Starting phenix.real_space_refine on Wed Mar 4 20:31:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wum_21916/03_2026/6wum_21916.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wum_21916/03_2026/6wum_21916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wum_21916/03_2026/6wum_21916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wum_21916/03_2026/6wum_21916.map" model { file = "/net/cci-nas-00/data/ceres_data/6wum_21916/03_2026/6wum_21916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wum_21916/03_2026/6wum_21916.cif" } resolution = 3.6 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= 0.024 sd= 0.131 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 30 5.16 5 C 10420 2.51 5 N 2924 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16414 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2284 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 22, 'TRANS': 272} Chain breaks: 2 Chain: "b" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2614 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain breaks: 3 Chain: "a" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3309 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "A" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2284 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 22, 'TRANS': 272} Chain breaks: 2 Chain: "C" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2614 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain breaks: 3 Chain: "B" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3309 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Time building chain proxies: 3.53, per 1000 atoms: 0.22 Number of scatterers: 16414 At special positions: 0 Unit cell: (156.88, 121.9, 115.54, 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 30 16.00 O 3040 8.00 N 2924 7.00 C 10420 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: 1.46 Conformation dependent library (CDL) restraints added in 771.7 milliseconds 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 26 sheets defined 37.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.782A pdb=" N ARG E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 82 removed outlier: 4.662A pdb=" N TRP E 75 " --> pdb=" O GLY E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 150 through 174 removed outlier: 3.840A pdb=" N ALA E 158 " --> pdb=" O GLN E 154 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E 160 " --> pdb=" O TYR E 156 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG E 165 " --> pdb=" O THR E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 178 through 187 Processing helix chain 'E' and resid 193 through 213 removed outlier: 4.135A pdb=" N ALA E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN E 211 " --> pdb=" O ALA E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 255 removed outlier: 3.762A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.907A pdb=" N TYR E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 285 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 300 through 307 removed outlier: 3.699A pdb=" N MET E 304 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 321 Processing helix chain 'b' and resid 18 through 32 removed outlier: 3.766A pdb=" N LEU b 22 " --> pdb=" O ASP b 18 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 47 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 106 through 121 Processing helix chain 'b' and resid 125 through 130 removed outlier: 3.731A pdb=" N LEU b 129 " --> pdb=" O PRO b 125 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 148 Processing helix chain 'b' and resid 153 through 156 removed outlier: 3.830A pdb=" N TRP b 156 " --> pdb=" O PRO b 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 153 through 156' Processing helix chain 'b' and resid 157 through 171 removed outlier: 3.593A pdb=" N ALA b 161 " --> pdb=" O THR b 157 " (cutoff:3.500A) Processing helix chain 'b' and resid 239 through 254 removed outlier: 3.674A pdb=" N VAL b 249 " --> pdb=" O ALA b 245 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL b 252 " --> pdb=" O GLU b 248 " (cutoff:3.500A) Processing helix chain 'b' and resid 255 through 257 No H-bonds generated for 'chain 'b' and resid 255 through 257' Processing helix chain 'b' and resid 268 through 284 removed outlier: 3.715A pdb=" N LEU b 274 " --> pdb=" O GLU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 299 removed outlier: 3.545A pdb=" N ILE b 295 " --> pdb=" O TRP b 291 " (cutoff:3.500A) Processing helix chain 'b' and resid 300 through 315 removed outlier: 3.765A pdb=" N CYS b 304 " --> pdb=" O TYR b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 316 through 319 Processing helix chain 'b' and resid 328 through 333 removed outlier: 4.432A pdb=" N ALA b 333 " --> pdb=" O ALA b 329 " (cutoff:3.500A) Processing helix chain 'b' and resid 338 through 352 Processing helix chain 'b' and resid 356 through 378 removed outlier: 4.738A pdb=" N TRP b 360 " --> pdb=" O LEU b 356 " (cutoff:3.500A) Processing helix chain 'b' and resid 386 through 407 removed outlier: 3.696A pdb=" N TYR b 407 " --> pdb=" O