Starting phenix.real_space_refine on Fri Jul 3 16:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ipr_35641/07_2026/8ipr_35641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ipr_35641/07_2026/8ipr_35641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ipr_35641/07_2026/8ipr_35641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ipr_35641/07_2026/8ipr_35641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ipr_35641/07_2026/8ipr_35641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ipr_35641/07_2026/8ipr_35641.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ipr_35641/07_2026/8ipr_35641.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ipr_35641/07_2026/8ipr_35641.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 58 5.16 5 C 9412 2.51 5 N 2692 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14894 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3639 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 31, 'TRANS': 472} Chain: "C" Number of atoms: 3744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3744 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 482} Chain: "D" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3639 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 31, 'TRANS': 472} Chain: "E" Number of atoms: 3744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3744 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 482} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.31, per 1000 atoms: 0.22 Number of scatterers: 14894 At special positions: 0 Unit cell: (92.352, 120.64, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 12 15.00 Mg 4 11.99 O 2716 8.00 N 2692 7.00 C 9412 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: 1.28 Conformation dependent library (CDL) restraints added in 722.9 milliseconds 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3720 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 8 sheets defined 72.2% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 20 through 41 removed outlier: 3.562A pdb=" N PHE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 108 Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.828A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 114' Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 126 through 161 Proline residue: A 142 - end of helix removed outlier: 4.267A pdb=" N VAL A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 202 removed outlier: 3.659A pdb=" N VAL A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 4.440A pdb=" N ALA A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 removed outlier: 5.925A pdb=" N ALA A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 220 through 269 removed outlier: 3.587A pdb=" N VAL A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Proline residue: A 245 - end of helix Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 277 through 319 removed outlier: 3.938A pdb=" N ALA A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.520A pdb=" N THR A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.514A pdb=" N ALA A 431 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 449 Processing helix chain 'A' and resid 464 through 477 removed outlier: 4.785A pdb=" N ARG A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'C' and resid -4 through 24 Processing helix chain 'C' and resid 35 through 80 removed outlier: 3.933A pdb=" N LEU C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 101 through 104 Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 112 through 134 removed outlier: 3.544A pdb=" N THR C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 134 through 142 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 183 removed outlier: 3.571A pdb=" N ILE C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 Processing helix chain 'C' and resid 195 through 246 removed outlier: 4.008A pdb=" N ARG C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 293 Proline residue: C 262 - end of helix removed outlier: 3.845A pdb=" N PHE C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Proline residue: C 267 - end of helix removed outlier: 3.997A pdb=" N HIS C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP C 280 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 345 Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 409 through 416 removed outlier: 3.816A pdb=" N GLU C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 462 through 479 Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 20 through 41 removed outlier: 3.582A pdb=" N PHE D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 