Starting phenix.real_space_refine on Sun Aug 24 05:35:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxo_27771/08_2025/8dxo_27771.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxo_27771/08_2025/8dxo_27771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dxo_27771/08_2025/8dxo_27771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxo_27771/08_2025/8dxo_27771.map" model { file = "/net/cci-nas-00/data/ceres_data/8dxo_27771/08_2025/8dxo_27771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxo_27771/08_2025/8dxo_27771.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 11561 2.51 5 N 2760 2.21 5 O 3031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17499 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2481 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2501 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "D" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2497 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "E" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "F" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2516 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain breaks: 2 Chain: "G" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2490 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain breaks: 2 Time building chain proxies: 4.49, per 1000 atoms: 0.26 Number of scatterers: 17499 At special positions: 0 Unit cell: (122.1, 114.4, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 3031 8.00 N 2760 7.00 C 11561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 115 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 308 " distance=2.03 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 832.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 7 sheets defined 72.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 22 through 48 removed outlier: 4.063A pdb=" N VAL A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.614A pdb=" N TYR A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.702A pdb=" N LYS A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 126' Processing helix chain 'A' and resid 126 through 148 removed outlier: 3.682A pdb=" N TRP A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.396A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 253 Processing helix chain 'A' and resid 259 through 283 removed outlier: 3.764A pdb=" N ALA A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 342 Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 368 through 381 removed outlier: 4.149A pdb=" N GLN A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.543A pdb=" N ARG A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 removed outlier: 4.515A pdb=" N GLU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 Proline residue: B 22 - end of helix Processing helix chain 'B' and resid 23 through 48 removed outlier: 5.311A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.856A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.654A pdb=" N LYS B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.665A pdb=" N SER B 142 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.625A pdb=" N LYS B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.426A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 259 through 283 removed outlier: 3.745A pdb=" N LEU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 341 removed outlier: 3.687A pdb=" N SER B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 367 through 381 removed outlier: 3.628A pdb=" N ALA B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.502A pdb=" N ARG B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 removed outlier: 4.106A pdb=" N GLU B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 47 removed outlier: 4.187A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 45 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.855A pdb=" N TYR C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 143 removed outlier: 3.708A pdb=" N LYS C 125 " --> pdb=" O HIS C 121 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 126 " --> pdb=" O TRP C 122 " (cutoff:3.500A) Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.844A pdb=" N ASP C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 175 removed outlier: 4.398A pdb=" N THR C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU C 175 " --> pdb=" O THR C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 removed outlier: 4.185A pdb=" N GLU C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 283 removed outlier: 4.212A pdb=" N TYR C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 removed outlier: 4.074A pdb=" N VAL C 287 " --> pdb=" O VAL C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 313 through 343 removed outlier: 3.628A pdb=" N PHE C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 343 " --> pdb=" O TYR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.829A pdb=" N ALA C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'D' and resid 22 through 47 removed outlier: 3.548A pdb=" N VAL D 26 " --> pdb=" O PRO D 22 