Starting phenix.real_space_refine on Sun Jun 15 12:13:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxo_27771/06_2025/8dxo_27771.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxo_27771/06_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_27771/06_2025/8dxo_27771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxo_27771/06_2025/8dxo_27771.map" model { file = "/net/cci-nas-00/data/ceres_data/8dxo_27771/06_2025/8dxo_27771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxo_27771/06_2025/8dxo_27771.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.25, per 1000 atoms: 0.59 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: 3.94 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.71 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: 5.15 Time building geometry restraints manager: 4.76 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.120 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.027 0.001 TRP D 145 HIS 0.008 0.001 HIS B 375 PHE 0.023 0.001 PHE G 289 TYR 0.015 0.001 TYR C 343 ARG 0.003 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.13857 ( 1049) hydrogen bonds : angle 5.80956 ( 3117) SS BOND : bond 0.00210 ( 14) SS BOND : angle 0.44414 ( 28) covalent geometry : bond 0.00237 (17969) covalent geometry : angle 0.52527 (24258) *********************** 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 : 1.960 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: 0.7625 (mm) REVERT: G 377 ILE cc_start: 0.8882 (tp) cc_final: 0.8544 (tp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.3145 time to fit residues: 163.6834 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 : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.183920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143727 restraints weight = 25857.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143484 restraints weight = 16601.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144215 restraints weight = 15149.549| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1401 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= 0.140 Angle : 0.527 8.345 24286 Z= 0.283 Chirality : 0.039 0.131 2647 Planarity : 0.003 0.056 2955 Dihedral : 4.090 30.173 2283 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.49 % Allowed : 10.10 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 2059 helix: 1.79 (0.15), residues: 1362 sheet: -0.29 (0.46), residues: 141 loop : -2.49 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 145 HIS 0.010 0.001 HIS A 157 PHE 0.029 0.002 PHE A 158 TYR 0.029 0.001 TYR A 279 ARG 0.007 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 1049) hydrogen bonds : angle 4.13045 ( 3117) SS BOND : bond 0.00179 ( 14) SS BOND : angle 0.46736 ( 28) covalent geometry : bond 0.00316 (17969) covalent geometry : angle 0.52667 (24258) *********************** 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 329 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 376 MET cc_start: 0.7879 (tpp) cc_final: 0.7307 (tpp) REVERT: D 143 ASN cc_start: 0.8370 (t0) cc_final: 0.7949 (t0) REVERT: D 158 PHE cc_start: 0.7607 (t80) cc_final: 0.7257 (t80) REVERT: F 363 ILE cc_start: 0.8035 (mm) cc_final: 0.7698 (mm) REVERT: G 242 PHE cc_start: 0.8380 (m-80) cc_final: 0.7834 (m-80) REVERT: G 377 ILE cc_start: 0.8982 (tp) cc_final: 0.8707 (tp) outliers start: 29 outliers final: 21 residues processed: 312 average time/residue: 0.3103 time to fit residues: 144.0343 Evaluate side-chains 288 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 267 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 279 TYR 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 141 CYS 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 198 optimal weight: 0.6980 chunk 195 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN A 368 ASN A 398 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.182241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.142697 restraints weight = 25652.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141171 restraints weight = 19315.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.142356 restraints weight = 17707.897| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1762 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= 0.145 Angle : 0.511 7.321 24286 Z= 0.275 Chirality : 0.039 0.133 2647 Planarity : 0.003 0.057 2955 Dihedral : 4.059 29.400 2283 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.37 % Allowed : 13.81 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 2059 helix: 1.77 (0.15), residues: 1375 sheet: -0.22 (0.46), residues: 139 loop : -2.63 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 170 HIS 0.006 0.001 HIS C 251 PHE 0.027 0.001 PHE A 158 TYR 0.025 0.001 TYR A 279 ARG 0.004 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 1049) hydrogen bonds : angle 3.95107 ( 3117) SS BOND : bond 0.00199 ( 14) SS BOND : angle 0.48033 ( 28) covalent geometry : bond 0.00333 (17969) covalent geometry : angle 0.51148 (24258) *********************** 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 334 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 TRP cc_start: 0.7050 (t60) cc_final: 0.6492 (t60) REVERT: D 37 MET cc_start: 0.7562 (tpt) cc_final: 0.7151 (tmm) REVERT: D 48 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6314 (ppp) REVERT: D 143 ASN cc_start: 0.8320 (t0) cc_final: 0.7899 (t0) REVERT: F 105 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9015 (tt) REVERT: F 363 ILE cc_start: 0.8113 (mm) cc_final: 0.7744 (mm) REVERT: G 242 PHE cc_start: 0.8282 (m-80) cc_final: 0.7793 (m-80) REVERT: G 246 LYS cc_start: 0.7846 (mmtm) cc_final: 0.7586 (mmtm) REVERT: G 377 ILE cc_start: 0.8959 (tp) cc_final: 0.8717 (tp) outliers start: 46 outliers final: 31 residues processed: 310 average time/residue: 0.3057 time to fit residues: 140.1540 Evaluate side-chains 302 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR 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 263 VAL Chi-restraints excluded: chain D residue 279 TYR 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 366 VAL 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 E residue 335 LEU Chi-restraints excluded: chain E residue 341 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 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 36 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 309 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 143 ASN F 305 ASN G 398 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.177870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138919 restraints weight = 25873.