GLY b 403 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 70 removed outlier: 3.664A pdb=" N LEU a 62 " --> pdb=" O ARG a 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE a 65 " --> pdb=" O LEU a 61 " (cutoff:3.500A) Proline residue: a 68 - end of helix Processing helix chain 'a' and resid 86 through 96 Processing helix chain 'a' and resid 211 through 214 removed outlier: 3.704A pdb=" N SER a 214 " --> pdb=" O PRO a 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 211 through 214' Processing helix chain 'a' and resid 257 through 261 Processing helix chain 'a' and resid 447 through 462 removed outlier: 3.540A pdb=" N THR a 462 " --> pdb=" O VAL a 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.782A pdb=" N ARG A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.663A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.841A pdb=" N ALA A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 193 through 213 removed outlier: 4.135A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.762A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.907A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 307 removed outlier: 3.699A pdb=" N MET A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'C' and resid 18 through 32 removed outlier: 3.767A pdb=" N LEU C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 106 through 121 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.731A pdb=" N LEU C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.831A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 171 removed outlier: 3.594A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.674A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 268 through 284 removed outlier: 3.714A pdb=" N LEU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.546A pdb=" N ILE C 295 " --> pdb=" O TRP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.766A pdb=" N CYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 328 through 333 removed outlier: 4.432A pdb=" N ALA C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 356 through 378 removed outlier: 4.738A pdb=" N TRP C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 407 removed outlier: 3.695A pdb=" N TYR C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.664A pdb=" N LEU B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 86 through 96 Processing helix chain 'B' and resid 211 through 214 removed outlier: 3.704A pdb=" N SER B 214 " --> pdb=" O PRO B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.539A pdb=" N THR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 30 through 31 removed outlier: 5.668A pdb=" N ARG E 30 " --> pdb=" O LEU a 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 87 through 89 removed outlier: 6.484A pdb=" N LEU E 52 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'b' and resid 419 through 421 removed outlier: 5.861A pdb=" N THR a 48 " --> pdb=" O ILE a 128 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE a 130 " --> pdb=" O THR a 48 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU a 50 " --> pdb=" O ILE a 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 139 through 142 removed outlier: 4.324A pdb=" N TYR a 183 " --> pdb=" O ARG a 205 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG a 205 " --> pdb=" O TYR a 183 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER a 242 " --> pdb=" O ALA a 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE a 291 " --> pdb=" O ARG a 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 198 through 210 removed outlier: 3.689A pdb=" N GLU a 217 " --> pdb=" O THR a 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 290 through 297 Processing sheet with id=AA8, first strand: chain 'a' and resid 311 through 316 removed outlier: 4.135A pdb=" N LEU a 339 " --> pdb=" O ALA a 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 319 through 320 Processing sheet with id=AB1, first strand: chain 'a' and resid 356 through 357 Processing sheet with id=AB2, first strand: chain 'a' and resid 396 through 397 removed outlier: 3.863A pdb=" N ARG a 426 " --> pdb=" O ALA a 397 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 400 through 401 removed outlier: 4.053A pdb=" N VAL a 401 " --> pdb=" O ALA a 422 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 405 through 406 Processing sheet with id=AB5, first strand: chain 'A' and resid 30 through 31 removed outlier: 5.703A pdb=" N ARG A 30 " --> pdb=" O LEU B 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.484A pdb=" N LEU A 52 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB8, first strand: chain 'C' and resid 417 through 421 removed outlier: 3.774A pdb=" N GLN C 418 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR B 48 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE B 130 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU B 50 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 139 through 142 removed outlier: 4.324A pdb=" N TYR B 183 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 205 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 242 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 291 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 198 through 210 removed outlier: 3.689A pdb=" N GLU B 217 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 290 through 297 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 316 removed outlier: 4.136A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AC6, first strand: chain 'B' and resid 396 through 397 removed outlier: 3.864A pdb=" N ARG B 426 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 400 through 401 removed outlier: 4.054A pdb=" N VAL B 401 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 405 through 406 631 hydrogen bonds defined for protein. 