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.718A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.528A pdb=" N LYS D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 142 removed outlier: 3.971A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 167 removed outlier: 3.949A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 4.153A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 removed outlier: 3.891A pdb=" N LEU D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 282 removed outlier: 3.632A pdb=" N VAL D 263 " --> pdb=" O TYR D 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 341 removed outlier: 3.990A pdb=" N LYS D 318 " --> pdb=" O HIS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 359 removed outlier: 3.869A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 380 Processing helix chain 'D' and resid 383 through 390 removed outlier: 3.515A pdb=" N ARG D 387 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 removed outlier: 3.953A pdb=" N GLU D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.759A pdb=" N VAL E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.634A pdb=" N TYR E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 142 removed outlier: 3.511A pdb=" N VAL E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 167 removed outlier: 3.952A pdb=" N PHE E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 176 removed outlier: 3.778A pdb=" N THR E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 253 removed outlier: 4.008A pdb=" N GLU E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 284 Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 312 through 344 removed outlier: 3.743A pdb=" N PHE E 316 " --> pdb=" O MET E 312 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS E 318 " --> pdb=" O HIS E 314 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 359 Processing helix chain 'E' and resid 367 through 381 removed outlier: 3.625A pdb=" N ALA E 371 " --> pdb=" O LYS E 367 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.924A pdb=" N PHE E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 405 removed outlier: 3.604A pdb=" N GLU E 397 " --> pdb=" O SER E 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 49 removed outlier: 3.889A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.689A pdb=" N TYR F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 143 Processing helix chain 'F' and resid 152 through 167 removed outlier: 3.599A pdb=" N GLU F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 177 removed outlier: 3.583A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU F 177 " --> pdb=" O ARG F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 253 removed outlier: 3.614A pdb=" N LEU F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 283 removed outlier: 3.718A pdb=" N ALA F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET F 261 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 342 removed outlier: 3.835A pdb=" N PHE F 316 " --> pdb=" O MET F 312 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 342 " --> pdb=" O LEU F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 359 removed outlier: 3.552A pdb=" N ARG F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 removed outlier: 3.674A pdb=" N ALA F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 379 " --> pdb=" O HIS F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.957A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 405 removed outlier: 3.724A pdb=" N LEU F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 47 removed outlier: 3.827A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 47 " --> pdb=" O CYS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.767A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.820A pdb=" N LYS G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR G 126 " --> pdb=" O TRP G 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 121 through 126' Processing helix chain 'G' and resid 126 through 142 removed outlier: 3.643A pdb=" N LEU G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 165 removed outlier: 3.849A pdb=" N ILE G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 235 through 253 removed outlier: 3.561A pdb=" N ALA G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 283 removed outlier: 3.696A pdb=" N VAL G 263 " --> pdb=" O TYR G 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER G 281 " --> pdb=" O ILE G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 287 removed outlier: 3.679A pdb=" N VAL G 287 " --> pdb=" O VAL G 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 284 through 287' Processing helix chain 'G' and resid 312 through 343 removed outlier: 3.908A pdb=" N PHE G 316 " --> pdb=" O MET G 312 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER G 317 " --> pdb=" O ALA G 313 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS G 318 " --> pdb=" O HIS G 314 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE G 321 " --> pdb=" O SER G 317 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 359 Processing helix chain 'G' and resid 367 through 379 removed outlier: 3.958A pdb=" N