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134696 restraints weight = 18398.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136328 restraints weight = 20564.751| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17983 Z= 0.227 Angle : 0.585 7.542 24286 Z= 0.316 Chirality : 0.041 0.142 2647 Planarity : 0.003 0.059 2955 Dihedral : 4.288 28.678 2283 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.20 % Allowed : 15.77 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 2059 helix: 1.56 (0.14), residues: 1383 sheet: -0.21 (0.46), residues: 135 loop : -2.80 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 145 HIS 0.007 0.001 HIS G 375 PHE 0.031 0.002 PHE F 41 TYR 0.024 0.002 TYR A 279 ARG 0.005 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.05154 ( 1049) hydrogen bonds : angle 4.13283 ( 3117) SS BOND : bond 0.00285 ( 14) SS BOND : angle 0.63466 ( 28) covalent geometry : bond 0.00544 (17969) covalent geometry : angle 0.58508 (24258) *********************** 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 327 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 145 TRP cc_start: 0.6954 (t60) cc_final: 0.6541 (t60) REVERT: C 243 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7046 (mm-30) REVERT: C 246 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7773 (mttm) REVERT: D 37 MET cc_start: 0.7611 (tpt) cc_final: 0.7138 (tmm) REVERT: D 48 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6458 (ppp) REVERT: D 143 ASN cc_start: 0.8408 (t0) cc_final: 0.7917 (t0) REVERT: E 108 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: F 105 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8957 (tt) REVERT: G 108 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8630 (m-10) REVERT: G 242 PHE cc_start: 0.8608 (m-80) cc_final: 0.8126 (m-80) REVERT: G 246 LYS cc_start: 0.7875 (mmtm) cc_final: 0.7534 (mmtm) REVERT: G 377 ILE cc_start: 0.9047 (tp) cc_final: 0.8727 (tp) outliers start: 62 outliers final: 41 residues processed: 301 average time/residue: 0.3023 time to fit residues: 135.9368 Evaluate side-chains 300 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR 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 A residue 279 TYR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 284 VAL 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 C residue 276 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 48 MET 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 312 MET Chi-restraints excluded: chain D residue 335 LEU 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 334 CYS 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 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 366 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 273 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 368 ASN B 237 GLN C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN G 398 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.178436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139776 restraints weight = 26140.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135079 restraints weight = 18982.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137680 restraints weight = 19360.423| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17983 Z= 0.185 Angle : 0.545 7.382 24286 Z= 0.294 Chirality : 0.040 0.137 2647 Planarity : 0.003 0.057 2955 Dihedral : 4.227 29.369 2283 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.92 % Allowed : 17.22 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 2059 helix: 1.57 (0.14), residues: 1384 sheet: -0.25 (0.46), residues: 135 loop : -2.79 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 170 HIS 0.006 0.001 HIS C 251 PHE 0.032 0.002 PHE G 158 TYR 0.024 0.001 TYR A 279 ARG 0.004 0.000 ARG A 344 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 1049) hydrogen bonds : angle 4.01586 ( 3117) SS BOND : bond 0.00267 ( 14) SS BOND : angle 0.52988 ( 28) covalent geometry : bond 0.00439 (17969) covalent geometry : angle 0.54456 (24258) *********************** 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 341 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 TRP cc_start: 0.6892 (t60) cc_final: 0.6526 (t60) REVERT: C 243 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7036 (mm-30) REVERT: C 246 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7822 (mttm) REVERT: C 273 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7962 (t80) REVERT: C 376 MET cc_start: 0.7863 (tpp) cc_final: 0.6912 (mpp) REVERT: D 37 MET cc_start: 0.7612 (tpt) cc_final: 0.7122 (tmm) REVERT: D 48 MET cc_start: 0.6798 (ppp) cc_final: 0.6377 (ppp) REVERT: D 143 ASN cc_start: 0.8369 (t0) cc_final: 0.7920 (t0) REVERT: D 351 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: F 105 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8927 (tt) REVERT: G 108 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8511 (m-10) REVERT: G 242 PHE cc_start: 0.8594 (m-80) cc_final: 0.8131 (m-80) REVERT: G 246 LYS cc_start: 0.7808 (mmtm) cc_final: 0.7475 (mmtm) REVERT: G 377 ILE cc_start: 0.9065 (tp) cc_final: 0.8728 (tp) REVERT: G 403 LEU cc_start: 0.8894 (mm) cc_final: 0.8681 (mm) outliers start: 76 outliers final: 57 residues processed: 312 average time/residue: 0.3116 time to fit residues: 144.0714 Evaluate side-chains 309 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 2.011 ------------------------------------------------------------------------------- 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 279 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 295 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 38 ILE 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 C residue 273 PHE Chi-restraints excluded: chain C residue 337 THR 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 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 312 MET 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 334 CYS Chi-restraints excluded: chain E residue 335 LEU 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 47 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 284 VAL Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 114 optimal weight: 10.0000 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 368 ASN B 106 GLN C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.183192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143469 restraints weight = 25827.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.141722 restraints weight = 16885.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142989 restraints weight = 17170.876| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2362 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= 0.107 Angle : 0.485 7.073 24286 Z= 0.259 Chirality : 0.037 0.150 2647 Planarity : 0.003 0.054 2955 Dihedral : 4.028 29.484 2283 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.25 % Allowed : 18.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 2059 helix: 1.75 (0.15), residues: 1379 sheet: -0.41 (0.46), residues: 141 loop : -2.62 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 170 HIS 0.006 0.001 HIS C 251 PHE 0.026 0.001 PHE A 158 TYR 0.026 0.001 TYR A 279 ARG 0.005 0.000 ARG A 344 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1049) hydrogen bonds : angle 3.74178 ( 3117) SS BOND : bond 0.00186 ( 14) SS BOND : angle 0.40757 ( 28) covalent geometry : bond 0.00232 (17969) covalent geometry : angle 0.48494 (24258) *********************** 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 355 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7086 (t80) REVERT: B 145 TRP cc_start: 0.6817 (t60) cc_final: 0.6414 (t60) REVERT: C 108 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: C 273 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7830 (t80) REVERT: C 376 MET cc_start: 0.7809 (tpp) cc_final: 0.6956 (tpp) REVERT: D 37 MET cc_start: 0.7535 (tpt) cc_final: 0.7075 (tmm) REVERT: D 143 ASN cc_start: 0.8329 (t0) cc_final: 0.7939 (t0) REVERT: D 247 LYS cc_start: 0.8527 (pttm) cc_final: 0.8224 (ptmt) REVERT: F 363 ILE cc_start: 0.8213 (mm) cc_final: 0.7855 (mm) REVERT: G 108 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: G 377 ILE cc_start: 0.9010 (tp) cc_final: 0.8683 (tp) outliers start: 63 outliers final: 41 residues processed: 328 average time/residue: 0.3682 time to fit residues: 180.9343 Evaluate side-chains 316 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain B residue 132 LEU 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 108 TYR Chi-restraints excluded: chain C residue 273 PHE 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 49 GLN 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 136 LEU 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 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 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain G residue 108 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 309 ASN A 368 ASN B 106 GLN B 237 GLN C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 157 HIS F 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.178717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139537 restraints weight = 25849.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136337 restraints weight = 19658.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137727 restraints weight = 20990.970| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17983 Z= 0.189 Angle : 0.564 11.328 24286 Z= 0.301 Chirality : 0.040 0.159 2647 Planarity : 0.003 0.055 2955 Dihedral : 4.145 29.011 2283 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.92 % Allowed : 19.07 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 2059 helix: 1.59 (0.15), residues: 1385 sheet: -0.26 (0.46), residues: 135 loop : -2.76 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 170 HIS 0.006 0.001 HIS C 251 PHE 0.024 0.002 PHE B 351 TYR 0.024 0.002 TYR A 279 ARG 0.003 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 1049) hydrogen bonds : angle 3.93575 ( 3117) SS BOND : bond 0.00251 ( 14) SS BOND : angle 0.51316 ( 28) covalent geometry : bond 0.00452 (17969) covalent geometry : angle 0.56445 (24258) *********************** 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 344 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 268 time to evaluate : 2.140 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7138 (t80) REVERT: B 145 TRP cc_start: 0.6813 (t60) cc_final: 0.6420 (t60) REVERT: B 273 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7261 (t80) REVERT: C 108 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: C 273 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7982 (t80) REVERT: C 376 MET cc_start: 0.7828 (tpp) cc_final: 0.6863 (mpp) REVERT: D 37 MET cc_start: 0.7621 (tpt) cc_final: 0.7143 (tmm) REVERT: D 48 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6389 (ppp) REVERT: D 143 ASN cc_start: 0.8404 (t0) cc_final: 0.7981 (t0) REVERT: D 158 PHE cc_start: 0.7705 (t80) cc_final: 0.7219 (t80) REVERT: D 351 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.6560 (m-80) REVERT: E 156 GLU cc_start: 0.8663 (tt0) cc_final: 0.8031 (tm-30) REVERT: G 108 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8497 (m-10) REVERT: G 377 ILE cc_start: 0.9053 (tp) cc_final: 0.8713 (tp) outliers start: 76 outliers final: 55 residues processed: 313 average time/residue: 0.3069 time to fit residues: 143.6823 Evaluate side-chains 321 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 TYR Chi-restraints excluded: chain C residue 133 ILE 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 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 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 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 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 319 LEU Chi-restraints excluded: chain E residue 335 LEU 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 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 243 GLU 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 159 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 151 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN B 106 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.181447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142371 restraints weight = 25596.