Starting phenix.real_space_refine on Fri Jun 13 11:34:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ipr_35641/06_2025/8ipr_35641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ipr_35641/06_2025/8ipr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ipr_35641/06_2025/8ipr_35641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ipr_35641/06_2025/8ipr_35641.map" model { file = "/net/cci-nas-00/data/ceres_data/8ipr_35641/06_2025/8ipr_35641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ipr_35641/06_2025/8ipr_35641.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.32, per 1000 atoms: 0.63 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: 3.58 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.39 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: 4.47 Time building geometry restraints manager: 4.25 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 - 17.85: 7950 17.85 - 35.71: 938 35.71 - 53.56: 247 53.56 - 71.42: 53 71.42 - 89.27: 18 Dihedral angle restraints: 9206 sinusoidal: 3440 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 9203 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: 0.04 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: 2.460 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.900 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 16.937 89.274 5486 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP C 369 HIS 0.003 0.001 HIS C 460 PHE 0.006 0.001 PHE D 291 TYR 0.006 0.001 TYR D 102 ARG 0.014 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.12250 ( 1074) hydrogen bonds : angle 4.83382 ( 3171) covalent geometry : bond 0.00421 (15152) covalent geometry : angle 0.70733 (20770) *********************** 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 : 1.459 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: 0.7679 (m-40) REVERT: E 24 ASN cc_start: 0.7987 (m-40) cc_final: 0.7751 (m-40) outliers start: 2 outliers final: 2 residues processed: 193 average time/residue: 1.0529 time to fit residues: 227.0916 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 : 1.465 ------------------------------------------------------------------------------- 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 170 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN C 53 GLN E 53 GLN E 56 GLN E 296 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.051125 restraints weight = 51333.124| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.72 r_work: 0.2703 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15152 Z= 0.149 Angle : 0.657 9.509 20770 Z= 0.319 Chirality : 0.040 0.148 2592 Planarity : 0.005 0.048 2656 Dihedral : 8.335 88.564 2342 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.61 % Allowed : 24.30 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.20), residues: 2030 helix: 2.45 (0.14), residues: 1368 sheet: 0.16 (0.50), residues: 132 loop : -2.15 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 135 HIS 0.003 0.001 HIS C 16 PHE 0.025 0.002 PHE C 151 TYR 0.011 0.002 TYR E 133 ARG 0.007 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.04990 ( 1074) hydrogen bonds : angle 4.19762 ( 3171) covalent geometry : bond 0.00323 (15152) covalent geometry : angle 0.65656 (20770) *********************** 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 187 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 118 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8930 (tm-30) REVERT: A 140 LEU cc_start: 0.8813 (mm) cc_final: 0.8368 (mm) REVERT: D 82 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8941 (tm-30) REVERT: D 191 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8902 (tm-30) REVERT: D 384 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9037 (p) REVERT: E 488 HIS cc_start: 0.8918 (OUTLIER) cc_final: 0.8656 (p-80) outliers start: 69 outliers final: 19 residues processed: 171 average time/residue: 1.0146 time to fit residues: 198.8223 Evaluate side-chains 121 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 171 CYS 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 D residue 62 THR Chi-restraints excluded: chain D residue 171 CYS 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 141 VAL 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 79 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3364 r_free = 0.3364 target = 0.069402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.049429 restraints weight = 51791.097| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.66 r_work: 0.2660 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15152 Z= 0.204 Angle : 0.649 8.723 20770 Z= 0.318 Chirality : 0.040 0.135 2592 Planarity : 0.005 0.037 2656 Dihedral : 7.605 89.243 2338 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.54 % Allowed : 23.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.20), residues: 2030 helix: 2.54 (0.14), residues: 1366 sheet: 0.10 (0.51), residues: 132 loop : -2.09 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 135 HIS 0.004 0.001 HIS A 87 PHE 0.013 0.002 PHE D 291 TYR 0.011 0.002 TYR E 133 ARG 0.004 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.05148 ( 1074) hydrogen bonds : angle 4.14436 ( 3171) covalent geometry : bond 0.00462 (15152) covalent geometry : angle 0.64940 (20770) *********************** 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 172 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 104 time to evaluate : 1.613 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: 0.9313 (tm-30) cc_final: 0.8996 (tm-30) REVERT: A 130 ASP cc_start: 0.8962 (m-30) cc_final: 0.8627 (p0) REVERT: A 140 LEU cc_start: 0.8796 (mm) cc_final: 0.8370 (mm) REVERT: C 332 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.9074 (m110) REVERT: D 82 GLN cc_start: 0.9304 (tm-30) cc_final: 0.8987 (tm-30) REVERT: D 191 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8939 (tm-30) REVERT: D 384 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.9048 (p) outliers start: 68 outliers final: 26 residues processed: 156 average