (ttm-80) REVERT: A 229 ASP cc_start: 0.7133 (p0) cc_final: 0.6542 (m-30) outliers start: 14 outliers final: 3 residues processed: 96 average time/residue: 0.5778 time to fit residues: 59.6420 Evaluate side-chains 84 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain B residue 252 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 99 optimal weight: 0.0370 chunk 100 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 155 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.213305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168775 restraints weight = 9730.994| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.86 r_work: 0.3762 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9565 Z= 0.093 Angle : 0.457 6.989 12958 Z= 0.242 Chirality : 0.039 0.150 1423 Planarity : 0.003 0.032 1656 Dihedral : 3.750 22.293 1283 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.99 % Allowed : 13.84 % Favored : 84.16 % 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: 0.82 (0.25), residues: 1157 helix: 2.18 (0.25), residues: 448 sheet: 0.48 (0.35), residues: 224 loop : -1.03 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 324 TYR 0.022 0.001 TYR R 145 PHE 0.011 0.001 PHE N 108 TRP 0.010 0.001 TRP R 241 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 9560) covalent geometry : angle 0.45542 (12948) SS BOND : bond 0.00192 ( 5) SS BOND : angle 1.57372 ( 10) hydrogen bonds : bond 0.04230 ( 419) hydrogen bonds : angle 3.66158 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.359 Fit side-chains REVERT: R 37 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6562 (tppt) REVERT: R 334 ARG cc_start: 0.6596 (ttm170) cc_final: 0.5765 (ttm170) REVERT: R 384 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6962 (m-80) REVERT: A 53 LYS cc_start: 0.6112 (tttt) cc_final: 0.5080 (mtmm) REVERT: A 229 ASP cc_start: 0.7220 (p0) cc_final: 0.6563 (m-30) REVERT: B 59 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: N 91 THR cc_start: 0.5272 (m) cc_final: 0.5021 (p) outliers start: 20 outliers final: 6 residues processed: 100 average time/residue: 0.5846 time to fit residues: 62.6248 Evaluate side-chains 89 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 384 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.209752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.166370 restraints weight = 9575.202| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.89 r_work: 0.3689 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9565 Z= 0.114 Angle : 0.494 7.778 12958 Z= 0.260 Chirality : 0.040 0.148 1423 Planarity : 0.003 0.033 1656 Dihedral : 3.881 21.133 1283 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.29 % Allowed : 15.34 % Favored : 82.37 % 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: 0.81 (0.25), residues: 1157 helix: 2.19 (0.25), residues: 450 sheet: 0.40 (0.36), residues: 224 loop : -1.03 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 324 TYR 0.020 0.001 TYR R 145 PHE 0.019 0.001 PHE N 108 TRP 0.010 0.001 TRP R 241 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9560) covalent geometry : angle 0.49092 (12948) SS BOND : bond 0.00262 ( 5) SS BOND : angle 1.88351 ( 10) hydrogen bonds : bond 0.04729 ( 419) hydrogen bonds : angle 3.69528 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.243 Fit side-chains REVERT: R 37 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6598 (tppt) REVERT: R 334 ARG cc_start: 0.6747 (ttm170) cc_final: 0.5843 (ttm170) REVERT: A 38 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6943 (ptm-80) REVERT: A 53 LYS cc_start: 0.6183 (tttt) cc_final: 0.5337 (mtmm) REVERT: A 229 ASP cc_start: 0.7135 (p0) cc_final: 0.6493 (m-30) REVERT: A 309 GLU cc_start: 0.5130 (pm20) cc_final: 0.4928 (mp0) REVERT: N 91 THR cc_start: 0.5208 (m) cc_final: 0.4869 (p) outliers start: 23 outliers final: 9 residues processed: 96 average time/residue: 0.5728 time to fit residues: 58.9544 Evaluate side-chains 92 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 153 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 155 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.212390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.165883 restraints weight = 9723.754| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.00 r_work: 0.3747 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9565 Z= 0.099 Angle : 0.467 7.579 12958 Z= 0.247 Chirality : 0.040 0.142 1423 Planarity : 0.003 0.033 1656 Dihedral : 3.819 22.169 1283 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.19 % Allowed : 15.74 % Favored : 82.07 % 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: 0.98 (0.25), residues: 1157 helix: 2.33 (0.25), residues: 447 sheet: 0.53 (0.36), residues: 227 loop : -0.93 