108 Processing helix chain 'D' and resid 109 through 114 removed outlier: 3.826A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 114' Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 126 through 161 Proline residue: D 142 - end of helix removed outlier: 4.265A pdb=" N VAL D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 202 removed outlier: 3.654A pdb=" N VAL D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) Proline residue: D 180 - end of helix removed outlier: 4.409A pdb=" N ALA D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 removed outlier: 5.919A pdb=" N ALA D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 209 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 269 removed outlier: 3.627A pdb=" N VAL D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Proline residue: D 245 - end of helix Proline residue: D 253 - end of helix Processing helix chain 'D' and resid 277 through 319 removed outlier: 3.910A pdb=" N ALA D 281 " --> pdb=" O PRO D 277 " (cutoff:3.500A) Proline residue: D 287 - end of helix Proline residue: D 298 - end of helix Processing helix chain 'D' and resid 349 through 363 Processing helix chain 'D' and resid 385 through 391 Processing helix chain 'D' and resid 398 through 409 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.518A pdb=" N THR D 424 " --> pdb=" O GLY D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.800A pdb=" N VAL D 433 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 449 Processing helix chain 'D' and resid 464 through 477 removed outlier: 4.799A pdb=" N ARG D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLN D 470 " --> pdb=" O GLY D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid -4 through 24 Processing helix chain 'E' and resid 35 through 80 removed outlier: 3.944A pdb=" N LEU E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 91 Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 101 through 104 Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 112 through 134 removed outlier: 3.547A pdb=" N THR E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 134 through 142 Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 146 through 183 removed outlier: 3.571A pdb=" N ILE E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARG E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 Processing helix chain 'E' and resid 195 through 246 removed outlier: 4.004A pdb=" N ARG E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 293 Proline residue: E 262 - end of helix removed outlier: 3.829A pdb=" N PHE E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Proline residue: E 267 - end of helix removed outlier: 3.997A pdb=" N HIS E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP E 280 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 345 Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 399 through 408 Processing helix chain 'E' and resid 409 through 416 removed outlier: 3.822A pdb=" N GLU E 415 " --> pdb=" O GLU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 462 through 479 Processing helix chain 'E' and resid 489 through 494 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA2, first strand: chain 'C' and resid 318 through 320 Processing sheet with id=AA3, first strand: chain 'C' and resid 373 through 376 removed outlier: 6.213A pdb=" N ALA C 374 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL C 325 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL C 500 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 327 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 385 through 386 Processing sheet with id=AA5, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AA6, first strand: chain 'E' and resid 318 through 320 Processing sheet with id=AA7, first strand: chain 'E' and resid 373 through 376 removed outlier: 6.219A pdb=" N ALA E 374 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL E 325 " --> pdb=" O HIS E 498 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL E 500 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL E 327 " --> pdb=" O VAL E 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 385 through 386 1074 hydrogen bonds defined for protein. 