time/residue: 0.8169 time to fit residues: 147.9441 Evaluate side-chains 128 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain C residue 92 ASP 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 145 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 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 92 ASP 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 52 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 160 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 113 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3373 r_free = 0.3373 target = 0.069853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049935 restraints weight = 51692.850| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.68 r_work: 0.2673 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15152 Z= 0.159 Angle : 0.629 9.400 20770 Z= 0.303 Chirality : 0.039 0.128 2592 Planarity : 0.004 0.037 2656 Dihedral : 7.314 88.877 2338 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.07 % Allowed : 24.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.20), residues: 2030 helix: 2.53 (0.14), residues: 1372 sheet: 0.14 (0.51), residues: 132 loop : -2.07 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 54 HIS 0.003 0.001 HIS A 87 PHE 0.022 0.002 PHE C 151 TYR 0.008 0.002 TYR E 133 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 1074) hydrogen bonds : angle 4.05973 ( 3171) covalent geometry : bond 0.00353 (15152) covalent geometry : angle 0.62897 (20770) *********************** 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 165 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 104 time to evaluate : 1.505 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: 0.9317 (tm-30) cc_final: 0.8985 (tm-30) REVERT: A 140 LEU cc_start: 0.8810 (mm) cc_final: 0.8390 (mm) REVERT: A 283 LEU cc_start: 0.7114 (tm) cc_final: 0.6849 (tm) REVERT: A 284 MET cc_start: 0.8032 (mmt) cc_final: 0.7781 (mpt) REVERT: C 332 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.9046 (m110) REVERT: D 82 GLN cc_start: 0.9318 (tm-30) cc_final: 0.8997 (tm-30) REVERT: D 140 LEU cc_start: 0.8755 (mm) cc_final: 0.8384 (mm) REVERT: D 384 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9076 (p) outliers start: 61 outliers final: 29 residues processed: 150 average time/residue: 0.8614 time to fit residues: 148.8387 Evaluate side-chains 130 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 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 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 331 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 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 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 45 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3359 r_free = 0.3359 target = 0.069092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049266 restraints weight = 52482.776| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.67 r_work: 0.2656 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15152 Z= 0.178 Angle : 0.637 11.215 20770 Z= 0.306 Chirality : 0.040 0.137 2592 Planarity : 0.004 0.035 2656 Dihedral : 7.075 89.571 2338 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.47 % Allowed : 23.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.20), residues: 2030 helix: 2.63 (0.14), residues: 1370 sheet: 0.12 (0.51), residues: 132 loop : -2.07 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 135 HIS 0.003 0.001 HIS A 87 PHE 0.013 0.002 PHE D 291 TYR 0.008 0.002 TYR D 102 ARG 0.003 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 1074) hydrogen bonds : angle 4.00198 ( 3171) covalent geometry : bond 0.00404 (15152) covalent geometry : angle 0.63706 (20770) *********************** 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 169 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 102 time to evaluate : 1.733 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: 0.9336 (tm-30) cc_final: 0.9039 (tm-30) REVERT: A 130 ASP cc_start: 0.8982 (m-30) cc_final: 0.8599 (p0) REVERT: A 140 LEU cc_start: 0.8884 (mm) cc_final: 0.8435 (mm) REVERT: A 283 LEU cc_start: 0.7278 (tm) cc_final: 0.7026 (tm) REVERT: D 82 GLN cc_start: 0.9349 (tm-30) cc_final: 0.9059 (tm-30) REVERT: D 130 ASP cc_start: 0.9038 (m-30) cc_final: 0.8617 (p0) REVERT: D 140 LEU cc_start: 0.8813 (mm) cc_final: 0.8438 (mm) REVERT: D 384 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9092 (p) REVERT: E 56 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8646 (tp-100) outliers start: 67 outliers final: 38 residues processed: 149 average time/residue: 1.0087 time to fit residues: 173.5452 Evaluate side-chains 138 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 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 60 SER Chi-restraints excluded: chain C residue 92 ASP 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 504 SER Chi-restraints excluded: chain D residue 171 CYS 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 E residue 6 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 92 ASP 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 155 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 52 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 0 ASN D 458 GLN E 0 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.068715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.048961 restraints weight = 52283.655| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.66 r_work: 0.2648 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15152 Z= 0.188 Angle : 0.649 11.848 20770 Z= 0.312 Chirality : 0.040 0.147 2592 Planarity : 0.004 0.036 2656 Dihedral : 6.966 88.579 2338 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.14 % Allowed : 23.