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 324 TYR 0.020 0.001 TYR R 145 PHE 0.012 0.001 PHE N 108 TRP 0.011 0.001 TRP R 241 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9560) covalent geometry : angle 0.46439 (12948) SS BOND : bond 0.00213 ( 5) SS BOND : angle 1.72702 ( 10) hydrogen bonds : bond 0.04308 ( 419) hydrogen bonds : angle 3.62074 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: R 37 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6637 (tppt) REVERT: R 195 ASP cc_start: 0.6550 (OUTLIER) cc_final: 0.6314 (p0) REVERT: R 334 ARG cc_start: 0.6593 (ttm170) cc_final: 0.5708 (ttm170) REVERT: R 384 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: A 53 LYS cc_start: 0.5961 (tttt) cc_final: 0.5060 (mtmm) REVERT: A 229 ASP cc_start: 0.7192 (p0) cc_final: 0.6501 (m-30) REVERT: N 91 THR cc_start: 0.5016 (m) cc_final: 0.4643 (p) outliers start: 22 outliers final: 13 residues processed: 97 average time/residue: 0.5897 time to fit residues: 61.4169 Evaluate side-chains 99 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 384 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain P residue 1 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 155 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.212582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.172073 restraints weight = 9618.240| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.71 r_work: 0.3678 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9565 Z= 0.116 Angle : 0.497 7.828 12958 Z= 0.263 Chirality : 0.041 0.149 1423 Planarity : 0.003 0.033 1656 Dihedral : 3.951 22.310 1283 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.59 % Allowed : 15.84 % Favored : 81.57 % 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: 0.93 (0.25), residues: 1157 helix: 2.27 (0.25), residues: 446 sheet: 0.50 (0.36), residues: 227 loop : -0.94 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.019 0.001 TYR R 145 PHE 0.020 0.001 PHE N 108 TRP 0.011 0.001 TRP R 241 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9560) covalent geometry : angle 0.49488 (12948) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.82229 ( 10) hydrogen bonds : bond 0.04706 ( 419) hydrogen bonds : angle 3.67499 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: R 37 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6629 (tppt) REVERT: R 334 ARG cc_start: 0.6744 (ttm170) cc_final: 0.5865 (ttm170) REVERT: R 384 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: A 53 LYS cc_start: 0.6196 (tttt) cc_final: 0.5477 (mtmm) REVERT: A 229 ASP cc_start: 0.7188 (p0) cc_final: 0.6513 (m-30) REVERT: B 249 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7414 (m) outliers start: 26 outliers final: 13 residues processed: 100 average time/residue: 0.5713 time to fit residues: 61.4326 Evaluate side-chains 99 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 384 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain P residue 1 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 86 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.211911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170018 restraints weight = 9449.615| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.91 r_work: 0.3735 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.002 0.027 9565 Z= 0.094 Angle : 0.461 7.526 12958 Z= 0.245 Chirality : 0.039 0.138 1423 Planarity : 0.003 0.033 1656 Dihedral : 3.787 22.725 1283 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.89 % Allowed : 16.63 % Favored : 81.47 % 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: 1.05 (0.26), residues: 1157 helix: 2.42 (0.25), residues: 448 sheet: 0.54 (0.36), residues: 225 loop : -0.93 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 324 TYR 0.020 0.001 TYR R 145 PHE 0.010 0.001 PHE N 108 TRP 0.012 0.001 TRP R 241 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 9560) covalent geometry : angle 0.45794 (12948) SS BOND : bond 0.00237 ( 5) SS BOND : angle 1.81750 ( 10) hydrogen bonds : bond 0.04098 ( 419) hydrogen bonds : angle 3.51030 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: R 37 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6565 (tppt) REVERT: R 334 ARG cc_start: 0.6654 (ttm170) cc_final: 0.5801 (ttm170) REVERT: R 384 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: A 53 LYS cc_start: 0.5981 (tttt) cc_final: 0.5134 (mtmm) REVERT: A 229 ASP cc_start: 0.7298 (p0) cc_final: 0.6559 (m-30) REVERT: A 378 ASP cc_start: 0.6656 (m-30) cc_final: 0.6278 (m-30) outliers start: 19 outliers final: 11 residues processed: 94 average time/residue: 0.5985 time to fit residues: 60.3850 Evaluate side-chains 93 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 384 