GLN G 379 " --> pdb=" O HIS G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 390 removed outlier: 3.553A pdb=" N LYS G 386 " --> pdb=" O PRO G 382 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL G 390 " --> pdb=" O LYS G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 405 removed outlier: 3.743A pdb=" N LEU G 405 " --> pdb=" O LYS G 401 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 56 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 56 1049 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5197 1.34 - 1.46: 4695 1.46 - 1.58: 7853 1.58 - 1.70: 0 1.70 - 1.81: 224 Bond restraints: 17969 Sorted by residual: bond pdb=" N ASN B 368 " pdb=" CA ASN B 368 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.38e+00 bond pdb=" C ASP E 381 " pdb=" N PRO E 382 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.31e+00 bond pdb=" CB PHE A 273 " pdb=" CG PHE A 273 " ideal model delta sigma weight residual 1.502 1.479 0.023 2.30e-02 1.89e+03 9.84e-01 bond pdb=" C ASP A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.57e-01 bond pdb=" C VAL A 327 " pdb=" O VAL A 327 " ideal model delta sigma weight residual 1.237 1.227 0.010 1.17e-02 7.31e+03 7.72e-01 ... (remaining 17964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 23836 1.61 - 3.22: 355 3.22 - 4.84: 58 4.84 - 6.45: 7 6.45 - 8.06: 2 Bond angle restraints: 24258 Sorted by residual: angle pdb=" N LEU G 315 " pdb=" CA LEU G 315 " pdb=" C LEU G 315 " ideal model delta sigma weight residual 113.18 108.63 4.55 1.33e+00 5.65e-01 1.17e+01 angle pdb=" N MET G 48 " pdb=" CA MET G 48 " pdb=" C MET G 48 " ideal model delta sigma weight residual 113.18 108.98 4.20 1.33e+00 5.65e-01 9.99e+00 angle pdb=" N GLU E 254 " pdb=" CA GLU E 254 " pdb=" C GLU E 254 " ideal model delta sigma weight residual 114.56 110.69 3.87 1.27e+00 6.20e-01 9.29e+00 angle pdb=" C ALA F 278 " pdb=" N TYR F 279 " pdb=" CA TYR F 279 " ideal model delta sigma weight residual 120.68 115.61 5.07 1.70e+00 3.46e-01 8.91e+00 angle pdb=" C ALA A 278 " pdb=" N TYR A 279 " pdb=" CA TYR A 279 " ideal model delta sigma weight residual 122.06 116.58 5.48 1.86e+00 2.89e-01 8.68e+00 ... (remaining 24253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9417 17.93 - 35.87: 958 35.87 - 53.80: 166 53.80 - 71.74: 22 71.74 - 89.67: 19 Dihedral angle restraints: 10582 sinusoidal: 4307 harmonic: 6275 Sorted by residual: dihedral pdb=" CA ASP B 25 " pdb=" C ASP B 25 " pdb=" N VAL B 26 " pdb=" CA VAL B 26 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL G 47 " pdb=" C VAL G 47 " pdb=" N MET G 48 " pdb=" CA MET G 48 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ILE B 257 " pdb=" C ILE B 257 " pdb=" N LEU B 258 " pdb=" CA LEU B 258 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 10579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1953 0.035 - 0.070: 516 0.070 - 0.105: 138 0.105 - 0.140: 38 0.140 - 0.174: 2 Chirality restraints: 2647 Sorted by residual: chirality pdb=" CG LEU B 392 " pdb=" CB LEU B 392 " pdb=" CD1 LEU B 392 " pdb=" CD2 LEU B 392 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE G 363 " pdb=" N ILE G 363 " pdb=" C ILE G 363 " pdb=" CB ILE G 363 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 2644 not shown) Planarity restraints: 2955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 148 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO C 149 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 37 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C MET C 37 " -0.029 2.00e-02 2.50e+03 pdb=" O MET C 37 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE C 38 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 145 " -0.013 2.00e-02 2.50e+03 1.00e-02 2.52e+00 pdb=" CG TRP D 145 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 145 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP D 145 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 145 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 145 " -0.001 2.00e-02 2.50e+03 ... (remaining 2952 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1326 2.74 - 3.28: 17965 3.28 - 3.82: 28083 3.82 - 4.36: 31371 4.36 - 4.90: 55105 Nonbonded interactions: 133850 Sorted by model distance: nonbonded pdb=" O LYS C 239 " pdb=" OE1 GLU C 243 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR D 123 " pdb=" OD1 ASN D 280 " model vdw 2.199 3.040 nonbonded pdb=" NE2 HIS F 134 " pdb=" OH TYR F 279 " model vdw 2.201 3.120 nonbonded pdb=" NH2 ARG C 355 " pdb=" OD1 ASP C 365 " model vdw 2.212 3.120 nonbonded pdb=" OH TYR G 123 " pdb=" OD1 ASN G 280 " model vdw 2.233 3.040 ... (remaining 133845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'B' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'C' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'D' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'E' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'F' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'G' and (resid 16 through 175 or resid 177 or resid 235 through 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.750 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.370 