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.20), residues: 2030 helix: 2.62 (0.14), residues: 1370 sheet: 0.19 (0.50), residues: 138 loop : -2.07 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 135 HIS 0.003 0.001 HIS A 87 PHE 0.015 0.002 PHE C 151 TYR 0.008 0.002 TYR A 102 ARG 0.007 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.04974 ( 1074) hydrogen bonds : angle 4.01381 ( 3171) covalent geometry : bond 0.00426 (15152) covalent geometry : angle 0.64896 (20770) *********************** 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 163 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 101 time to evaluate : 3.208 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: 0.9347 (tm-30) cc_final: 0.9042 (tm-30) REVERT: A 140 LEU cc_start: 0.8874 (mm) cc_final: 0.8434 (mm) REVERT: A 283 LEU cc_start: 0.7212 (tm) cc_final: 0.6981 (tm) REVERT: D 82 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9044 (tm-30) REVERT: D 140 LEU cc_start: 0.8855 (mm) cc_final: 0.8474 (mm) REVERT: D 384 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.9105 (p) outliers start: 62 outliers final: 36 residues processed: 147 average time/residue: 1.1212 time to fit residues: 194.0519 Evaluate side-chains 134 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER 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 17 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 92 ASP 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 501 THR 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 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 92 ASP 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 11 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 0 ASN E 0 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.069202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.049462 restraints weight = 52627.961| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.69 r_work: 0.2665 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.150 Angle : 0.632 12.688 20770 Z= 0.302 Chirality : 0.039 0.132 2592 Planarity : 0.004 0.036 2656 Dihedral : 6.796 89.875 2338 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.94 % Allowed : 24.57 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.20), residues: 2030 helix: 2.69 (0.14), residues: 1370 sheet: 0.15 (0.51), residues: 136 loop : -1.97 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 135 HIS 0.003 0.001 HIS E 488 PHE 0.015 0.001 PHE C 151 TYR 0.008 0.002 TYR C -4 ARG 0.006 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 1074) hydrogen bonds : angle 3.95097 ( 3171) covalent geometry : bond 0.00331 (15152) covalent geometry : angle 0.63222 (20770) *********************** 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 159 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 100 time to evaluate : 3.992 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: A 82 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9035 (tm-30) REVERT: A 140 LEU cc_start: 0.8910 (mm) cc_final: 0.8498 (mm) REVERT: A 283 LEU cc_start: 0.7209 (tm) cc_final: 0.6993 (tm) REVERT: D 82 GLN cc_start: 0.9338 (tm-30) cc_final: 0.9039 (tm-30) REVERT: D 140 LEU cc_start: 0.8852 (mm) cc_final: 0.8651 (mm) REVERT: D 384 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9103 (p) outliers start: 59 outliers final: 32 residues processed: 144 average time/residue: 1.1225 time to fit residues: 188.1048 Evaluate side-chains 131 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER 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 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 501 THR 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 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 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 282 LYS Chi-restraints excluded: chain E residue 501 THR 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 86 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 4 optimal weight: 0.0770 chunk 169 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 0 ASN E 0 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.069573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.050027 restraints weight = 52041.572| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.68 r_work: 0.2699 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15152 Z= 0.138 Angle : 0.639 13.196 20770 Z= 0.302 Chirality : 0.039 0.144 2592 Planarity : 0.004 0.035 2656 Dihedral : 6.581 87.960 2338 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.54 % Allowed : 24.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.20), residues: 2030 helix: 2.74 (0.14), residues: 1370 sheet: 0.17 (0.51), residues: 136 loop : -1.93 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 135 HIS 0.002 0.001 HIS E 276 PHE 0.017 0.001 PHE A 24 TYR 0.008 0.001 TYR C -4 ARG 0.007 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 1074) hydrogen bonds : angle 3.88821 ( 3171) covalent geometry : bond 0.00301 (15152) covalent geometry : angle 0.63869 (20770) *********************** 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 159 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 1.501 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: 0.9329 (tm-30) cc_final: 0.9025 (tm-30) REVERT: A 130 ASP cc_start: 0.8965 (m-30) cc_final: 0.8556 (p0) REVERT: A 283 LEU cc_start: 0.7186 (tm) cc_final: 0.6971 (tm) REVERT: D 82 GLN cc_start: 0.9342 (tm-30) cc_final: 0.9040 (tm-30) REVERT: D 384 THR cc_start: 0.9497 (OUTLIER) cc_final: 0.9066 (p) REVERT: D 388 ASP cc_start: 0.9371 (t0) cc_final: 0.8914 (t0) REVERT: D 458 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8711 (mt0) outliers start: 53 outliers final: 32 residues processed: 142 average time/residue: 0.8503 time to fit residues: 139.3506 Evaluate side-chains 132 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 407 ASP 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 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 282 LYS Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 504 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 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 145 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3368 r_free = 0.3368 target = 0.069092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.049539 restraints weight = 