Starting phenix.real_space_refine on Mon Nov 18 00:01:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/11_2024/8ipr_35641.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/11_2024/8ipr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/11_2024/8ipr_35641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/11_2024/8ipr_35641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/11_2024/8ipr_35641.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/11_2024/8ipr_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.46, per 1000 atoms: 0.64 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: 4.13 Conformation dependent library (CDL) restraints added in 2.0 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: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 20 through 41 removed outlier: 3.562A pdb=" N PHE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 108 Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.828A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 114' Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 126 through 161 Proline residue: A 142 - end of helix removed outlier: 4.267A pdb=" N VAL A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 202 removed outlier: 3.659A pdb=" N VAL A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 4.440A pdb=" N ALA A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 removed outlier: 5.925A pdb=" N ALA A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 220 through 269 removed outlier: 3.587A pdb=" N VAL A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Proline residue: A 245 - end of helix Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 277 through 319 removed outlier: 3.938A pdb=" N ALA A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.520A pdb=" N THR A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.514A pdb=" N ALA A 431 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 449 Processing helix chain 'A' and resid 464 through 477 removed outlier: 4.785A pdb=" N ARG A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'C' and resid -4 through 24 Processing helix chain 'C' and resid 35 through 80 removed outlier: 3.933A pdb=" N LEU C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 101 through 104 Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 112 through 134 removed outlier: 3.544A pdb=" N THR C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 134 through 142 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 183 removed outlier: 3.571A pdb=" N ILE C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 Processing helix chain 'C' and resid 195 through 246 removed outlier: 4.008A pdb=" N ARG C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 293 Proline residue: C 262 - end of helix removed outlier: 3.845A pdb=" N PHE C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Proline residue: C 267 - end of helix removed outlier: 3.997A pdb=" N HIS C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP C 280 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 345 Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 409 through 416 removed outlier: 3.816A pdb=" N GLU C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 462 through 479 Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 20 through 41 removed outlier: 3.582A pdb=" N PHE D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 108 Processing helix chain 'D' and resid 109 through 114 removed outlier: 3.826A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 114' Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 126 through 161 Proline residue: D 142 - end of helix removed outlier: 4.265A pdb=" N VAL D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 202 removed outlier: 3.654A pdb=" N VAL D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) Proline residue: D 180 - end of helix removed outlier: 4.409A pdb=" N ALA D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 removed outlier: 5.919A pdb=" N ALA D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 209 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 269 removed outlier: 3.627A pdb=" N VAL D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Proline residue: D 245 - end of helix Proline residue: D 253 - end of helix Processing helix chain 'D' and resid 277 through 319 removed outlier: 3.910A pdb=" N ALA D 281 " --> pdb=" O PRO D 277 " (cutoff:3.500A) Proline residue: D 287 - end of helix Proline residue: D 298 - end of helix Processing helix chain 'D' and resid 349 through 363 Processing helix chain 'D' and resid 385 through 391 Processing helix chain 'D' and resid 398 through 409 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.518A pdb=" N THR D 424 " --> pdb=" O GLY D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.800A pdb=" N VAL D 433 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 449 Processing helix chain 'D' and resid 464 through 477 removed outlier: 4.799A pdb=" N ARG D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLN D 470 " --> pdb=" O GLY D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid -4 through 24 Processing helix chain 'E' and resid 35 through 80 removed outlier: 3.944A pdb=" N LEU E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 91 Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 101 through 104 Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 112 through 134 removed outlier: 3.547A pdb=" N THR E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 134 through 142 Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 146 through 183 removed outlier: 3.571A pdb=" N ILE E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARG E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 Processing helix chain 'E' and resid 195 through 246 removed outlier: 4.004A pdb=" N ARG E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 293 Proline residue: E 262 - end of helix removed outlier: 3.829A pdb=" N PHE E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Proline residue: E 267 - end of helix removed outlier: 3.997A pdb=" N HIS E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP E 280 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 345 Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 399 through 408 Processing helix chain 'E' and resid 409 through 416 removed outlier: 3.822A pdb=" N GLU E 415 " --> pdb=" O GLU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 462 through 479 Processing helix chain 'E' and resid 489 through 494 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA2, first strand: chain 'C' and resid 318 through 320 Processing sheet with id=AA3, first strand: chain 'C' and resid 373 through 376 removed outlier: 6.213A pdb=" N ALA C 374 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL C 325 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL C 500 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 327 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 385 through 386 Processing sheet with id=AA5, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AA6, first strand: chain 'E' and resid 318 through 320 Processing sheet with id=AA7, first strand: chain 'E' and resid 373 through 376 removed outlier: 6.219A pdb=" N ALA E 374 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL E 325 " --> pdb=" O HIS E 498 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL E 500 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL E 327 " --> pdb=" O VAL E 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 385 through 386 1074 hydrogen bonds defined for protein. 