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain P residue 1 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 0.0070 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.210308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168077 restraints weight = 9474.532| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.98 r_work: 0.3707 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9565 Z= 0.107 Angle : 0.483 7.715 12958 Z= 0.255 Chirality : 0.040 0.145 1423 Planarity : 0.003 0.033 1656 Dihedral : 3.854 21.584 1283 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.79 % Allowed : 16.83 % Favored : 81.37 % 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: 0.98 (0.25), residues: 1157 helix: 2.37 (0.25), residues: 447 sheet: 0.47 (0.36), residues: 225 loop : -0.95 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 324 TYR 0.019 0.001 TYR R 145 PHE 0.019 0.001 PHE N 108 TRP 0.010 0.001 TRP R 241 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9560) covalent geometry : angle 0.48024 (12948) SS BOND : bond 0.00234 ( 5) SS BOND : angle 1.87009 ( 10) hydrogen bonds : bond 0.04397 ( 419) hydrogen bonds : angle 3.55352 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: R 37 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6545 (tppt) REVERT: R 334 ARG cc_start: 0.6691 (ttm170) cc_final: 0.5846 (ttm170) REVERT: R 384 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: A 53 LYS cc_start: 0.6040 (tttt) cc_final: 0.5170 (mtmt) REVERT: A 229 ASP cc_start: 0.7300 (p0) cc_final: 0.6556 (m-30) outliers start: 18 outliers final: 12 residues processed: 95 average time/residue: 0.5402 time to fit residues: 55.1701 Evaluate side-chains 98 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 384 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain P residue 1 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.210311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167832 restraints weight = 9432.449| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.99 r_work: 0.3715 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9565 Z= 0.106 Angle : 0.481 7.684 12958 Z= 0.255 Chirality : 0.040 0.144 1423 Planarity : 0.003 0.033 1656 Dihedral : 3.853 21.955 1283 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.89 % Allowed : 16.83 % Favored : 81.27 % 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: 0.97 (0.25), residues: 1157 helix: 2.35 (0.25), residues: 447 sheet: 0.45 (0.36), residues: 226 loop : -0.93 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 324 TYR 0.019 0.001 TYR A 360 PHE 0.017 0.001 PHE N 108 TRP 0.010 0.001 TRP R 241 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9560) covalent geometry : angle 0.47825 (12948) SS BOND : bond 0.00230 ( 5) SS BOND : angle 1.85702 ( 10) hydrogen bonds : bond 0.04342 ( 419) hydrogen bonds : angle 3.56241 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 37 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6547 (tppt) REVERT: R 334 ARG cc_start: 0.6740 (ttm170) cc_final: 0.5904 (ttm170) REVERT: R 384 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7036 (m-80) REVERT: A 53 LYS cc_start: 0.6026 (tttt) cc_final: 0.5176 (mtmt) REVERT: A 229 ASP cc_start: 0.7288 (p0) cc_final: 0.6547 (m-30) outliers start: 19 outliers final: 12 residues processed: 97 average time/residue: 0.5592 time to fit residues: 58.3381 Evaluate side-chains 97 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 LYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 384 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain P residue 1 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.212097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.172268 restraints weight = 9565.709| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.66 r_work: 0.3664 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9565 Z= 0.120 Angle : 0.506 7.898 12958 Z= 0.267 Chirality : 0.041 0.148 1423 Planarity : 0.003 0.034 1656 Dihedral : 3.961 21.856 1283 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.79 % Allowed : 17.23 % Favored : 80.98 % 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: 0.89 (0.25), residues: 1157 helix: 2.26 (0.25), residues: 447 sheet: 0.39 (0.35), residues: 227 loop : -0.93 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 324 TYR 0.023 0.001 TYR A 360 PHE 0.021 0.001 PHE N 108 TRP 0.010 0.001 TRP N 47 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9560) covalent geometry : angle 0.50341 (12948) SS BOND : bond 0.00243 ( 5) SS BOND : angle 2.06964 ( 10) hydrogen bonds : bond 0.04712 ( 419) hydrogen bonds : angle 3.63898 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3386.61 seconds wall clock time: 58 minutes 26.65 seconds (3506.65 seconds total)