Starting phenix.real_space_refine on Wed Feb 4 18:03:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nxx_49911/02_2026/9nxx_49911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nxx_49911/02_2026/9nxx_49911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nxx_49911/02_2026/9nxx_49911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nxx_49911/02_2026/9nxx_49911.map" model { file = "/net/cci-nas-00/data/ceres_data/9nxx_49911/02_2026/9nxx_49911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nxx_49911/02_2026/9nxx_49911.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.044 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 36 5.16 5 C 7509 2.51 5 N 2045 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11910 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2893 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 7, 'TRANS': 347} Chain breaks: 1 Chain: "B" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3070 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 7, 'TRANS': 371} Chain: "C" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2890 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 1 Chain: "D" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3057 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 7, 'TRANS': 369} Time building chain proxies: 2.35, per 1000 atoms: 0.20 Number of scatterers: 11910 At special positions: 0 Unit cell: (146.832, 81.928, 127.68, 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 36 16.00 O 2320 8.00 N 2045 7.00 C 7509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 431.7 milliseconds 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 6 sheets defined 65.1% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 17 through 28 removed outlier: 3.669A pdb=" N ARG A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 23 " --> pdb=" O GLU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 87 removed outlier: 4.048A pdb=" N TRP A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 117 through 132 removed outlier: 3.659A pdb=" N ASP A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 removed outlier: 4.343A pdb=" N ASN A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TYR A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.882A pdb=" N ASP A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 210 removed outlier: 3.580A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 197 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.585A pdb=" N TYR A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.647A pdb=" N ASN A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 266 Processing helix chain 'A' and resid 271 through 295 removed outlier: 3.660A pdb=" N LEU A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 325 removed outlier: 3.674A pdb=" N TYR A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 345 Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.502A pdb=" N ALA A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'B' and resid 7 through 28 removed outlier: 5.910A pdb=" N ARG B 21 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 22 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 87 removed outlier: 3.888A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 117 through 123 removed outlier: 4.169A pdb=" N LYS B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.978A pdb=" N ASN B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 188 through 210 removed outlier: 3.546A pdb=" N ILE B 192 " --> pdb=" O HIS B 188 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 200 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.605A pdb=" N ILE B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 295 removed outlier: 3.709A pdb=" N ALA B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 325 removed outlier: 3.541A pdb=" N ARG B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.692A pdb=" N GLN B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 370 removed outlier: 3.593A pdb=" N LYS B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 19 through 28 removed outlier: 3.631A pdb=" N THR C 23 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 87 removed outlier: 4.131A pdb=" N TRP C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 106 through 115 removed outlier: 3.593A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 Processing helix chain 'C' and resid 136 through 147 removed outlier: 4.571A pdb=" N ASN C 141 " --> pdb=" O PRO C 137 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 168 through 181 removed outlier: 3.507A pdb=" N ARG C 181 " --> pdb=" O TYR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 210 Processing helix chain 'C' and resid 218 through 234 Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 271 through 295 removed outlier: 3.732A pdb=" N LEU C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 290 " --> pdb=" O LYS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 325 removed outlier: 3.636A pdb=" N TYR C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN C 307 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 345 removed outlier: 3.706A pdb=" N GLN C 335 " --> pdb=" O THR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 370 removed outlier: 3.520A pdb=" N ALA C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 28 removed outlier: 5.747A pdb=" N ARG D 21 " --> pdb=" O ILE D 17 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 87 removed outlier: 3.798A pdb=" N GLY D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 117 through 127 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 149 through 159 Processing helix chain 'D' and resid 168 through 181 Processing helix chain 'D' and resid 188 through 210 removed outlier: 3.516A pdb=" N ILE D 192 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 200 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 233 Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 261 through 268 removed outlier: 3.686A pdb=" N ILE D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 295 removed outlier: 3.723A pdb=" N ALA D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 302 through 325 removed outlier: 3.971A pdb=" N GLN D 319 " --> pdb=" O GLY D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 345 Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'D' and resid 356 through 370 Processing helix chain 'D' and resid 378 through 383 removed outlier: 3.842A pdb=" N LYS D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.516A pdb=" N PHE A 99 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR A 161 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE A 96 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 163 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU A 98 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.516A pdb=" N PHE A 99 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N CYS A 34 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU A 97 " --> pdb=" O CYS A 34 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY A 36 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE A 99 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 163 removed outlier: 8.477A pdb=" N THR B 161 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE B 96 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE B 163 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 98 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER B 51 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU B 97 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N PHE B 53 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE B 99 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN B 55 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 44 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 160 through 164 removed outlier: 7.741A pdb=" N THR C 161 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE C 96 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 163 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU C 98 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 95 " --> pdb=" O CYS C 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 97 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 35 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AA6, first strand: chain 'D' and resid 160 through 164 removed outlier: 8.436A pdb=" N THR D 161 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE D 96 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE D 163 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU D 98 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER D 51 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU D 97 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE D 53 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE D 99 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN D 55 " --> pdb=" O PHE D 99 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1899 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: 1.55 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3954 1.34 - 1.46: 2411 1.46 - 1.58: 5735 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 12148 Sorted by residual: bond pdb=" CA LEU C 40 " pdb=" CB LEU C 40 " ideal model delta sigma weight residual 1.524 1.573 -0.049 1.51e-02 4.39e+03 1.05e+01 bond pdb=" N HIS C 105 " pdb=" CA HIS C 105 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.69e+00 bond pdb=" N ILE C 163 " pdb=" CA ILE C 163 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.72e+00 bond pdb=" N TYR C 164 " pdb=" CA TYR C 164 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.22e-02 6.72e+03 6.72e+00 bond pdb=" N ASN C 101 " pdb=" CA ASN C 101 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.27e-02 6.20e+03 6.55e+00 ... (remaining 12143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 16325 2.80 - 5.60: 90 5.60 - 8.41: 4 8.41 - 11.21: 1 11.21 - 14.01: 2 Bond angle restraints: 16422 Sorted by residual: angle pdb=" C ILE D 17 " pdb=" N GLN D 18 " pdb=" CA GLN D 18 " ideal model