3171 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: 2.58 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2440 1.31 - 1.44: 3548 1.44 - 1.57: 9046 1.57 - 1.69: 20 1.69 - 1.82: 98 Bond restraints: 15152 Sorted by residual: bond pdb=" CA PRO A 56 " pdb=" C PRO A 56 " ideal model delta sigma weight residual 1.514 1.534 -0.020 5.50e-03 3.31e+04 1.31e+01 bond pdb=" N PHE E 55 " pdb=" CA PHE E 55 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.30e-02 5.92e+03 1.02e+01 bond pdb=" C ASP C 455 " pdb=" O ASP C 455 " ideal model delta sigma weight residual 1.231 1.187 0.044 1.41e-02 5.03e+03 9.96e+00 bond pdb=" O2B ATP D 602 " pdb=" PB ATP D 602 " ideal model delta sigma weight residual 1.529 1.460 0.069 2.20e-02 2.07e+03 9.81e+00 bond pdb=" O2B ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 1.529 1.460 0.069 2.20e-02 2.07e+03 9.76e+00 ... (remaining 15147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 20063 1.75 - 3.51: 542 3.51 - 5.26: 123 5.26 - 7.01: 37 7.01 - 8.77: 5 Bond angle restraints: 20770 Sorted by residual: angle pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " pdb=" O3G ATP E 602 " ideal model delta sigma weight residual 104.48 111.44 -6.96 1.14e+00 7.76e-01 3.76e+01 angle pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " pdb=" O3G ATP C 602 " ideal model delta sigma weight residual 104.48 111.44 -6.96 1.14e+00 7.76e-01 3.76e+01 angle pdb=" N GLN E 56 " pdb=" CA GLN E 56 " pdb=" C GLN E 56 " ideal model delta sigma weight residual 111.82 105.55 6.27 1.16e+00 7.43e-01 2.92e+01 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 134.55 5.32 1.00e+00 1.00e+00 2.83e+01 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 134.55 5.32 1.00e+00 1.00e+00 2.83e+01 ... (remaining 20765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 7921 17.68 - 35.36: 889 35.36 - 53.04: 219 53.04 - 70.72: 41 70.72 - 88.40: 12 Dihedral angle restraints: 9082 sinusoidal: 3316 harmonic: 5766 Sorted by residual: dihedral pdb=" CA GLY D 205 " pdb=" C GLY D 205 " pdb=" N MET D 206 " pdb=" CA MET D 206 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA GLY A 205 " pdb=" C GLY A 205 " pdb=" N MET A 206 " pdb=" CA MET A 206 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER D 199 " pdb=" C SER D 199 " pdb=" N GLN D 200 " pdb=" CA GLN D 200 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 9079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2189 0.058 - 0.116: 368 0.116 - 0.174: 27 0.174 - 0.232: 6 0.232 - 0.290: 2 Chirality restraints: 2592 Sorted by residual: chirality pdb=" CA LEU A 17 " pdb=" N LEU A 17 " pdb=" C LEU A 17 " pdb=" CB LEU A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL C 141 " pdb=" CA VAL C 141 " pdb=" CG1 VAL C 141 " pdb=" CG2 VAL C 141 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL D 135 " pdb=" CA VAL D 135 " pdb=" CG1 VAL D 135 " pdb=" CG2 VAL D 135 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2589 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 252 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO A 253 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C LEU A 136 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU A 136 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 137 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 506 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C LEU C 506 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU C 506 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL C 507 " -0.012 2.00e-02 2.50e+03 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 121 2.56 - 3.15: 11624 3.15 - 3.73: 24130 3.73 - 4.32: 31138 4.32 - 4.90: 53197 Nonbonded interactions: 120210 Sorted by model distance: nonbonded pdb=" OG SER C 337 " pdb="MG MG C 601 " model vdw 1.978 2.170 nonbonded pdb=" OG SER E 337 " pdb="MG MG E 601 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR D 351 " pdb="MG MG D 601 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR A 351 " pdb="MG MG A 601 " model vdw 2.054 2.170 nonbonded pdb=" O ASP E 497 " pdb=" OD1 ASP E 497 " model vdw 2.160 3.040 ... (remaining 120205 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.230 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 14.300 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15152 Z= 0.233 Angle : 0.707 8.768 20770 Z= 0.395 Chirality : 0.043 0.290 2592 Planarity : 0.005 0.074 2656 Dihedral : 16.108 88.398 5362 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 0.13 % Allowed : 24.43 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.20), residues: 2030 helix: 2.28 (0.14), residues: 1356 sheet: 0.28 (0.50), residues: 132 loop : -2.19 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 18 TYR 0.006 0.001 TYR D 102 PHE 0.006 0.001 PHE D 291 TRP 0.008 0.001 TRP C 369 HIS 0.003 0.001 HIS C 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.23 (15152) covalent geometry : angle 0.70733 / 0.39 (20770) hydrogen bonds : bond 0.12250 / 8.32 ( 1074) hydrogen bonds : angle 4.83382 / 3.62 ( 3171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ASN cc_start: 0.7952 (m-40) cc_final: 0.7680 (m-40) REVERT: E 24 ASN cc_start: 0.7987 (m-40) cc_final: 0.7752 (m-40) outliers start: 2 outliers final: 2 residues processed: 193 average time/residue: 0.5062 time to fit residues: 108.9073 Evaluate side-chains 111 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain E residue 55 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN C 53 GLN C 296 HIS E 53 GLN E 56 GLN E 296 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.071748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.051899 restraints weight = 50602.681| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.66 r_work: 0.2721 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15152 Z= 0.138 Angle : 0.652 9.162 20770 Z= 0.315 Chirality : 0.040 0.154 2592 Planarity : 0.005 0.049 2656 Dihedral : 4.650 55.224 2218 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.47 % Allowed : 23.97 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.20), residues: 2030 helix: 2.44 (0.14), residues: 1366 sheet: 0.13 (0.50), residues: 132 loop : -2.13 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 199 TYR 0.011 0.002 TYR E 133 PHE 0.025 0.002 PHE C 151 TRP 0.012 0.001 TRP E 135 HIS 0.003 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (15152) covalent geometry : angle 0.65162 / 0.32 (20770) hydrogen bonds : bond 0.04896 / 3.42 ( 1074) hydrogen bonds : angle 4.20116 / 3.17 ( 3171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8881 (tm-30) REVERT: D 82 GLN cc_start: 0.9206 (tm-30) cc_final: 0.9005 (tm-30) REVERT: D 191 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8896 (tm-30) REVERT: D 384 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.9028 (p) REVERT: E 488 HIS cc_start: 0.8867 (OUTLIER) cc_final: 0.8653 (p-80) outliers start: 67 outliers final: 17 residues processed: 171 average time/residue: 0.4289 time to fit residues: 83.0469 Evaluate side-chains 122 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 488 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 192 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 HIS A 370 GLN A 458 GLN C 0 ASN D 231 HIS E 0 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.069359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.049378 restraints weight = 52243.728| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.68 r_work: 0.2655 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15152 Z= 0.207 Angle : 0.654 8.659 20770 Z= 0.319 Chirality : 0.041 0.141 2592 Planarity : 0.005 0.039 2656 Dihedral : 4.401 55.661 2214 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.74 % Allowed : 22.90 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.20), residues: 2030 helix: 2.54 (0.14), residues: 1370 sheet: 0.08 (0.50), residues: 132 loop : -2.09 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 138 TYR 0.012 0.002 TYR E 133 PHE 0.018 0.002 PHE C 275 TRP 0.009 0.001 TRP C 135 HIS 0.005 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (15152) covalent geometry : angle 0.65409 / 0.32 (20770) hydrogen bonds : bond 0.05167 / 3.63 ( 1074) hydrogen bonds : angle 4.12785 / 3.11 ( 3171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 102 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8986 (tm-30) REVERT: A 130 ASP cc_start: 0.8980 (m-30) cc_final: 0.8642 (p0) REVERT: A 140 LEU cc_start: 0.8819 (mm) cc_final: 0.8394 (mm) REVERT: D 82 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8986 (tm-30) REVERT: D 191 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8912 (tm-30) REVERT: D 384 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9058 (p) outliers start: 71 outliers final: 23 residues processed: 156 average time/residue: 0.3586 time to fit residues: 64.3616 Evaluate side-chains 122 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 301 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 157 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN C 0 ASN D 458 GLN E 0 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.069649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.049813 restraints weight = 51965.717| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.67 r_work: 0.2668 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15152 Z= 0.163 Angle : 0.634 9.506 20770 Z= 0.304 Chirality : 0.040 0.132 2592 Planarity : 0.004 0.038 2656 Dihedral : 4.384 57.854 2214 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.61 % Allowed : 23.03 