1761 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: 2.86 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3799 1.33 - 1.45: 3522 1.45 - 1.57: 9421 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 16792 Sorted by residual: bond pdb=" C ASP A 148 " pdb=" N LEU A 149 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.48e-02 4.57e+03 4.43e+00 bond pdb=" C SER A 257 " pdb=" N GLU A 258 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.41e-02 5.03e+03 4.27e+00 bond pdb=" C ASP E 148 " pdb=" N LEU E 149 " ideal model delta sigma weight residual 1.331 1.300 0.030 1.48e-02 4.57e+03 4.24e+00 bond pdb=" C SER E 257 " pdb=" N GLU E 258 " ideal model delta sigma weight residual 1.332 1.305 0.028 1.41e-02 5.03e+03 3.87e+00 bond pdb=" C ALA C 2 " pdb=" N VAL C 3 " ideal model delta sigma weight residual 1.335 1.312 0.023 1.27e-02 6.20e+03 3.33e+00 ... (remaining 16787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 21285 1.70 - 3.40: 1326 3.40 - 5.10: 193 5.10 - 6.80: 38 6.80 - 8.50: 6 Bond angle restraints: 22848 Sorted by residual: angle pdb=" N LEU b 284 " pdb=" CA LEU b 284 " pdb=" C LEU b 284 " ideal model delta sigma weight residual 109.81 118.31 -8.50 2.21e+00 2.05e-01 1.48e+01 angle pdb=" N LEU C 284 " pdb=" CA LEU C 284 " pdb=" C LEU C 284 " ideal model delta sigma weight residual 109.81 118.29 -8.48 2.21e+00 2.05e-01 1.47e+01 angle pdb=" N ASN E 35 " pdb=" CA ASN E 35 " pdb=" C ASN E 35 " ideal model delta sigma weight residual 110.68 115.95 -5.27 1.39e+00 5.18e-01 1.44e+01 angle pdb=" N ASN A 35 " pdb=" CA ASN A 35 " pdb=" C ASN A 35 " ideal model delta sigma weight residual 110.68 115.92 -5.24 1.39e+00 5.18e-01 1.42e+01 angle pdb=" N ALA b 11 " pdb=" CA ALA b 11 " pdb=" C ALA b 11 " ideal model delta sigma weight residual 110.80 118.32 -7.52 2.13e+00 2.20e-01 1.25e+01 ... (remaining 22843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9060 17.97 - 35.93: 769 35.93 - 53.90: 105 53.90 - 71.87: 20 71.87 - 89.83: 18 Dihedral angle restraints: 9972 sinusoidal: 3814 harmonic: 6158 Sorted by residual: dihedral pdb=" CA LEU E 101 " pdb=" C LEU E 101 " pdb=" N PRO E 102 " pdb=" CA PRO E 102 " ideal model delta harmonic sigma weight residual -180.00 -144.60 -35.40 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta harmonic sigma weight residual -180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA TYR B 183 " pdb=" C TYR B 183 " pdb=" N ASN B 184 " pdb=" CA ASN B 184 " ideal model delta harmonic sigma weight residual 180.00 148.27 31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 9969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2238 0.074 - 0.148: 321 0.148 - 0.222: 11 0.222 - 0.295: 0 0.295 - 0.369: 2 Chirality restraints: 2572 Sorted by residual: chirality pdb=" CA GLU A 258 " pdb=" N GLU A 258 " pdb=" C GLU A 258 " pdb=" CB GLU A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA GLU E 258 " pdb=" N GLU E 258 " pdb=" C GLU E 258 " pdb=" CB GLU E 258 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA LEU b 52 " pdb=" N LEU b 52 " pdb=" C LEU b 52 " pdb=" CB LEU b 52 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2569 not shown) Planarity restraints: 2966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 258 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C GLU E 258 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU E 258 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 259 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 257 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C SER A 257 " 0.033 2.00e-02 2.50e+03 pdb=" O SER A 257 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A 258 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 383 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO B 384 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " 0.026 5.00e-02 4.00e+02 ... (remaining 2963 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 417 2.65 - 3.21: 15778 3.21 - 3.77: 23641 3.77 - 4.34: 32222 4.34 - 4.90: 54112 Nonbonded interactions: 126170 Sorted by model distance: nonbonded pdb=" O HIS b 51 " pdb=" OG1 THR b 54 " model vdw 2.086 3.040 nonbonded pdb=" O HIS C 51 " pdb=" OG1 THR C 54 " model vdw 2.087 3.040 nonbonded pdb=" OG SER A 96 " pdb=" O THR A 98 " model vdw 2.159 3.040 nonbonded pdb=" OG SER E 96 " pdb=" O THR E 98 " model vdw 2.160 3.040 nonbonded pdb=" NE1 TRP b 420 " pdb=" OD1 ASP a 63 " model vdw 2.169 3.120 ... (remaining 126165 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: 0.05 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' } ncs_group { reference = chain 'b' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.700 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.008 0.074 16792 Z= 0.365 Angle : 0.923 8.499 22848 Z= 0.527 Chirality : 0.050 0.369 2572 Planarity : 0.005 0.047 2966 Dihedral : 13.760 89.834 6020 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.45 % Favored : 83.46 % Rotamer: Outliers : 1.01 % Allowed : 7.35 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.30 % 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: -4.27 (0.16), residues: 2128 helix: -1.31 (0.17), residues: 740 sheet: -3.68 (0.21), residues: 442 loop : -3.64 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 332 TYR 0.027 0.002 TYR b 37 PHE 0.028 0.002 PHE a 396 TRP 0.021 0.002 TRP C 361 HIS 0.007 0.002 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00794 (16792) covalent geometry : angle 0.92311 (22848) hydrogen bonds : bond 0.16469 ( 631) hydrogen bonds : angle 7.13029 ( 1761) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 248 ASP cc_start: 0.7418 (t0) cc_final: 0.7190 (t0) REVERT: b 251 ASP cc_start: 0.7662 (m-30) cc_final: 0.7358 (m-30) REVERT: a 419 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7340 (tt0) REVERT: a 445 MET cc_start: 0.8335 (mtp) cc_final: 0.8073 (mtp) REVERT: A 248 ASP cc_start: 0.7447 (t0) cc_final: 0.7212 (t0) REVERT: C 166 MET cc_start: 0.8850 (mmm) cc_final: 0.8511 (mmm) REVERT: B 140 PHE cc_start: 0.8223 (t80) cc_final: 0.7830 (t80) REVERT: B 378 LYS cc_start: 0.8817 (tttt) cc_final: 0.8569 (tttm) REVERT: B 419 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7305 (tt0) REVERT: B 445 MET cc_start: 0.8316 (mtp) cc_final: 0.8055 (mtp) outliers start: 17 outliers final: 3 residues processed: 236 average time/residue: 0.1376 time to fit residues: 47.2511 Evaluate side-chains 174 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 ASN E 178 HIS A 166 ASN A 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106249 restraints weight = 28081.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108730 restraints weight = 19029.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110386 restraints weight = 14964.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111466 restraints weight = 12830.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111798 restraints weight = 11618.216| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16792 Z= 0.270 Angle : 0.815 11.628 22848 Z= 0.414 Chirality : 0.049 0.228 2572 Planarity : 0.006 0.049 2966 Dihedral : 6.666 53.310 2363 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.04 % Favored : 84.87 % Rotamer: Outliers : 2.55 % Allowed : 11.49 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.15 % 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: -3.32 (0.17), residues: 2128 helix: -0.23 (0.19), residues: 744 sheet: -3.27 (0.23), residues: 430 loop : -3.33 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 319 TYR 0.019 0.002 TYR C 37 PHE 0.024 0.002 PHE a 140 TRP 0.017 0.002 TRP C 361 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00637 (16792) covalent geometry : angle 0.81480 (22848) hydrogen bonds : bond 0.04643 ( 631) hydrogen bonds : angle 5.03102 ( 1761) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.8414 (mm) cc_final: 0.7942 (mm) REVERT: E 193 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8592 (p) REVERT: b 247 ARG cc_start: 0.7265 (ptp-110) cc_final: 0.6800 (ptp-110) REVERT: b 251 ASP cc_start: 0.7527 (m-30) cc_final: 0.7161 (m-30) REVERT: a 64 GLN cc_start: 0.7593 (tp40) cc_final: 0.7061 (tp40) REVERT: a 419 GLN cc_start: 0.7420 (tp-100) cc_final: 0.7121 (tt0) REVERT: a 497 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: C 166 MET cc_start: 0.8810 (mmm) cc_final: 0.8604 (mmt) REVERT: B 64 GLN cc_start: 0.7280 (tp40) cc_final: 0.6874 (tp40) REVERT: B 419 GLN cc_start: 0.7577 (tp-100) cc_final: 0.7135 (tt0) REVERT: B 497 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7044 (mt-10) outliers start: 43 outliers final: 32 residues processed: 216 average time/residue: 0.1222 time to fit residues: 39.9600 Evaluate side-chains 203 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 172 HIS Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 243 VAL Chi-restraints excluded: chain a residue 255 SER Chi-restraints excluded: chain a residue 441 GLU Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 505 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 93 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 286 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109769 restraints weight = 28066.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112475 restraints weight = 18337.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114264 restraints weight = 14131.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115412 restraints weight = 11973.