delta sigma weight residual 122.15 134.63 -12.48 2.83e+00 1.25e-01 1.95e+01 angle pdb=" CA GLY C 165 " pdb=" C GLY C 165 " pdb=" O GLY C 165 " ideal model delta sigma weight residual 121.41 117.88 3.53 8.80e-01 1.29e+00 1.61e+01 angle pdb=" CA LEU C 40 " pdb=" CB LEU C 40 " pdb=" CG LEU C 40 " ideal model delta sigma weight residual 116.30 130.31 -14.01 3.50e+00 8.16e-02 1.60e+01 angle pdb=" CA PHE C 99 " pdb=" CB PHE C 99 " pdb=" CG PHE C 99 " ideal model delta sigma weight residual 113.80 117.80 -4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" N LEU C 98 " pdb=" CA LEU C 98 " pdb=" C LEU C 98 " ideal model delta sigma weight residual 109.63 103.70 5.93 1.49e+00 4.50e-01 1.58e+01 ... (remaining 16417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6075 17.91 - 35.82: 904 35.82 - 53.73: 245 53.73 - 71.64: 50 71.64 - 89.56: 20 Dihedral angle restraints: 7294 sinusoidal: 2979 harmonic: 4315 Sorted by residual: dihedral pdb=" CA ILE B 17 " pdb=" C ILE B 17 " pdb=" N GLN B 18 " pdb=" CA GLN B 18 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ILE D 17 " pdb=" C ILE D 17 " pdb=" N GLN D 18 " pdb=" CA GLN D 18 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ARG C 21 " pdb=" C ARG C 21 " pdb=" N LEU C 22 " pdb=" CA LEU C 22 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 7291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1208 0.034 - 0.069: 465 0.069 - 0.103: 92 0.103 - 0.137: 28 0.137 - 0.172: 7 Chirality restraints: 1800 Sorted by residual: chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CG LEU C 97 " pdb=" CB LEU C 97 " pdb=" CD1 LEU C 97 " pdb=" CD2 LEU C 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA LEU C 98 " pdb=" N LEU C 98 " pdb=" C LEU C 98 " pdb=" CB LEU C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 1797 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 100 " -0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C THR C 100 " 0.082 2.00e-02 2.50e+03 pdb=" O THR C 100 " -0.030 2.00e-02 2.50e+03 pdb=" N ASN C 101 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 103 " 0.356 9.50e-02 1.11e+02 1.59e-01 1.56e+01 pdb=" NE ARG C 103 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 103 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 103 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 103 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 96 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C PHE C 96 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE C 96 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 97 " 0.011 2.00e-02 2.50e+03 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1009 2.74 - 3.28: 11504 3.28 - 3.82: 19795 3.82 - 4.36: 23441 4.36 - 4.90: 40896 Nonbonded interactions: 96645 Sorted by model distance: nonbonded pdb=" OH TYR A 177 " pdb=" OE2 GLU A 229 " model vdw 2.200 3.040 nonbonded pdb=" O PHE B 37 " pdb=" OG1 THR B 214 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR B 177 " pdb=" OE2 GLU B 229 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR D 177 " pdb=" OE2 GLU D 229 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR C 177 " pdb=" OE2 GLU C 229 " model vdw 2.236 3.040 ... (remaining 96640 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 41 or resid 63 through 383)) selection = (chain 'B' and (resid 10 through 41 or resid 63 through 383)) selection = (chain 'C' and (resid 10 through 41 or resid 63 through 383)) selection = (chain 'D' and (resid 10 through 41 or resid 63 through 383)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.260 Find NCS groups from input model: 0.180 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.003 0.049 12148 Z= 0.172 Angle : 0.551 14.011 16422 Z= 0.314 Chirality : 0.039 0.172 1800 Planarity : 0.005 0.159 2112 Dihedral : 18.461 89.555 4506 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 0.68 % Allowed : 23.33 % Favored : 75.99 % 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 (0.23), residues: 1453 helix: 0.46 (0.18), residues: 929 sheet: -0.18 (0.66), residues: 83 loop : -1.72 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 328 TYR 0.013 0.001 TYR B 261 PHE 0.016 0.001 PHE A 325 TRP 0.009 0.001 TRP C 12 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00335 (12148) covalent geometry : angle 0.55102 (16422) hydrogen bonds : bond 0.18870 ( 640) hydrogen bonds : angle 5.97016 ( 1899) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7468 (pm20) cc_final: 0.7260 (pm20) REVERT: B 17 ILE cc_start: 0.7147 (mp) cc_final: 0.6926 (mt) REVERT: C 21 ARG cc_start: 0.7088 (ptm160) cc_final: 0.6883 (ptm160) REVERT: C 162 TYR cc_start: 0.8156 (t80) cc_final: 0.7847 (t80) REVERT: C 257 ASP cc_start: 0.8127 (t70) cc_final: 0.7847 (t0) REVERT: D 352 ASN cc_start: 0.8174 (m110) cc_final: 0.7882 (m110) outliers start: 9 outliers final: 3 residues processed: 99 average time/residue: 0.1177 time to fit residues: 16.2638 Evaluate side-chains 95 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 103 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN D 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.207134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126864 restraints weight = 12093.246| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.36 r_work: 0.3032 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12148 Z= 0.142 Angle : 0.490 12.675 16422 Z= 0.258 Chirality : 0.038 0.149 1800 Planarity : 0.003 0.040 2112 Dihedral : 4.486 53.217 1611 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.66 % Allowed : 22.04 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.13 (0.23), residues: 1453 helix: 0.93 (0.18), residues: 943 sheet: -0.33 (0.65), residues: 83 loop : -1.68 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.013 0.001 TYR B 261 PHE 0.014 0.001 PHE C 241 TRP 0.005 0.001 TRP C 74 HIS 0.003 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00340 (12148) covalent geometry : angle 0.49005 (16422) hydrogen bonds : bond 0.04492 ( 640) hydrogen bonds : angle 3.79970 ( 1899) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 81 MET cc_start: 0.7458 (tpt) cc_final: 0.6741 (tmm) REVERT: A 284 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8503 (mm-30) REVERT: B 217 ARG cc_start: 0.7461 (mtt-85) cc_final: 0.6898 (mtp-110) REVERT: C 257 ASP cc_start: 0.8358 (t70) cc_final: 0.8131 (t0) outliers start: 35 outliers final: 23 residues processed: 121 average time/residue: 0.1043 time to fit residues: 18.0738 Evaluate side-chains 108 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 0.0050 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.204966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131497 restraints weight = 12255.415| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.17 r_work: 0.3076 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12148 Z= 0.128 Angle : 0.465 12.677 16422 Z= 0.244 Chirality : 0.037 0.143 1800 Planarity : 0.003 0.040 2112 Dihedral : 4.196 55.490 1607 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.12 % Allowed : 21.66 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.23), residues: 1453 helix: 1.18 (0.18), residues: 947 sheet: -0.14 (0.63), residues: 88 loop : -1.75 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.012 0.001 TYR B 261 PHE 0.012 0.001 PHE A 325 TRP 0.005 0.001 TRP C 74 HIS 0.002 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00305 (12148) covalent geometry : angle 0.46527 (16422) hydrogen bonds : bond 0.04069 ( 640) hydrogen bonds : angle 3.57301 ( 1899) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7511 (tpt) cc_final: 0.6686 (tmm) REVERT: A 193 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8028 (mmp) REVERT: A 217 ARG cc_start: 0.8570 (mtp85) cc_final: 0.8214 (mtp85) REVERT: B 129 LEU cc_start: 0.1770 (OUTLIER) cc_final: 0.1385 (mp) REVERT: B 217 ARG cc_start: 0.7392 (mtt-85) cc_final: 0.6784 (mtp-110) REVERT: B 247 GLU cc_start: 0.8449 (pt0) cc_final: 0.8134 (pm20) REVERT: C 174 ARG cc_start: 0.7407 (ttm170) cc_final: 0.7187 (ttt180) REVERT: C 247 GLU cc_start: 0.7890 (pm20) cc_final: 0.7524 (pm20) REVERT: C 257 ASP cc_start: 0.8281 (t70) cc_final: 0.8066 (t0) REVERT: D 351 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8464 (mm-30) outliers start: 41 outliers final: 24 residues processed: 128 average time/residue: 0.1141 time to fit residues: 20.7940 Evaluate side-chains 120 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain C residue 12 TRP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS C 243 ASN ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.206072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131891 restraints weight = 12156.881| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.42 r_work: 0.3042 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12148 Z= 0.132 Angle : 0.466 13.268 16422 Z= 0.242 Chirality : 0.037 0.144 1800 Planarity : 0.003 0.040 2112 Dihedral : 4.168 56.298 1607 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.65 % Allowed : 21.43 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.54 (0.23), residues: 1453 helix: 1.30 (0.18), residues: 946 sheet: -0.00 (0.63), residues: 88 loop : -1.73 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.013 0.001 TYR B 261 PHE 0.011 0.001 PHE A 325 TRP 0.005 0.001 TRP C 74 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00316 (12148) covalent geometry : angle 0.46612 (16422) hydrogen bonds : bond 0.03968 ( 640) hydrogen bonds : angle 3.50349 ( 1899) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7078 (mm-30) REVERT: A 193 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8081 (mmp) REVERT: A 247 GLU cc_start: 0.7562 (pm20) cc_final: 0.7165 (pm20) REVERT: A 284 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8380 (mm-30) REVERT: B 129 LEU cc_start: 0.2052 (OUTLIER) cc_final: 0.1685 (mp) REVERT: B 217 ARG cc_start: 0.7393 (mtt-85) cc_final: 0.6773 (mtp-110) REVERT: B 247 GLU cc_start: 0.8471 (pt0) cc_final: 0.8149 (pm20) REVERT: C 40 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7330 (pp) REVERT: C 247 GLU cc_start: 0.7882 (pm20) cc_final: 0.7500 (pm20) REVERT: D 351 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8471 (mm-30) outliers start: 48 outliers final: 32 residues processed: 139 average time/residue: 0.1060 time to fit residues: 20.9914 Evaluate side-chains 127 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain C residue 12 TRP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 113 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 81 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: B 234 GLN C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.204396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128777 restraints weight = 12236.229| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.58 r_work: 0.3005 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12148 Z= 0.139 Angle : 0.471 12.714 16422 Z= 0.246 Chirality : 0.038 0.225 1800 Planarity : 0.003 0.040 2112 Dihedral : 4.166 56.679 1607 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.34 % Allowed : 22.04 % Favored : 74.62 % 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: 0.56 (0.23), residues: 1453 helix: 1.28 (0.18), residues: 956 sheet: 0.06 (0.66), residues: 82 loop : -1.71 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.014 0.001 TYR B 261 PHE 0.013 0.001 PHE A 325 TRP 0.005 0.001 TRP C 74 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00336 (12148) covalent geometry : angle 0.47141 (16422) hydrogen bonds : bond 0.03997 ( 640) hydrogen bonds : angle 3.49361 ( 1899) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7059 (mm-30) REVERT: A 81 MET cc_start: 0.7127 (tpp) cc_final: 0.6348 (tpt) REVERT: A 193 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8070 (mmp) REVERT: A 284 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8390 (mm-30) REVERT: B 129 LEU cc_start: 0.1901 (OUTLIER) cc_final: 0.1535 (mp) REVERT: B 217 ARG cc_start: 0.7349 (mtt-85) cc_final: 0.6853 (mtp-110) REVERT: B 234 GLN cc_start: 0.5980 (OUTLIER) cc_final: 0.4980 (tt0) REVERT: B 247 GLU cc_start: 0.8242 (pt0) cc_final: 0.8032 (pm20) REVERT: C 40 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7195 (pp) REVERT: C 243 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7542 (m110) REVERT: C 247 GLU cc_start: 0.7890 (pm20) cc_final: 0.7526 (pm20) REVERT: D 351 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8394 (mm-30) outliers start: 44 outliers final: 35 residues processed: 133 average time/residue: 0.0974 time to fit residues: 18.9935 Evaluate side-chains 132 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain C residue 12 TRP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 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 322 HIS C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.204184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129771 restraints weight = 12217.139| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.25 r_work: 0.3024 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12148 Z= 0.138 Angle : 0.466 12.681 16422 Z= 0.243 Chirality : 0.038 0.179 1800 Planarity : 0.003 0.040 2112 Dihedral : 4.153 57.050 1607 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.88 % Allowed : 21.81 % Favored : 74.32 % 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: 0.63 (0.23), residues: 1453 helix: 1.34 (0.18), residues: 954 sheet: 0.16 (0.66), residues: 82 loop : -1.70 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.014 0.001 TYR B 261 PHE 0.013 0.001 PHE C 325 TRP 0.005 0.001 TRP C 74 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00334 (12148) covalent geometry : angle 0.46583 (16422) hydrogen bonds : bond 0.03967 ( 640) hydrogen bonds : angle 3.45694 ( 1899) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 92 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6956 (mm-30) REVERT: A 81 MET cc_start: 0.7145 (tpp) cc_final: 0.6329 (tpt) REVERT: A 193 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7997 (mmp) REVERT: A 284 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8303 (mm-30) REVERT: B 120 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.5063 (tp30) REVERT: B 129 LEU cc_start: 0.2148 (OUTLIER) cc_final: 0.1795 (mp) REVERT: B 164 TYR cc_start: 0.5654 (OUTLIER) cc_final: 0.5089 (m-10) REVERT: B 217 ARG cc_start: 0.7316 (mtt-85) cc_final: 0.6688 (mtp-110) REVERT: B 247 GLU cc_start: 0.8419 (pt0) cc_final: 0.8108 (pm20) REVERT: C 40 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7193 (pp) REVERT: C 88 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: C 247 GLU cc_start: 0.7830 (pm20) cc_final: 0.7410 (pm20) REVERT: D 351 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8417 (mm-30) outliers start: 51 outliers final: 39 residues processed: 136 average time/residue: 0.1055 time to fit residues: 20.9570 Evaluate side-chains 134 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 89 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain C residue 12 