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.002 0.029 17983 Z= 0.116 Angle : 0.525 8.061 24286 Z= 0.293 Chirality : 0.035 0.174 2647 Planarity : 0.003 0.050 2955 Dihedral : 14.798 89.672 6478 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 2059 helix: 1.45 (0.15), residues: 1328 sheet: -0.14 (0.46), residues: 139 loop : -2.52 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.015 0.001 TYR C 343 PHE 0.023 0.001 PHE G 289 TRP 0.027 0.001 TRP D 145 HIS 0.008 0.001 HIS B 375 Details of bonding type rmsd covalent geometry : bond 0.00237 (17969) covalent geometry : angle 0.52527 (24258) SS BOND : bond 0.00210 ( 14) SS BOND : angle 0.44414 ( 28) hydrogen bonds : bond 0.13857 ( 1049) hydrogen bonds : angle 5.80956 ( 3117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.701 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: D 143 ASN cc_start: 0.7896 (t0) cc_final: 0.7519 (t0) REVERT: F 363 ILE cc_start: 0.7979 (mm) cc_final: 0.7626 (mm) REVERT: G 377 ILE cc_start: 0.8882 (tp) cc_final: 0.8545 (tp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.1521 time to fit residues: 79.2028 Evaluate side-chains 281 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 309 ASN A 310 HIS A 368 ASN B 46 GLN B 237 GLN C 49 GLN C 113 GLN C 251 HIS C 314 HIS D 112 ASN D 157 HIS E 106 GLN E 112 ASN F 309 ASN G 298 GLN G 310 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.181384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141810 restraints weight = 25748.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.139459 restraints weight = 16893.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141066 restraints weight = 17540.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.141180 restraints weight = 11422.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141510 restraints weight = 10356.282| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17983 Z= 0.174 Angle : 0.552 8.384 24286 Z= 0.297 Chirality : 0.040 0.141 2647 Planarity : 0.004 0.059 2955 Dihedral : 4.152 30.026 2283 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.65 % Allowed : 10.77 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.20), residues: 2059 helix: 1.73 (0.15), residues: 1360 sheet: -0.26 (0.46), residues: 139 loop : -2.57 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 387 TYR 0.028 0.002 TYR A 279 PHE 0.027 0.002 PHE A 158 TRP 0.014 0.001 TRP D 145 HIS 0.009 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00402 (17969) covalent geometry : angle 0.55171 (24258) SS BOND : bond 0.00210 ( 14) SS BOND : angle 0.53364 ( 28) hydrogen bonds : bond 0.04894 ( 1049) hydrogen bonds : angle 4.23637 ( 3117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 293 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 376 MET cc_start: 0.7837 (tpp) cc_final: 0.7267 (tpp) REVERT: D 143 ASN cc_start: 0.8411 (t0) cc_final: 0.7980 (t0) REVERT: D 158 PHE cc_start: 0.7676 (t80) cc_final: 0.7340 (t80) REVERT: F 363 ILE cc_start: 0.8054 (mm) cc_final: 0.7676 (mm) REVERT: G 377 ILE cc_start: 0.8980 (tp) cc_final: 0.8702 (tp) outliers start: 32 outliers final: 23 residues processed: 310 average time/residue: 0.1255 time to fit residues: 57.7228 Evaluate side-chains 290 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 267 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 207 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 113 GLN A 309 ASN A 398 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN C 251 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.183427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.143750 restraints weight = 25958.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140064 restraints weight = 17989.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141484 restraints weight = 18542.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142753 restraints weight = 11491.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142862 restraints weight = 10219.215| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17983 Z= 0.123 Angle : 0.491 6.795 24286 Z= 0.264 Chirality : 0.038 0.131 2647 Planarity : 0.003 0.056 2955 Dihedral : 4.043 29.535 2283 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.27 % Allowed : 13.81 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.20), residues: 2059 helix: 1.79 (0.15), residues: 1377 sheet: -0.22 (0.46), residues: 139 loop : -2.62 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.027 0.001 TYR A 279 PHE 0.028 0.001 PHE A 158 TRP 0.019 0.001 TRP B 170 HIS 0.009 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00275 (17969) covalent geometry : angle 0.49132 (24258) SS BOND : bond 0.00192 ( 14) SS BOND : angle 0.44318 ( 28) hydrogen bonds : bond 0.04086 ( 1049) hydrogen bonds : angle 3.88735 ( 3117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 297 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 TRP cc_start: 0.6993 (t60) cc_final: 0.6397 (t60) REVERT: B 351 PHE cc_start: 0.6956 (m-80) cc_final: 0.6681 (m-80) REVERT: C 248 PHE cc_start: 0.6837 (t80) cc_final: 0.6623 (t80) REVERT: C 330 