52612.647| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.70 r_work: 0.2682 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15152 Z= 0.167 Angle : 0.653 14.974 20770 Z= 0.310 Chirality : 0.040 0.156 2592 Planarity : 0.004 0.035 2656 Dihedral : 6.573 89.113 2338 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.60 % Allowed : 25.10 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.20), residues: 2030 helix: 2.74 (0.14), residues: 1370 sheet: 0.17 (0.51), residues: 136 loop : -1.93 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 369 HIS 0.003 0.001 HIS A 87 PHE 0.016 0.001 PHE A 24 TYR 0.008 0.001 TYR D 102 ARG 0.005 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 1074) hydrogen bonds : angle 3.91381 ( 3171) covalent geometry : bond 0.00378 (15152) covalent geometry : angle 0.65330 (20770) *********************** 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 155 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 101 time to evaluate : 1.500 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: A 82 GLN cc_start: 0.9337 (tm-30) cc_final: 0.9028 (tm-30) REVERT: A 130 ASP cc_start: 0.8953 (m-30) cc_final: 0.8610 (p0) REVERT: A 283 LEU cc_start: 0.7247 (tm) cc_final: 0.7040 (tm) REVERT: D 82 GLN cc_start: 0.9359 (tm-30) cc_final: 0.9058 (tm-30) REVERT: D 130 ASP cc_start: 0.8971 (m-30) cc_final: 0.8558 (p0) REVERT: D 384 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9155 (p) REVERT: E 56 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8779 (tp40) outliers start: 54 outliers final: 30 residues processed: 142 average time/residue: 0.8951 time to fit residues: 146.2846 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 : 1.620 ------------------------------------------------------------------------------- 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 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 128 VAL Chi-restraints excluded: chain C residue 141 VAL 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 282 LYS Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 504 SER 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 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 501 THR 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 200 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 191 optimal weight: 0.0670 chunk 42 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3388 r_free = 0.3388 target = 0.070208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.050733 restraints weight = 52240.926| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.72 r_work: 0.2708 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15152 Z= 0.133 Angle : 0.660 15.437 20770 Z= 0.309 Chirality : 0.039 0.150 2592 Planarity : 0.004 0.035 2656 Dihedral : 6.463 88.513 2338 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.67 % Allowed : 25.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.20), residues: 2030 helix: 2.74 (0.14), residues: 1370 sheet: 0.20 (0.51), residues: 136 loop : -1.89 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 369 HIS 0.002 0.000 HIS E 276 PHE 0.016 0.001 PHE A 24 TYR 0.009 0.002 TYR E 112 ARG 0.006 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 1074) hydrogen bonds : angle 3.85819 ( 3171) covalent geometry : bond 0.00288 (15152) covalent geometry : angle 0.65990 (20770) ********************** 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 140 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 1.516 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: A 82 GLN cc_start: 0.9330 (tm-30) cc_final: 0.8952 (tm-30) REVERT: A 130 ASP cc_start: 0.8950 (m-30) cc_final: 0.8585 (p0) REVERT: A 283 LEU cc_start: 0.7256 (tm) cc_final: 0.7053 (tm) REVERT: C 212 MET cc_start: 0.9463 (mmt) cc_final: 0.8739 (mmm) REVERT: D 82 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8973 (tm-30) REVERT: D 130 ASP cc_start: 0.8958 (m-30) cc_final: 0.8539 (p0) REVERT: D 283 LEU cc_start: 0.7358 (tm) cc_final: 0.6988 (tm) REVERT: D 384 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9062 (p) REVERT: D 388 ASP cc_start: 0.9364 (t0) cc_final: 0.8922 (t0) REVERT: E 56 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8756 (tp-100) REVERT: E 130 MET cc_start: 0.8685 (tpp) cc_final: 0.8470 (tpt) outliers start: 40 outliers final: 28 residues processed: 124 average time/residue: 0.9942 time to fit residues: 141.0795 Evaluate side-chains 128 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 353 MET 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 145 LEU 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 501 THR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 384 THR 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 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 501 THR 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 111 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 0 ASN D 458 GLN E 0 ASN E 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.069111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.049696 restraints weight = 52827.772| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.69 r_work: 0.2686 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15152 Z= 0.170 Angle : 0.672 14.920 20770 Z= 0.317 Chirality : 0.040 0.146 2592 Planarity : 0.004 0.034 2656 Dihedral : 6.495 88.323 2338 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.60 % Allowed : 26.23 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.20), residues: 2030 helix: 2.75 (0.14), residues: 1370 sheet: 0.20 (0.51), residues: 136 loop : -1.89 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 135 HIS 0.003 0.001 HIS A 87 PHE 0.015 0.001 PHE A 24 TYR 0.008 0.001 TYR D 102 ARG 0.006 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 1074) hydrogen bonds : angle 3.89319 ( 3171) covalent geometry : bond 0.00386 (15152) covalent geometry : angle 0.67220 (20770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8767.60 seconds wall clock time: 153 minutes 16.85 seconds (9196.85 seconds total)