TRP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.202843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127110 restraints weight = 12154.895| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.54 r_work: 0.2990 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12148 Z= 0.176 Angle : 0.498 13.026 16422 Z= 0.259 Chirality : 0.039 0.154 1800 Planarity : 0.003 0.040 2112 Dihedral : 4.257 57.329 1607 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.80 % Allowed : 21.88 % Favored : 74.32 % 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: 0.51 (0.23), residues: 1453 helix: 1.21 (0.18), residues: 958 sheet: 0.33 (0.67), residues: 83 loop : -1.74 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.016 0.001 TYR B 261 PHE 0.015 0.001 PHE C 325 TRP 0.005 0.001 TRP C 12 HIS 0.003 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00433 (12148) covalent geometry : angle 0.49781 (16422) hydrogen bonds : bond 0.04410 ( 640) hydrogen bonds : angle 3.58449 ( 1899) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 94 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 81 MET cc_start: 0.7169 (tpp) cc_final: 0.6321 (tpt) REVERT: A 193 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8194 (mmp) REVERT: A 247 GLU cc_start: 0.7506 (pm20) cc_final: 0.7136 (pm20) REVERT: B 120 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5055 (tp30) REVERT: B 129 LEU cc_start: 0.2305 (OUTLIER) cc_final: 0.1973 (mp) REVERT: B 164 TYR cc_start: 0.5700 (OUTLIER) cc_final: 0.5056 (m-10) REVERT: B 217 ARG cc_start: 0.7474 (mtt-85) cc_final: 0.6964 (mtp-110) REVERT: B 234 GLN cc_start: 0.6217 (OUTLIER) cc_final: 0.5208 (tt0) REVERT: B 247 GLU cc_start: 0.8414 (pt0) cc_final: 0.8078 (pm20) REVERT: C 40 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7244 (pp) REVERT: C 88 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5703 (mp0) REVERT: C 217 ARG cc_start: 0.8726 (mtp85) cc_final: 0.8411 (mtp180) REVERT: C 247 GLU cc_start: 0.7896 (pm20) cc_final: 0.7486 (pm20) REVERT: D 247 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: D 351 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8484 (mm-30) outliers start: 50 outliers final: 40 residues processed: 137 average time/residue: 0.1156 time to fit residues: 22.9982 Evaluate side-chains 138 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain C residue 12 TRP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 20 optimal weight: 0.1980 chunk 84 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.206940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127197 restraints weight = 12144.822| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.25 r_work: 0.3078 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12148 Z= 0.105 Angle : 0.445 13.062 16422 Z= 0.234 Chirality : 0.037 0.156 1800 Planarity : 0.003 0.040 2112 Dihedral : 4.070 57.293 1607 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.74 % Allowed : 23.10 % Favored : 74.16 % 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 (0.23), residues: 1453 helix: 1.53 (0.18), residues: 948 sheet: 0.33 (0.67), residues: 82 loop : -1.72 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.011 0.001 TYR B 261 PHE 0.012 0.001 PHE A 325 TRP 0.006 0.001 TRP C 74 HIS 0.002 0.000 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00244 (12148) covalent geometry : angle 0.44466 (16422) hydrogen bonds : bond 0.03514 ( 640) hydrogen bonds : angle 3.36717 ( 1899) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7001 (mm-30) REVERT: A 81 MET cc_start: 0.7163 (tpp) cc_final: 0.6282 (tpt) REVERT: A 193 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7857 (mmp) REVERT: A 247 GLU cc_start: 0.7572 (pm20) cc_final: 0.7299 (pm20) REVERT: A 284 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8282 (mm-30) REVERT: B 129 LEU cc_start: 0.2174 (OUTLIER) cc_final: 0.1762 (mp) REVERT: B 247 GLU cc_start: 0.8336 (pt0) cc_final: 0.8014 (pm20) REVERT: C 40 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7154 (pp) REVERT: C 88 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5779 (mp0) REVERT: C 193 MET cc_start: 0.7653 (mmp) cc_final: 0.7435 (mmp) REVERT: C 247 GLU cc_start: 0.7861 (pm20) cc_final: 0.7497 (pm20) REVERT: D 247 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7717 (mp0) outliers start: 36 outliers final: 28 residues processed: 127 average time/residue: 0.1073 time to fit residues: 20.1811 Evaluate side-chains 127 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain C residue 12 TRP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 132 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: A 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.204294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123681 restraints weight = 12121.754| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.27 r_work: 0.3040 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12148 Z= 0.134 Angle : 0.464 12.868 16422 Z= 0.243 Chirality : 0.038 0.152 1800 Planarity : 0.003 0.040 2112 Dihedral : 3.819 26.963 1603 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.04 % Allowed : 22.87 % Favored : 74.09 % 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: 0.77 (0.23), residues: 1453 helix: 1.46 (0.18), residues: 956 sheet: 0.42 (0.65), residues: 83 loop : -1.76 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.014 0.001 TYR B 261 PHE 0.014 0.001 PHE C 325 TRP 0.005 0.001 TRP C 12 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00323 (12148) covalent geometry : angle 0.46416 (16422) hydrogen bonds : bond 0.03896 ( 640) hydrogen bonds : angle 3.41177 ( 1899) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6974 (mm-30) REVERT: A 81 MET cc_start: 0.7161 (tpp) cc_final: 0.6270 (tpt) REVERT: A 93 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6780 (p0) REVERT: A 193 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7992 (mmp) REVERT: A 284 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 129 LEU cc_start: 0.2375 (OUTLIER) cc_final: 0.2048 (mp) REVERT: B 217 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6785 (mtp-110) REVERT: B 247 GLU cc_start: 0.8340 (pt0) cc_final: 0.8035 (pm20) REVERT: C 40 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7178 (pp) REVERT: C 88 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.5865 (mp0) REVERT: C 247 GLU cc_start: 0.7839 (pm20) cc_final: 0.7409 (pm20) REVERT: D 247 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7673 (mp0) outliers start: 40 outliers final: 33 residues processed: 127 average time/residue: 0.1041 time to fit residues: 19.7477 Evaluate side-chains 129 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain C residue 12 TRP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 45 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.204176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130804 restraints weight = 12236.786| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.42 r_work: 0.3027 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12148 Z= 0.136 Angle : 0.468 12.792 16422 Z= 0.245 Chirality : 0.038 0.151 1800 Planarity : 0.003 0.039 2112 Dihedral : 3.827 26.866 1603 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.27 % Allowed : 22.72 % Favored : 74.01 % 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: 0.78 (0.23), residues: 1453 helix: 1.47 (0.18), residues: 956 sheet: 0.44 (0.65), residues: 83 loop : -1.76 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.014 0.001 TYR B 261 PHE 0.015 0.001 PHE A 96 TRP 0.005 0.001 TRP C 12 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00330 (12148) covalent geometry : angle 0.46838 (16422) hydrogen bonds : bond 0.03894 ( 640) hydrogen bonds : angle 3.41388 ( 1899) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 93 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7007 (mm-30) REVERT: A 81 MET cc_start: 0.7165 (tpp) cc_final: 0.6273 (tpt) REVERT: A 93 ASN cc_start: 0.7051 (OUTLIER) cc_final: 0.6821 (p0) REVERT: A 193 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.8012 (mmp) REVERT: A 284 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8346 (mm-30) REVERT: B 129 LEU cc_start: 0.2373 (OUTLIER) cc_final: 0.2051 (mp) REVERT: B 164 TYR cc_start: 0.5568 (OUTLIER) cc_final: 0.5009 (m-10) REVERT: B 217 ARG cc_start: 0.7324 (mtt-85) cc_final: 0.6837 (mtp-110) REVERT: B 247 GLU cc_start: 0.8344 (pt0) cc_final: 0.8048 (pm20) REVERT: C 40 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7162 (pp) REVERT: C 88 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5946 (mp0) REVERT: C 247 GLU cc_start: 0.7859 (pm20) cc_final: 0.7449 (pm20) REVERT: D 247 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7668 (mp0) outliers start: 43 outliers final: 35 residues processed: 129 average time/residue: 0.1038 time to fit residues: 19.9516 Evaluate side-chains 135 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain C residue 12 TRP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 85 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.204346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129227 restraints weight = 12211.952| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.38 r_work: 0.2997 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 12148 Z= 0.140 Angle : 0.758 59.198 16422 Z= 0.431 Chirality : 0.038 0.294 1800 Planarity : 0.003 0.052 2112 Dihedral : 3.932 34.932 1603 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.50 % Allowed : 22.42 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.79 (0.23), residues: 1453 helix: 1.48 (0.18), residues: 956 sheet: 0.49 (0.65), residues: 83 loop : -1.77 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.013 0.001 TYR B 261 PHE 0.014 0.001 PHE C 325 TRP 0.005 0.001 TRP C 74 HIS 0.003 0.000 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00329 (12148) covalent geometry : angle 0.75773 (16422) hydrogen bonds : bond 0.03826 ( 640) hydrogen bonds : angle 3.42147 ( 1899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3444.43 seconds wall clock time: 59 minutes 40.38 seconds (3580.38 seconds total)