TYR cc_start: 0.8109 (t80) cc_final: 0.7879 (t80) REVERT: C 355 ARG cc_start: 0.6332 (mtt180) cc_final: 0.6028 (mtm110) REVERT: C 376 MET cc_start: 0.7852 (tpp) cc_final: 0.6814 (mpp) REVERT: D 37 MET cc_start: 0.7549 (tpt) cc_final: 0.7119 (tmm) REVERT: D 143 ASN cc_start: 0.8341 (t0) cc_final: 0.7931 (t0) REVERT: D 243 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7156 (mm-30) REVERT: F 105 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9032 (tt) REVERT: F 363 ILE cc_start: 0.8061 (mm) cc_final: 0.7709 (mm) REVERT: G 242 PHE cc_start: 0.8522 (m-80) cc_final: 0.8299 (m-80) REVERT: G 377 ILE cc_start: 0.8984 (tp) cc_final: 0.8708 (tp) outliers start: 44 outliers final: 28 residues processed: 318 average time/residue: 0.1216 time to fit residues: 57.6034 Evaluate side-chains 299 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 166 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 207 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN B 106 GLN C 251 HIS F 305 ASN F 309 ASN G 398 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.184989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145256 restraints weight = 26014.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144073 restraints weight = 17397.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145021 restraints weight = 16610.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145523 restraints weight = 11372.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145677 restraints weight = 10313.140| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17983 Z= 0.106 Angle : 0.468 7.918 24286 Z= 0.251 Chirality : 0.037 0.133 2647 Planarity : 0.003 0.055 2955 Dihedral : 3.924 29.177 2283 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.89 % Allowed : 15.57 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.20), residues: 2059 helix: 1.89 (0.15), residues: 1370 sheet: -0.23 (0.45), residues: 141 loop : -2.57 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.026 0.001 TYR A 279 PHE 0.028 0.001 PHE F 41 TRP 0.017 0.001 TRP E 170 HIS 0.007 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00233 (17969) covalent geometry : angle 0.46857 (24258) SS BOND : bond 0.00164 ( 14) SS BOND : angle 0.39737 ( 28) hydrogen bonds : bond 0.03669 ( 1049) hydrogen bonds : angle 3.71028 ( 3117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 306 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 TRP cc_start: 0.6905 (t60) cc_final: 0.6402 (t60) REVERT: C 243 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6735 (mm-30) REVERT: C 246 LYS cc_start: 0.7999 (mtmm) cc_final: 0.7653 (mttm) REVERT: C 248 PHE cc_start: 0.7050 (t80) cc_final: 0.6826 (t80) REVERT: C 376 MET cc_start: 0.7819 (tpp) cc_final: 0.6833 (tpp) REVERT: D 37 MET cc_start: 0.7476 (tpt) cc_final: 0.7068 (tmm) REVERT: D 143 ASN cc_start: 0.8209 (t0) cc_final: 0.7818 (t0) REVERT: D 347 ARG cc_start: 0.7482 (ttm170) cc_final: 0.6337 (mpp-170) REVERT: F 105 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9099 (tt) REVERT: F 363 ILE cc_start: 0.8030 (mm) cc_final: 0.7675 (mm) REVERT: F 373 MET cc_start: 0.7409 (mmm) cc_final: 0.7188 (mmm) REVERT: G 242 PHE cc_start: 0.8357 (m-80) cc_final: 0.8048 (m-80) REVERT: G 377 ILE cc_start: 0.8976 (tp) cc_final: 0.8723 (tp) outliers start: 56 outliers final: 38 residues processed: 331 average time/residue: 0.1349 time to fit residues: 66.5851 Evaluate side-chains 317 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 354 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 92 optimal weight: 0.0070 chunk 191 optimal weight: 0.0000 chunk 163 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 309 ASN C 251 HIS G 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.185311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.145661 restraints weight = 25825.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143951 restraints weight = 16944.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145052 restraints weight = 16842.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145577 restraints weight = 11306.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145736 restraints weight = 10357.469| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17983 Z= 0.105 Angle : 0.468 7.201 24286 Z= 0.252 Chirality : 0.037 0.146 2647 Planarity : 0.003 0.053 2955 Dihedral : 3.874 29.037 2283 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.04 % Allowed : 16.70 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.20), residues: 2059 helix: 1.89 (0.15), residues: 1374 sheet: -0.16 (0.46), residues: 141 loop : -2.56 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 344 TYR 0.023 0.001 TYR A 279 PHE 0.027 0.001 PHE G 158 TRP 0.017 0.001 TRP E 170 HIS 0.006 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00231 (17969) covalent geometry : angle 0.46797 (24258) SS BOND : bond 0.00155 ( 14) SS BOND : angle 0.36070 ( 28) hydrogen bonds : bond 0.03562 ( 1049) hydrogen bonds : angle 3.65953 ( 3117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.7048 (mtp) cc_final: 0.6801 (mtp) REVERT: B 145 TRP cc_start: 