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.20), residues: 2030 helix: 2.58 (0.14), residues: 1370 sheet: 0.09 (0.51), residues: 132 loop : -2.06 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 98 TYR 0.009 0.002 TYR E 133 PHE 0.013 0.002 PHE C 275 TRP 0.010 0.001 TRP E 54 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15152) covalent geometry : angle 0.63417 / 0.30 (20770) hydrogen bonds : bond 0.04921 / 3.46 ( 1074) hydrogen bonds : angle 4.04579 / 3.05 ( 3171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 100 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9318 (tm-30) cc_final: 0.8976 (tm-30) REVERT: A 140 LEU cc_start: 0.8834 (mm) cc_final: 0.8421 (mm) REVERT: C 332 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.9032 (m110) REVERT: D 82 GLN cc_start: 0.9326 (tm-30) cc_final: 0.8993 (tm-30) REVERT: D 140 LEU cc_start: 0.8739 (mm) cc_final: 0.8385 (mm) REVERT: D 384 THR cc_start: 0.9461 (OUTLIER) cc_final: 0.9082 (p) outliers start: 69 outliers final: 30 residues processed: 150 average time/residue: 0.3719 time to fit residues: 64.2886 Evaluate side-chains 129 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 144 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 125 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 0 ASN E 0 ASN E 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.049554 restraints weight = 52472.260| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.68 r_work: 0.2667 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15152 Z= 0.164 Angle : 0.636 10.997 20770 Z= 0.303 Chirality : 0.040 0.134 2592 Planarity : 0.004 0.036 2656 Dihedral : 4.335 58.360 2214 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.41 % Allowed : 23.56 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 2030 helix: 2.62 (0.14), residues: 1372 sheet: 0.08 (0.51), residues: 132 loop : -2.04 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 324 TYR 0.008 0.002 TYR D 102 PHE 0.012 0.002 PHE E 151 TRP 0.007 0.001 TRP C 135 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15152) covalent geometry : angle 0.63595 / 0.30 (20770) hydrogen bonds : bond 0.04858 / 3.42 ( 1074) hydrogen bonds : angle 3.99965 / 3.02 ( 3171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 101 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8966 (tm-30) REVERT: A 130 ASP cc_start: 0.8980 (m-30) cc_final: 0.8627 (p0) REVERT: A 140 LEU cc_start: 0.8869 (mm) cc_final: 0.8440 (mm) REVERT: C 332 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8999 (m110) REVERT: D 82 GLN cc_start: 0.9336 (tm-30) cc_final: 0.8990 (tm-30) REVERT: D 130 ASP cc_start: 0.9019 (m-30) cc_final: 0.8573 (p0) REVERT: D 140 LEU cc_start: 0.8795 (mm) cc_final: 0.8417 (mm) REVERT: D 384 THR cc_start: 0.9461 (OUTLIER) cc_final: 0.9085 (p) REVERT: D 458 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8785 (mt0) REVERT: E 56 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8640 (tp-100) outliers start: 66 outliers final: 37 residues processed: 149 average time/residue: 0.3878 time to fit residues: 66.6900 Evaluate side-chains 140 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN C 0 ASN E 0 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.048554 restraints weight = 52636.791| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.64 r_work: 0.2639 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15152 Z= 0.214 Angle : 0.666 11.797 20770 Z= 0.321 Chirality : 0.041 0.136 2592 Planarity : 0.004 0.036 2656 Dihedral : 4.387 59.457 2214 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.21 % Allowed : 23.90 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 2030 helix: 2.62 (0.14), residues: 1370 sheet: 0.18 (0.50), residues: 138 loop : -2.10 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 138 TYR 0.009 0.002 TYR A 102 PHE 0.014 0.002 PHE A 24 TRP 0.007 0.001 TRP E 135 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (15152) covalent geometry : angle 0.66593 / 0.32 (20770) hydrogen bonds : bond 0.05101 / 3.59 ( 1074) hydrogen bonds : angle 4.04351 / 3.04 ( 3171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 101 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9336 (tm-30) cc_final: 0.9036 (tm-30) REVERT: A 140 LEU cc_start: 0.8911 (mm) cc_final: 0.8488 (mm) REVERT: C 332 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.8991 (m110) REVERT: D 82 GLN cc_start: 0.9338 (tm-30) cc_final: 0.9041 (tm-30) REVERT: D 140 LEU cc_start: 0.8867 (mm) cc_final: 0.8494 (mm) REVERT: D 384 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9096 (p) REVERT: D 458 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8880 (mt0) outliers start: 63 outliers final: 37 residues processed: 148 average time/residue: 0.3599 time to fit residues: 61.6892 Evaluate side-chains 136 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 124 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 117 optimal weight: 30.0000 chunk 50 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 164 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN C 0 ASN E 0 ASN E 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.069711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.050250 restraints weight = 52327.941| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.67 r_work: 0.2695 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15152 Z= 0.137 Angle : 0.627 12.795 20770 Z= 0.298 Chirality : 0.039 0.140 2592 Planarity : 0.004 0.035 2656 Dihedral : 4.301 58.849 2214 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.14 % Allowed : 24.23 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.20), residues: 2030 helix: 2.72 (0.14), residues: 1370 sheet: 0.16 (0.51), residues: 136 loop : -1.97 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 138 TYR 0.008 0.002 TYR C -4 PHE 0.015 0.001 PHE A 24 TRP 0.006 0.001 TRP E 369 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15152) covalent geometry : angle 0.62673 / 0.30 (20770) hydrogen bonds : bond 0.04701 / 3.31 ( 1074) hydrogen bonds : angle 3.92638 / 2.97 ( 3171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 104 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8956 (tm-30) REVERT: A 283 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6971 (tm) REVERT: C 332 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.9011 (m110) REVERT: D 82 GLN cc_start: 0.9347 (tm-30) cc_final: 0.9001 (tm-30) REVERT: D 140 LEU cc_start: 0.8856 (mm) cc_final: 0.8634 (mm) REVERT: D 384 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9138 (p) REVERT: E 56 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8790 (tp40) outliers start: 62 outliers final: 25 residues processed: 151 average time/residue: 0.3877 time to fit residues: 67.5399 Evaluate side-chains 126 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 100 optimal weight: 0.0170 chunk 150 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN C 0 ASN D 458 GLN E 0 ASN E 53 GLN E 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.069207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049692 restraints weight = 53095.585| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.68 r_work: 0.2680 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15152 Z= 0.160 Angle : 0.656 14.499 20770 Z= 0.311 Chirality : 0.040 0.140 2592 Planarity : 0.004 0.090 2656 Dihedral : 4.282 58.414 2214 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.40 % Allowed : 25.17 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.20), residues: 2030 helix: 2.73 (0.14), residues: 1370 sheet: 0.17 (0.51), residues: 136 loop : -1.96 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 69 TYR 0.008 0.001 TYR D 102 PHE 0.014 0.002 PHE A 24 TRP 0.007 0.001 TRP E 135 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (15152) covalent geometry : angle 0.65637 / 0.31 (20770) hydrogen bonds : bond 0.04777 / 3.36 ( 1074) hydrogen bonds : angle 3.91982 / 2.96 ( 3171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9330 (tm-30) cc_final: 0.9015 (tm-30) REVERT: A 130 ASP cc_start: 0.8947 (m-30) cc_final: 0.8591 (p0) REVERT: A 283 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6983 (tm) REVERT: C 332 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.9009 (m110) REVERT: D 82 GLN cc_start: 0.9345 (tm-30) cc_final: 0.9045 (tm-30) REVERT: D 130 ASP cc_start: 0.8918 (m-30) cc_final: 0.8544 (p0) REVERT: D 140 LEU cc_start: 0.8882 (mm) cc_final: 0.8677 (mm) REVERT: D 384 THR cc_start: 0.9506 (OUTLIER) cc_final: 0.9143 (p) REVERT: E 56 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8840 (tp-100) outliers start: 51 outliers final: 29 residues processed: 133 average time/residue: 0.3652 time to fit residues: 55.9539 Evaluate side-chains 129 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 156 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN C 0 ASN ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN E 0 ASN E 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.068700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049176 restraints weight = 52910.581| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.67 r_work: 0.2665 