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116178 restraints weight = 10768.099| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16792 Z= 0.143 Angle : 0.707 8.650 22848 Z= 0.354 Chirality : 0.045 0.199 2572 Planarity : 0.005 0.047 2966 Dihedral : 6.179 54.683 2363 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.12 % Favored : 87.78 % Rotamer: Outliers : 2.19 % Allowed : 12.03 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.72 % Twisted General : 0.15 % 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: -2.71 (0.18), residues: 2128 helix: 0.41 (0.20), residues: 740 sheet: -2.89 (0.24), residues: 426 loop : -3.11 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 495 TYR 0.010 0.001 TYR b 407 PHE 0.027 0.002 PHE B 140 TRP 0.011 0.001 TRP C 361 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00327 (16792) covalent geometry : angle 0.70660 (22848) hydrogen bonds : bond 0.03723 ( 631) hydrogen bonds : angle 4.61018 ( 1761) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 247 ARG cc_start: 0.7259 (ptp-110) cc_final: 0.7052 (ptp-110) REVERT: a 64 GLN cc_start: 0.7566 (tp40) cc_final: 0.7030 (tp40) REVERT: a 419 GLN cc_start: 0.7348 (tp-100) cc_final: 0.7128 (tt0) REVERT: a 497 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: A 31 ILE cc_start: 0.8835 (mm) cc_final: 0.8104 (mt) REVERT: A 62 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7145 (ttm110) REVERT: C 166 MET cc_start: 0.8797 (mmm) cc_final: 0.8484 (mmm) REVERT: C 247 ARG cc_start: 0.7379 (ptp-110) cc_final: 0.7171 (ptp-110) REVERT: B 64 GLN cc_start: 0.7265 (tp40) cc_final: 0.6836 (tp40) REVERT: B 419 GLN cc_start: 0.7396 (tp-100) cc_final: 0.7145 (tt0) REVERT: B 497 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6932 (mt-10) outliers start: 37 outliers final: 29 residues processed: 218 average time/residue: 0.1146 time to fit residues: 39.1857 Evaluate side-chains 202 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 395 VAL Chi-restraints excluded: chain a residue 441 GLU Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 497 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 38 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107582 restraints weight = 28130.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110135 restraints weight = 18989.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111835 restraints weight = 14913.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112767 restraints weight = 12780.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113564 restraints weight = 11630.816| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16792 Z= 0.216 Angle : 0.743 11.417 22848 Z= 0.372 Chirality : 0.047 0.210 2572 Planarity : 0.005 0.047 2966 Dihedral : 6.227 56.632 2362 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.55 % Favored : 84.35 % Rotamer: Outliers : 3.38 % Allowed : 13.45 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.10 % 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: -2.58 (0.18), residues: 2128 helix: 0.50 (0.20), residues: 742 sheet: -2.70 (0.25), residues: 424 loop : -3.10 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 495 TYR 0.013 0.002 TYR C 37 PHE 0.027 0.002 PHE B 487 TRP 0.015 0.001 TRP C 361 HIS 0.005 0.001 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00513 (16792) covalent geometry : angle 0.74322 (22848) hydrogen bonds : bond 0.03993 ( 631) hydrogen bonds : angle 4.55394 ( 1761) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 62 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7392 (ttm110) REVERT: b 247 ARG cc_start: 0.7272 (ptp-110) cc_final: 0.6701 (ptm160) REVERT: b 251 ASP cc_start: 0.7585 (m-30) cc_final: 0.7179 (m-30) REVERT: a 64 GLN cc_start: 0.7648 (tp40) cc_final: 0.7084 (tp40) REVERT: a 497 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: A 31 ILE cc_start: 0.8841 (mm) cc_final: 0.8425 (mm) REVERT: C 166 MET cc_start: 0.8820 (mmm) cc_final: 0.8476 (mmm) REVERT: C 247 ARG cc_start: 0.7341 (ptp-110) cc_final: 0.7064 (ptp-110) REVERT: B 64 GLN cc_start: 0.7410 (tp40) cc_final: 0.6916 (tp40) REVERT: B 497 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7031 (mt-10) outliers start: 57 outliers final: 43 residues processed: 224 average time/residue: 0.1107 time to fit residues: 38.9208 Evaluate side-chains 217 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 172 HIS Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 243 VAL Chi-restraints excluded: chain a residue 271 THR Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 395 VAL Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 497 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 156 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 163 optimal weight: 0.1980 chunk 196 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 GLN a 419 GLN a 504 GLN C 317 GLN B 419 GLN B 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109822 restraints weight = 28083.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112529 restraints weight = 18478.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114293 restraints weight = 14157.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115269 restraints weight = 11951.