0.6903 (t60) cc_final: 0.6406 (t60) REVERT: C 248 PHE cc_start: 0.7045 (t80) cc_final: 0.6818 (t80) REVERT: D 37 MET cc_start: 0.7478 (tpt) cc_final: 0.7096 (tmm) REVERT: D 143 ASN cc_start: 0.8193 (t0) cc_final: 0.7837 (t0) REVERT: D 347 ARG cc_start: 0.7433 (ttm170) cc_final: 0.6267 (mpp-170) REVERT: F 363 ILE cc_start: 0.8041 (mm) cc_final: 0.7681 (mm) REVERT: G 108 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.7997 (m-80) REVERT: G 377 ILE cc_start: 0.8977 (tp) cc_final: 0.8757 (tp) REVERT: G 403 LEU cc_start: 0.8870 (mm) cc_final: 0.8625 (mm) outliers start: 59 outliers final: 44 residues processed: 326 average time/residue: 0.1311 time to fit residues: 63.7915 Evaluate side-chains 320 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 370 PHE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 376 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 109 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN A 368 ASN C 251 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.183487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143330 restraints weight = 25654.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141445 restraints weight = 16822.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142854 restraints weight = 17697.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143151 restraints weight = 11706.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.143463 restraints weight = 10426.315| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17983 Z= 0.123 Angle : 0.500 11.179 24286 Z= 0.263 Chirality : 0.038 0.144 2647 Planarity : 0.003 0.053 2955 Dihedral : 3.875 28.947 2283 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.45 % Allowed : 17.16 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.20), residues: 2059 helix: 1.84 (0.15), residues: 1377 sheet: -0.15 (0.46), residues: 141 loop : -2.57 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 344 TYR 0.022 0.001 TYR A 279 PHE 0.027 0.001 PHE D 158 TRP 0.019 0.001 TRP D 23 HIS 0.008 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00284 (17969) covalent geometry : angle 0.49965 (24258) SS BOND : bond 0.00176 ( 14) SS BOND : angle 0.40717 ( 28) hydrogen bonds : bond 0.03742 ( 1049) hydrogen bonds : angle 3.66113 ( 3117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 290 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 250 LEU cc_start: 0.7642 (pp) cc_final: 0.7327 (mt) REVERT: B 145 TRP cc_start: 0.6927 (t60) cc_final: 0.6430 (t60) REVERT: C 273 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7912 (t80) REVERT: D 37 MET cc_start: 0.7467 (tpt) cc_final: 0.7096 (tmm) REVERT: D 143 ASN cc_start: 0.8250 (t0) cc_final: 0.7867 (t0) REVERT: D 347 ARG cc_start: 0.7370 (ttm170) cc_final: 0.6218 (mpp-170) REVERT: D 351 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: E 108 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8723 (m-80) REVERT: F 342 PHE cc_start: 0.8195 (m-10) cc_final: 0.7802 (m-10) REVERT: F 363 ILE cc_start: 0.8074 (mm) cc_final: 0.7700 (mm) REVERT: G 108 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: G 377 ILE cc_start: 0.9009 (tp) cc_final: 0.8723 (tp) outliers start: 67 outliers final: 47 residues processed: 326 average time/residue: 0.1255 time to fit residues: 61.8938 Evaluate side-chains 330 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 3 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 173 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.184146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.143610 restraints weight = 25851.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.142728 restraints weight = 18887.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143514 restraints weight = 16379.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144079 restraints weight = 11636.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144277 restraints weight = 10241.672| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17983 Z= 0.116 Angle : 0.507 10.671 24286 Z= 0.266 Chirality : 0.038 0.163 2647 Planarity : 0.003 0.052 2955 Dihedral : 3.871 29.085 2283 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.20 % Allowed : 18.04 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.20), residues: 2059 helix: 1.82 (0.15), residues: 1377 sheet: -0.15 (0.46), residues: 141 loop : -2.53 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 387 TYR 0.022 0.001 TYR A 279 PHE 0.028 0.001 PHE D 158 TRP 0.020 0.001 TRP D 23 HIS 0.008 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00264 (17969) covalent geometry : angle 0.50696 (24258) SS BOND : bond 0.00167 ( 14) SS BOND : angle 0.36904 ( 28) hydrogen bonds : bond 0.03612 ( 1049) hydrogen bonds : angle 3.64591 ( 3117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 0.713 Fit side-chains REVERT: A 250 LEU cc_start: 0.7645 (pp) cc_final: 0.7312 (mt) REVERT: B 145 TRP cc_start: 0.6930 (t60) cc_final: 0.6402 (t60) REVERT: C 248 PHE cc_start: 0.7009 (t80) cc_final: 0.6719 (t80) REVERT: D 37 MET cc_start: 0.7439 (tpt) cc_final: 0.7113 (tmm) REVERT: D 351 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: F 342 PHE cc_start: 0.8187 (m-10) cc_final: 0.7761 (m-10) REVERT: F 363 ILE cc_start: 0.8124 (mm) cc_final: 0.7744 (mm) REVERT: F 373 MET cc_start: 0.7356 (mmm) cc_final: 0.7111 (mmm) REVERT: G 18 ARG cc_start: 0.7750 (ppt170) cc_final: 0.7451 (ppt170) REVERT: G 108 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: G 377 ILE cc_start: 0.8974 (tp) cc_final: 0.8761 (tp) REVERT: G 403 LEU cc_start: 0.8840 (mm) cc_final: 0.8625 (mm) outliers start: 62 outliers final: 52 residues processed: 325 average time/residue: 0.1360 time to fit residues: 66.4612 Evaluate side-chains 333 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 279 TYR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 334 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 100 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN C 251 HIS ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS ** F 106 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 = 0.4204 r_free = 0.4204 target = 0.179388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.139596 restraints weight = 25778.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137233 restraints weight = 22145.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138582 restraints weight = 19169.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139454 restraints weight = 12141.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139759 restraints weight = 11177.579| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17983 Z= 0.187 Angle : 0.570 10.186 24286 Z= 0.302 Chirality : 0.041 0.222 2647 Planarity : 0.003 0.053 2955 Dihedral : 4.045 28.952 2283 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.25 % Allowed : 18.20 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.20), residues: 2059 helix: 1.66 (0.15), residues: 1385 sheet: -0.14 (0.46), residues: 137 loop : -2.64 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 387 TYR 0.020 0.001 TYR A 279 PHE 0.028 0.002 PHE D 158 TRP 0.023 0.002 TRP D 23 HIS 0.007 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00446 (17969) covalent geometry : angle 0.56968 (24258) SS BOND : bond 0.00251 ( 14) SS BOND : angle 0.52778 ( 28) hydrogen bonds : bond 0.04466 ( 1049) hydrogen bonds : angle 3.85338 ( 3117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 280 time to evaluate : 0.522 Fit side-chains REVERT: A 250 LEU cc_start: 0.7673 (pp) cc_final: 0.7406 (mt) REVERT: A 273 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7110 (t80) REVERT: A 373 MET cc_start: 0.7025 (mtp) cc_final: 0.6781 (mtp) REVERT: B 145 TRP cc_start: 0.6816 (t60) cc_final: 0.6390 (t60) REVERT: D 37 MET cc_start: 0.7526 (tpt) cc_final: 0.7154 (tmm) REVERT: D 143 ASN cc_start: 0.8282 (t0) cc_final: 0.7883 (t0) REVERT: D 351 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6219 (m-80) REVERT: E 156 GLU cc_start: 0.8514 (tt0) cc_final: 0.7971 (tm-30) REVERT: F 363 ILE cc_start: 0.8202 (mm) cc_final: 0.7814 (mm) REVERT: F 373 MET cc_start: 0.7389 (mmm) cc_final: 0.7152 (mmm) REVERT: G 108 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8594 (m-10) REVERT: G 377 ILE cc_start: 0.8998 (tp) cc_final: 0.8703 (tp) outliers start: 63 outliers final: 51 residues processed: 315 average time/residue: 0.1236 time to fit residues: 59.0501 Evaluate side-chains 321 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 334 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 184 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.182291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141921 restraints weight = 25662.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140120 restraints weight = 17669.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141649 restraints weight = 17636.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141722 restraints weight = 11998.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142414 restraints weight = 10601.282| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17983 Z= 0.132 Angle : 0.539 10.025 24286 Z= 0.283 Chirality : 0.038 0.159 2647 Planarity : 0.003 0.051 2955 Dihedral : 4.011 29.305 2283 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.35 % Allowed : 18.81 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.20), residues: 2059 helix: 1.75 (0.15), residues: 1370 sheet: -0.06 (0.46), residues: 137 loop : -2.53 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.022 0.001 TYR A 279 PHE 0.031 0.001 PHE G 158 TRP 0.024 0.002 TRP D 23 HIS 0.007 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00303 (17969) covalent geometry : angle 0.53873 (24258) SS BOND : bond 0.00202 ( 14) SS BOND : angle 0.42922 ( 28) hydrogen bonds : bond 0.03901 ( 1049) hydrogen bonds : angle 3.77610 ( 3117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 285 time to evaluate : 0.715 Fit side-chains REVERT: A 250 LEU cc_start: 0.7714 (pp) cc_final: 0.7457 (mt) REVERT: A 273 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7088 (t80) REVERT: A 373 MET cc_start: 0.7146 (mtp) cc_final: 0.6876 (mtp) REVERT: B 145 TRP cc_start: 0.6800 (t60) cc_final: 0.6370 (t60) REVERT: C 