3171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 4.72 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: 0.00 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: 2.960 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: 0.110 Set scattering table: 0.130 Process input model: 35.550 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- 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= 0.277 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 *********************** 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 : 1.646 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: 1.1671 time to fit residues: 251.6104 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 : 1.641 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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= 0.212 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 *********************** 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 : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ASN cc_start: 0.8067 (m-40) cc_final: 0.7794 (m-40) REVERT: E 24 ASN cc_start: 0.8093 (m-40) cc_final: 0.7852 (m-40) outliers start: 69 outliers final: 19 residues processed: 171 average time/residue: 1.0273 time to fit residues: 199.6565 Evaluate side-chains 120 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15152 Z= 0.281 Angle : 0.646 8.655 20770 Z= 0.316 Chirality : 0.040 0.144 2592 Planarity : 0.005 0.037 2656 Dihedral : 7.521 87.871 2338 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.74 % Allowed : 23.23 % 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: 1.89 (0.20), residues: 2030 helix: 2.54 (0.14), residues: 1366 sheet: 0.10 (0.50), residues: 132 loop : -2.08 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 135 HIS 0.003 0.001 HIS D 87 PHE 0.013 0.002 PHE D 291 TYR 0.012 0.002 TYR E 133 ARG 0.005 0.000 ARG A 138 *********************** 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 174 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 103 time to evaluate : 1.776 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 257 MET cc_start: 0.7678 (tmm) cc_final: 0.7419 (tmm) REVERT: C 24 ASN cc_start: 0.8120 (m-40) cc_final: 0.7845 (m-40) outliers start: 71 outliers final: 26 residues processed: 158 average time/residue: 0.8229 time to fit residues: 151.8483 Evaluate side-chains 124 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 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 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 181 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15152 Z= 0.217 Angle : 0.625 9.366 20770 Z= 0.301 Chirality : 0.039 0.137 2592 Planarity : 0.004 0.039 2656 Dihedral : 7.238 88.021 2338 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.21 % Allowed : 23.83 % Favored : 71.96 % 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: 1.94 (0.20), residues: 2030 helix: 2.55 (0.14), residues: 1372 sheet: 0.16 (0.51), residues: 132 loop : -2.04 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 54 HIS 0.004 0.001 HIS D 87 PHE 0.012 0.001 PHE C 151 TYR 0.008 0.002 TYR C -4 ARG 0.004 0.000 ARG A 98 *********************** 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: 63 poor density : 102 time to evaluate : 1.931 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 257 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7410 (tmm) REVERT: A 283 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7369 (tm) outliers start: 63 outliers final: 31 residues processed: 145 average time/residue: 0.9306 time to fit residues: 155.8977 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 : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 283 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 301 HIS Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 331 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 141 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 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 162 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 175 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15152 Z= 0.259 Angle : 0.634 10.785 20770 Z= 0.307 Chirality : 0.040 0.145 2592 Planarity : 0.004 0.035 2656 Dihedral : 7.028 89.094 2338 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.61 % Allowed : 23.50 % 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: 2.02 (0.20), residues: 2030 helix: 2.64 (0.14), residues: 1370 sheet: 0.12 (0.51), residues: 132 loop : -2.04 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 135 HIS 0.003 0.001 HIS D 87 PHE 0.013 0.002 PHE D 291 TYR 0.009 0.002 TYR D 102 ARG 0.003 0.000 ARG A 98 *********************** 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 170 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 101 time to evaluate : 1.689 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 257 MET cc_start: 0.7774 (tmm) cc_final: 0.7523 (tmm) REVERT: A 283 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7412 (tm) outliers start: 69 outliers final: 40 residues processed: 150 average time/residue: 0.8911 time to fit residues: 155.1593 Evaluate side-chains 137 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 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 C residue 507 VAL Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 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 501 THR 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 65 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2315 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= 0.235 Angle : 0.633 11.711 20770 Z= 0.306 Chirality : 0.040 0.135 2592 Planarity : 0.004 0.038 2656 Dihedral : 6.883 89.336 2338 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.21 % Allowed : 24.17 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.05 (0.20), residues: 2030 helix: 2.64 (0.14), residues: 1374 sheet: 0.11 (0.51), residues: 132 loop : -2.01 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 135 HIS 0.003 0.001 HIS E 488 PHE 0.014 0.001 PHE E 151 TYR 0.008 0.002 TYR E -4 ARG 0.008 0.000 ARG A 138 *********************** 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: 63 poor density : 100 time to evaluate : 1.601 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 257 MET cc_start: 0.7766 (tmm) cc_final: 0.7477 (tmm) REVERT: A 283 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7408 (tm) outliers start: 63 outliers final: 36 residues processed: 148 average time/residue: 0.8967 time to fit residues: 153.1934 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 : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 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 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 223 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 