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116221 restraints weight = 10755.623| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16792 Z= 0.115 Angle : 0.661 8.474 22848 Z= 0.330 Chirality : 0.043 0.209 2572 Planarity : 0.005 0.045 2966 Dihedral : 5.830 56.510 2362 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.57 % Favored : 89.33 % Rotamer: Outliers : 2.61 % Allowed : 15.05 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.23 (0.19), residues: 2128 helix: 0.79 (0.20), residues: 740 sheet: -2.28 (0.28), residues: 380 loop : -3.02 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 62 TYR 0.009 0.001 TYR b 37 PHE 0.026 0.001 PHE a 487 TRP 0.008 0.001 TRP C 361 HIS 0.004 0.001 HIS a 215 Details of bonding type rmsd covalent geometry : bond 0.00255 (16792) covalent geometry : angle 0.66147 (22848) hydrogen bonds : bond 0.03199 ( 631) hydrogen bonds : angle 4.34849 ( 1761) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 248 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: b 166 MET cc_start: 0.8704 (mmm) cc_final: 0.8289 (mmm) REVERT: b 247 ARG cc_start: 0.7227 (ptp-110) cc_final: 0.6954 (ptp-110) REVERT: a 64 GLN cc_start: 0.7568 (tp40) cc_final: 0.6972 (tp40) REVERT: a 497 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: A 31 ILE cc_start: 0.8864 (mm) cc_final: 0.8345 (mm) REVERT: A 173 TYR cc_start: 0.9026 (m-80) cc_final: 0.8776 (m-80) REVERT: A 248 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: C 166 MET cc_start: 0.8812 (mmm) cc_final: 0.8446 (mmm) REVERT: B 64 GLN cc_start: 0.7375 (tp40) cc_final: 0.6878 (tp40) REVERT: B 497 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6904 (mt-10) outliers start: 44 outliers final: 32 residues processed: 227 average time/residue: 0.1128 time to fit residues: 39.9239 Evaluate side-chains 206 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 497 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 148 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 101 optimal weight: 0.3980 chunk 34 optimal weight: 0.3980 chunk 199 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 GLN E 203 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.134804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111005 restraints weight = 28056.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113700 restraints weight = 18373.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115501 restraints weight = 14055.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116678 restraints weight = 11846.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117375 restraints weight = 10592.837| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16792 Z= 0.110 Angle : 0.640 8.129 22848 Z= 0.320 Chirality : 0.042 0.211 2572 Planarity : 0.005 0.044 2966 Dihedral : 5.571 55.998 2362 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.94 % Favored : 87.97 % Rotamer: Outliers : 2.55 % Allowed : 15.70 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.06 (0.19), residues: 2128 helix: 0.83 (0.20), residues: 750 sheet: -2.13 (0.27), residues: 398 loop : -2.89 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 495 TYR 0.008 0.001 TYR C 37 PHE 0.030 0.001 PHE a 487 TRP 0.007 0.001 TRP C 361 HIS 0.004 0.001 HIS a 215 Details of bonding type rmsd covalent geometry : bond 0.00242 (16792) covalent geometry : angle 0.64015 (22848) hydrogen bonds : bond 0.02963 ( 631) hydrogen bonds : angle 4.21831 ( 1761) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 248 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: b 247 ARG cc_start: 0.7216 (ptp-110) cc_final: 0.6933 (ptp-110) REVERT: a 64 GLN cc_start: 0.7587 (tp40) cc_final: 0.6994 (tp40) REVERT: a 497 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: A 31 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 248 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: C 166 MET cc_start: 0.8808 (mmm) cc_final: 0.8422 (mmm) REVERT: B 64 GLN cc_start: 0.7366 (tp40) cc_final: 0.6831 (tp40) outliers start: 43 outliers final: 32 residues processed: 216 average time/residue: 0.1081 time to fit residues: 36.2302 Evaluate side-chains 201 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 485 LEU Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 465 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 110 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106755 restraints weight = 28131.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109412 restraints weight = 18006.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111190 restraints weight = 13664.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112359 restraints weight = 11443.