248 PHE cc_start: 0.6897 (t80) cc_final: 0.6561 (t80) REVERT: D 37 MET cc_start: 0.7445 (tpt) cc_final: 0.7026 (tmm) REVERT: D 143 ASN cc_start: 0.8322 (t0) cc_final: 0.7955 (t0) REVERT: D 351 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.6438 (m-80) REVERT: E 156 GLU cc_start: 0.8559 (tt0) cc_final: 0.7989 (tm-30) REVERT: F 342 PHE cc_start: 0.8283 (m-10) cc_final: 0.7817 (m-10) REVERT: F 363 ILE cc_start: 0.8142 (mm) cc_final: 0.7768 (mm) REVERT: G 18 ARG cc_start: 0.7773 (ppt170) cc_final: 0.7509 (ppt170) REVERT: G 108 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8375 (m-10) REVERT: G 248 PHE cc_start: 0.7735 (t80) cc_final: 0.7435 (t80) REVERT: G 377 ILE cc_start: 0.8956 (tp) cc_final: 0.8684 (tp) outliers start: 65 outliers final: 53 residues processed: 322 average time/residue: 0.1251 time to fit residues: 61.1939 Evaluate side-chains 334 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 334 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.5980 chunk 188 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 193 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 HIS C 368 ASN D 309 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.182605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.141651 restraints weight = 25589.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141099 restraints weight = 17435.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141851 restraints weight = 15831.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.142085 restraints weight = 11973.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.142337 restraints weight = 10218.176| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17983 Z= 0.125 Angle : 0.539 10.007 24286 Z= 0.283 Chirality : 0.038 0.159 2647 Planarity : 0.003 0.051 2955 Dihedral : 3.976 29.156 2283 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.04 % Allowed : 19.69 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 2059 helix: 1.79 (0.15), residues: 1370 sheet: -0.04 (0.46), residues: 137 loop : -2.57 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 344 TYR 0.022 0.001 TYR A 279 PHE 0.033 0.001 PHE G 158 TRP 0.024 0.001 TRP D 23 HIS 0.009 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00286 (17969) covalent geometry : angle 0.53887 (24258) SS BOND : bond 0.00193 ( 14) SS BOND : angle 0.39372 ( 28) hydrogen bonds : bond 0.03759 ( 1049) hydrogen bonds : angle 3.73647 ( 3117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 281 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7088 (t80) REVERT: B 145 TRP cc_start: 0.6787 (t60) cc_final: 0.6343 (t60) REVERT: C 248 PHE cc_start: 0.6956 (t80) cc_final: 0.6625 (t80) REVERT: D 37 MET cc_start: 0.7460 (tpt) cc_final: 0.7028 (tmm) REVERT: D 347 ARG cc_start: 0.7545 (ttm170) cc_final: 0.6350 (mpp-170) REVERT: D 351 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: E 156 GLU cc_start: 0.8545 (tt0) cc_final: 0.7877 (tm-30) REVERT: F 342 PHE cc_start: 0.8289 (m-10) cc_final: 0.7810 (m-10) REVERT: F 363 ILE cc_start: 0.8133 (mm) cc_final: 0.7765 (mm) REVERT: G 18 ARG cc_start: 0.7806 (ppt170) cc_final: 0.7552 (ppt170) REVERT: G 108 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8384 (m-80) REVERT: G 248 PHE cc_start: 0.7723 (t80) cc_final: 0.7447 (t80) REVERT: G 377 ILE cc_start: 0.8948 (tp) cc_final: 0.8679 (tp) outliers start: 59 outliers final: 53 residues processed: 314 average time/residue: 0.1257 time to fit residues: 59.9553 Evaluate side-chains 333 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 343 TYR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 334 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 108 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.181520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141234 restraints weight = 25770.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139238 restraints weight = 17743.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140687 restraints weight = 18625.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140787 restraints weight = 11914.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.141271 restraints weight = 10493.511| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17983 Z= 0.142 Angle : 0.547 8.805 24286 Z= 0.289 Chirality : 0.039 0.159 2647 Planarity : 0.003 0.052 2955 Dihedral : 3.996 29.115 2283 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.14 % Allowed : 19.79 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.20), residues: 2059 helix: 1.73 (0.15), residues: 1372 sheet: -0.05 (0.46), residues: 137 loop : -2.56 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 387 TYR 0.022 0.001 TYR A 279 PHE 0.033 0.001 PHE G 158 TRP 0.024 0.002 TRP B 170 HIS 0.010 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00332 (17969) covalent geometry : angle 0.54734 (24258) SS BOND : bond 0.00214 ( 14) SS BOND : angle 0.40862 ( 28) hydrogen bonds : bond 0.03980 ( 1049) hydrogen bonds : angle 3.78109 ( 3117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.84 seconds wall clock time: 43 minutes 36.57 seconds (2616.57 seconds total)