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15152 Z= 0.188 Angle : 0.681 15.153 20770 Z= 0.321 Chirality : 0.040 0.141 2592 Planarity : 0.004 0.035 2656 Dihedral : 4.287 59.186 2214 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.40 % Allowed : 24.97 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.20), residues: 2030 helix: 2.71 (0.14), residues: 1370 sheet: 0.14 (0.50), residues: 140 loop : -1.98 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 138 TYR 0.009 0.001 TYR D 102 PHE 0.014 0.002 PHE A 24 TRP 0.007 0.001 TRP C 375 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (15152) covalent geometry : angle 0.68132 / 0.32 (20770) hydrogen bonds : bond 0.04913 / 3.46 ( 1074) hydrogen bonds : angle 3.96286 / 2.99 ( 3171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9041 (tm-30) REVERT: A 130 ASP cc_start: 0.8948 (m-30) cc_final: 0.8588 (p0) REVERT: A 283 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7009 (tm) REVERT: C 212 MET cc_start: 0.9465 (mmt) cc_final: 0.8771 (mmm) REVERT: C 332 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.9013 (m110) REVERT: D 82 GLN cc_start: 0.9361 (tm-30) cc_final: 0.9050 (tm-30) REVERT: D 130 ASP cc_start: 0.8927 (m-30) cc_final: 0.8613 (p0) REVERT: D 384 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9138 (p) REVERT: E 56 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8887 (tp-100) outliers start: 51 outliers final: 28 residues processed: 135 average time/residue: 0.3973 time to fit residues: 61.6650 Evaluate side-chains 129 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 89 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 133 optimal weight: 0.0040 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN C 0 ASN D 458 GLN E 0 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.050757 restraints weight = 52080.798| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.72 r_work: 0.2711 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15152 Z= 0.133 Angle : 0.672 14.242 20770 Z= 0.313 Chirality : 0.039 0.181 2592 Planarity : 0.004 0.036 2656 Dihedral : 4.232 58.420 2214 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.27 % Allowed : 26.50 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.20), residues: 2030 helix: 2.72 (0.14), residues: 1370 sheet: 0.14 (0.51), residues: 136 loop : -1.91 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 69 TYR 0.008 0.001 TYR C -4 PHE 0.013 0.001 PHE A 24 TRP 0.009 0.001 TRP E 135 HIS 0.003 0.000 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (15152) covalent geometry : angle 0.67150 / 0.31 (20770) hydrogen bonds : bond 0.04580 / 3.22 ( 1074) hydrogen bonds : angle 3.87748 / 2.94 ( 3171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9328 (tm-30) cc_final: 0.8950 (tm-30) REVERT: A 130 ASP cc_start: 0.8958 (m-30) cc_final: 0.8595 (p0) REVERT: A 283 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6994 (tm) REVERT: D 82 GLN cc_start: 0.9345 (tm-30) cc_final: 0.8972 (tm-30) REVERT: D 130 ASP cc_start: 0.8966 (m-30) cc_final: 0.8545 (p0) REVERT: D 283 LEU cc_start: 0.7352 (tm) cc_final: 0.6983 (tm) REVERT: D 384 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9059 (p) REVERT: D 388 ASP cc_start: 0.9350 (t0) cc_final: 0.8905 (t0) outliers start: 34 outliers final: 23 residues processed: 124 average time/residue: 0.3802 time to fit residues: 54.1857 Evaluate side-chains 124 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN C 0 ASN D 458 GLN E 0 ASN E 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.069820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050375 restraints weight = 52455.036| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.72 r_work: 0.2700 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15152 Z= 0.144 Angle : 0.673 15.219 20770 Z= 0.314 Chirality : 0.040 0.166 2592 Planarity : 0.004 0.066 2656 Dihedral : 4.180 56.997 2214 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.67 % Allowed : 25.97 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.20), residues: 2030 helix: 2.73 (0.14), residues: 1370 sheet: 0.15 (0.51), residues: 136 loop : -1.90 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 69 TYR 0.008 0.001 TYR C -4 PHE 0.012 0.001 PHE A 24 TRP 0.006 0.000 TRP E 369 HIS 0.003 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (15152) covalent geometry : angle 0.67257 / 0.31 (20770) hydrogen bonds : bond 0.04571 / 3.22 ( 1074) hydrogen bonds : angle 3.87438 / 2.93 ( 3171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.50 seconds wall clock time: 59 minutes 49.92 seconds (3589.92 seconds total)