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113043 restraints weight = 10203.610| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16792 Z= 0.162 Angle : 0.689 9.989 22848 Z= 0.343 Chirality : 0.045 0.239 2572 Planarity : 0.005 0.044 2966 Dihedral : 5.742 57.007 2362 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.88 % Favored : 87.03 % Rotamer: Outliers : 3.02 % Allowed : 16.47 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.08 (0.19), residues: 2128 helix: 0.85 (0.20), residues: 748 sheet: -2.28 (0.27), residues: 418 loop : -2.85 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 62 TYR 0.020 0.001 TYR E 156 PHE 0.029 0.002 PHE a 487 TRP 0.032 0.001 TRP A 328 HIS 0.005 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00384 (16792) covalent geometry : angle 0.68854 (22848) hydrogen bonds : bond 0.03405 ( 631) hydrogen bonds : angle 4.23754 ( 1761) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 248 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6706 (m-30) REVERT: b 247 ARG cc_start: 0.7191 (ptp-110) cc_final: 0.6882 (ptp-110) REVERT: a 64 GLN cc_start: 0.7605 (tp40) cc_final: 0.6994 (tp40) REVERT: a 497 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: A 31 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A 248 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6734 (m-30) REVERT: C 166 MET cc_start: 0.8839 (mmm) cc_final: 0.8421 (mmm) REVERT: B 64 GLN cc_start: 0.7336 (tp40) cc_final: 0.6822 (tp40) outliers start: 51 outliers final: 41 residues processed: 203 average time/residue: 0.1087 time to fit residues: 34.1809 Evaluate side-chains 209 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 172 HIS Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 271 THR Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 395 VAL Chi-restraints excluded: chain a residue 458 VAL Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 485 LEU Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 465 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 135 optimal weight: 0.4980 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 34 optimal weight: 0.0670 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110090 restraints weight = 28173.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112898 restraints weight = 17435.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114793 restraints weight = 12953.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116043 restraints weight = 10714.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116555 restraints weight = 9460.430| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16792 Z= 0.109 Angle : 0.646 9.621 22848 Z= 0.321 Chirality : 0.043 0.237 2572 Planarity : 0.005 0.057 2966 Dihedral : 5.510 56.514 2362 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.37 % Favored : 88.53 % Rotamer: Outliers : 2.49 % Allowed : 17.42 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.19), residues: 2128 helix: 0.92 (0.20), residues: 750 sheet: -1.99 (0.28), residues: 394 loop : -2.82 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 62 TYR 0.013 0.001 TYR E 156 PHE 0.029 0.001 PHE a 487 TRP 0.043 0.001 TRP A 328 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00242 (16792) covalent geometry : angle 0.64613 (22848) hydrogen bonds : bond 0.02908 ( 631) hydrogen bonds : angle 4.14238 ( 1761) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 248 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6762 (m-30) REVERT: E 306 LYS cc_start: 0.7703 (pttm) cc_final: 0.7283 (ptmm) REVERT: b 247 ARG cc_start: 0.7148 (ptp-110) cc_final: 0.6486 (ptp-110) REVERT: b 251 ASP cc_start: 0.7405 (m-30) cc_final: 0.7072 (m-30) REVERT: a 64 GLN cc_start: 0.7611 (tp40) cc_final: 0.6973 (tp40) REVERT: a 134 GLU cc_start: 0.7406 (tp30) cc_final: 0.7181 (mm-30) REVERT: a 497 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: A 31 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8315 (mm) REVERT: A 306 LYS cc_start: 0.7774 (pttm) cc_final: 0.7356 (ptmm) outliers start: 42 outliers final: 32 residues processed: 208 average time/residue: 0.1137 time to fit residues: 36.7526 Evaluate side-chains 200 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 271 THR Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 465 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 99 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 210 optimal weight: 20.0000 chunk 161 optimal weight: 30.0000 chunk 84 optimal weight: 0.1980 chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** 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 = 0.3640 r_free = 0.3640 target = 0.131389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107669 restraints weight = 28348.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110359 restraints weight = 17966.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112149 restraints weight = 13554.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113305 restraints weight = 11344.