142 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 89 optimal weight: 0.0070 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2451 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= 0.184 Angle : 0.628 12.616 20770 Z= 0.300 Chirality : 0.039 0.140 2592 Planarity : 0.004 0.040 2656 Dihedral : 6.624 89.790 2338 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.81 % Allowed : 24.70 % 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: 2.15 (0.20), residues: 2030 helix: 2.71 (0.14), residues: 1370 sheet: 0.18 (0.51), residues: 136 loop : -1.93 (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 0.014 0.001 PHE C 151 TYR 0.014 0.002 TYR E -4 ARG 0.012 0.000 ARG D 408 *********************** 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 165 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 108 time to evaluate : 1.753 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 257 MET cc_start: 0.7791 (tmm) cc_final: 0.7493 (tmm) REVERT: A 283 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7395 (tm) outliers start: 57 outliers final: 27 residues processed: 146 average time/residue: 0.9371 time to fit residues: 157.8343 Evaluate side-chains 126 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 321 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 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 223 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 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 120 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15152 Z= 0.279 Angle : 0.659 13.294 20770 Z= 0.317 Chirality : 0.040 0.134 2592 Planarity : 0.004 0.047 2656 Dihedral : 6.659 89.846 2338 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.74 % Allowed : 25.03 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.20), residues: 2030 helix: 2.71 (0.14), residues: 1370 sheet: 0.23 (0.51), residues: 136 loop : -1.94 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 135 HIS 0.003 0.001 HIS D 87 PHE 0.014 0.001 PHE E 151 TYR 0.012 0.002 TYR E -4 ARG 0.011 0.000 ARG D 408 *********************** 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 156 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 100 time to evaluate : 1.591 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 257 MET cc_start: 0.7776 (tmm) cc_final: 0.7476 (tmm) REVERT: A 283 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7390 (tm) REVERT: C 130 MET cc_start: 0.7945 (tpp) cc_final: 0.7510 (ttm) REVERT: C 376 MET cc_start: 0.8278 (tpp) cc_final: 0.7978 (ttt) outliers start: 56 outliers final: 30 residues processed: 141 average time/residue: 0.9122 time to fit residues: 149.0685 Evaluate side-chains 128 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 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 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 6 CYS 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 282 LYS Chi-restraints excluded: chain E residue 501 THR 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 177 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 170 optimal weight: 0.0370 chunk 181 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15152 Z= 0.189 Angle : 0.648 13.677 20770 Z= 0.307 Chirality : 0.039 0.137 2592 Planarity : 0.004 0.040 2656 Dihedral : 6.438 89.478 2338 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.87 % Allowed : 25.83 % 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: 2.22 (0.20), residues: 2030 helix: 2.77 (0.14), residues: 1368 sheet: 0.25 (0.51), residues: 136 loop : -1.94 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 369 HIS 0.002 0.000 HIS E 276 PHE 0.013 0.001 PHE A 24 TYR 0.012 0.002 TYR E -4 ARG 0.010 0.000 ARG D 408 *********************** 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 145 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 1.379 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 257 MET cc_start: 0.7767 (tmm) cc_final: 0.7477 (tmm) REVERT: A 283 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7387 (tm) REVERT: C 376 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7934 (ttt) REVERT: E 376 MET cc_start: 0.8075 (tpp) cc_final: 0.7825 (ttt) outliers start: 43 outliers final: 22 residues processed: 131 average time/residue: 0.9652 time to fit residues: 144.0719 Evaluate side-chains 125 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 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 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 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 119 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15152 Z= 0.244 Angle : 0.676 14.758 20770 Z= 0.321 Chirality : 0.040 0.142 2592 Planarity : 0.004 0.041 2656 Dihedral : 6.457 88.236 2338 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.67 % Allowed : 26.17 % 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: 2.23 (0.20), residues: 2030 helix: 2.76 (0.14), residues: 1370 sheet: 0.22 (0.50), 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 0.014 0.001 PHE A 24 TYR 0.010 0.002 TYR E -4 ARG 0.009 0.000 ARG D 408 ********************** 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 139 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 1.687 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 257 MET cc_start: 0.7781 (tmm) cc_final: 0.7486 (tmm) REVERT: A 283 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7424 (tm) REVERT: C 212 MET cc_start: 0.8203 (mmt) cc_final: 0.7951 (mmm) REVERT: C 376 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7994 (ttt) REVERT: D 283 LEU cc_start: 0.7674 (tm) cc_final: 0.7307 (tm) REVERT: E 130 MET cc_start: 0.7756 (tpt) cc_final: 0.7490 (tpt) outliers start: 40 outliers final: 25 residues processed: 127 average time/residue: 0.9397 time to fit residues: 136.9930 Evaluate side-chains 123 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 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 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 376 MET Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 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 127 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 147 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.070871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.051482 restraints weight = 52296.311| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.73 r_work: 0.2739 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2861 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= 0.183 Angle : 0.665 14.025 20770 Z= 0.313 Chirality : 0.039 0.157 2592 Planarity : 0.004 0.037 2656 Dihedral : 6.280 88.827 2338 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.00 % Allowed : 27.04 % Favored : 70.96 % 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: 2.22 (0.20), residues: 2030 helix: 2.76 (0.14), residues: 1372 sheet: 0.22 (0.50), residues: 136 loop : -1.93 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 369 HIS 0.003 0.000 HIS E 276 PHE 0.012 0.001 PHE A 24 TYR 0.012 0.001 TYR E -4 ARG 0.012 0.000 ARG A 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3769.42 seconds wall clock time: 70 minutes 7.56 seconds (4207.56 seconds total)