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114089 restraints weight = 10116.241| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16792 Z= 0.147 Angle : 0.678 10.155 22848 Z= 0.336 Chirality : 0.044 0.239 2572 Planarity : 0.005 0.048 2966 Dihedral : 5.613 57.138 2362 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.45 % Favored : 87.45 % Rotamer: Outliers : 2.61 % Allowed : 17.54 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.19), residues: 2128 helix: 0.91 (0.20), residues: 756 sheet: -1.97 (0.28), residues: 394 loop : -2.81 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 62 TYR 0.012 0.001 TYR E 156 PHE 0.027 0.001 PHE a 487 TRP 0.043 0.002 TRP A 328 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00346 (16792) covalent geometry : angle 0.67769 (22848) hydrogen bonds : bond 0.03193 ( 631) hydrogen bonds : angle 4.14508 ( 1761) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 248 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: b 247 ARG cc_start: 0.7164 (ptp-110) cc_final: 0.6855 (ptp-110) REVERT: a 64 GLN cc_start: 0.7675 (tp40) cc_final: 0.7039 (tp40) REVERT: a 134 GLU cc_start: 0.7452 (tp30) cc_final: 0.7242 (mm-30) REVERT: a 497 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: A 31 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8413 (mm) REVERT: B 134 GLU cc_start: 0.7456 (tp30) cc_final: 0.7233 (mm-30) outliers start: 44 outliers final: 39 residues processed: 196 average time/residue: 0.1169 time to fit residues: 35.3463 Evaluate side-chains 203 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 255 SER Chi-restraints excluded: chain a residue 271 THR Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 465 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 187 optimal weight: 0.0870 chunk 93 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 overall best weight: 2.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 144 HIS ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107356 restraints weight = 28543.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110147 restraints weight = 17874.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111984 restraints weight = 13300.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113170 restraints weight = 11077.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113797 restraints weight = 9842.214| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16792 Z= 0.155 Angle : 0.685 10.319 22848 Z= 0.341 Chirality : 0.044 0.229 2572 Planarity : 0.005 0.051 2966 Dihedral : 5.673 57.860 2362 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.45 % Favored : 87.45 % Rotamer: Outliers : 2.49 % Allowed : 18.01 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.19), residues: 2128 helix: 0.91 (0.20), residues: 756 sheet: -2.05 (0.28), residues: 402 loop : -2.79 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 62 TYR 0.011 0.001 TYR E 156 PHE 0.026 0.001 PHE a 487 TRP 0.043 0.001 TRP E 328 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00367 (16792) covalent geometry : angle 0.68528 (22848) hydrogen bonds : bond 0.03245 ( 631) hydrogen bonds : angle 4.17015 ( 1761) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 248 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: b 247 ARG cc_start: 0.7173 (ptp-110) cc_final: 0.6873 (ptp-110) REVERT: a 64 GLN cc_start: 0.7703 (tp40) cc_final: 0.7054 (tp40) REVERT: a 497 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: A 31 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8498 (mm) REVERT: A 306 LYS cc_start: 0.7852 (pttm) cc_final: 0.7362 (ptmm) REVERT: B 64 GLN cc_start: 0.7400 (tp40) cc_final: 0.6883 (tp40) REVERT: B 134 GLU cc_start: 0.7427 (tp30) cc_final: 0.7179 (mm-30) outliers start: 42 outliers final: 38 residues processed: 197 average time/residue: 0.1165 time to fit residues: 35.4188 Evaluate side-chains 202 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 255 SER Chi-restraints excluded: chain a residue 271 THR Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 395 VAL Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 465 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 100 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** 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 = 0.3665 r_free = 0.3665 target = 0.133808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110295 restraints weight = 28079.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113135 restraints weight = 17150.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115063 restraints weight = 12665.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116263 restraints weight = 10443.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116964 restraints weight = 9255.339| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16792 Z= 0.111 Angle : 0.649 10.179 22848 Z= 0.322 Chirality : 0.043 0.232 2572 Planarity : 0.005 0.071 2966 Dihedral : 5.453 58.381 2362 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.14 % Favored : 88.77 % Rotamer: Outliers : 2.49 % Allowed : 18.07 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.19), residues: 2128 helix: 0.94 (0.20), residues: 768 sheet: -1.95 (0.27), residues: 420 loop : -2.88 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 62 TYR 0.011 0.001 TYR A 156 PHE 0.025 0.001 PHE a 487 TRP 0.033 0.001 TRP A 328 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00248 (16792) covalent geometry : angle 0.64871 (22848) hydrogen bonds : bond 0.02859 ( 631) hydrogen bonds : angle 4.08481 ( 1761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.61 seconds wall clock time: 38 minutes 50.99 seconds (2330.99 seconds total)