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138890 restraints weight = 19091.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.141101 restraints weight = 19927.788| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2540 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= 0.123 Angle : 0.530 11.662 24286 Z= 0.279 Chirality : 0.038 0.222 2647 Planarity : 0.003 0.053 2955 Dihedral : 4.051 29.357 2283 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.40 % Allowed : 20.26 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 2059 helix: 1.71 (0.15), residues: 1375 sheet: -0.46 (0.46), residues: 141 loop : -2.62 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 170 HIS 0.007 0.001 HIS C 251 PHE 0.031 0.001 PHE G 158 TYR 0.026 0.001 TYR A 279 ARG 0.002 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1049) hydrogen bonds : angle 3.75888 ( 3117) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.42539 ( 28) covalent geometry : bond 0.00277 (17969) covalent geometry : angle 0.53032 (24258) *********************** 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 355 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 289 time to evaluate : 1.997 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7121 (t80) REVERT: B 145 TRP cc_start: 0.6770 (t60) cc_final: 0.6363 (t60) REVERT: C 108 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: C 248 PHE cc_start: 0.6930 (t80) cc_final: 0.6661 (t80) REVERT: C 273 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7900 (t80) REVERT: C 376 MET cc_start: 0.7808 (tpp) cc_final: 0.6949 (tpp) REVERT: D 37 MET cc_start: 0.7524 (tpt) cc_final: 0.7069 (tmm) REVERT: D 48 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6373 (ppp) REVERT: D 143 ASN cc_start: 0.8364 (t0) cc_final: 0.7979 (t0) REVERT: D 351 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: E 156 GLU cc_start: 0.8638 (tt0) cc_final: 0.7995 (tm-30) REVERT: F 363 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7834 (mm) REVERT: G 18 ARG cc_start: 0.7804 (ppt170) cc_final: 0.7496 (ppt170) REVERT: G 108 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8530 (m-10) REVERT: G 377 ILE cc_start: 0.9013 (tp) cc_final: 0.8699 (tp) outliers start: 66 outliers final: 55 residues processed: 328 average time/residue: 0.3067 time to fit residues: 151.9825 Evaluate side-chains 336 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 274 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 295 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 108 TYR Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 337 THR 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 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 351 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU 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 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 243 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 159 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 93 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 17 optimal weight: 0.0570 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 153 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN B 237 GLN C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.183085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.143907 restraints weight = 25884.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141711 restraints weight = 17742.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142913 restraints weight = 17118.353| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2646 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= 0.114 Angle : 0.517 8.464 24286 Z= 0.275 Chirality : 0.038 0.160 2647 Planarity : 0.003 0.053 2955 Dihedral : 3.958 29.157 2283 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.99 % Allowed : 20.93 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 2059 helix: 1.76 (0.15), residues: 1373 sheet: -0.33 (0.46), residues: 141 loop : -2.54 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 170 HIS 0.006 0.001 HIS C 251 PHE 0.024 0.001 PHE G 248 TYR 0.026 0.001 TYR A 279 ARG 0.007 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1049) hydrogen bonds : angle 3.70957 ( 3117) SS BOND : bond 0.00167 ( 14) SS BOND : angle 0.39468 ( 28) covalent geometry : bond 0.00252 (17969) covalent geometry : angle 0.51720 (24258) *********************** 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 341 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 1.906 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7124 (t80) REVERT: B 145 TRP cc_start: 0.6738 (t60) cc_final: 0.6253 (t60) REVERT: C 248 PHE cc_start: 0.6933 (t80) cc_final: 0.6613 (t80) REVERT: C 273 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.7872 (t80) REVERT: C 376 MET cc_start: 0.7695 (tpp) cc_final: 0.6781 (tpp) REVERT: D 37 MET cc_start: 0.7531 (tpt) cc_final: 0.7108 (tmm) REVERT: D 48 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6352 (ppp) REVERT: D 143 ASN cc_start: 0.8302 (t0) cc_final: 0.7955 (t0) REVERT: D 347 ARG cc_start: 0.7583 (ttm170) cc_final: 0.6388 (mpp-170) REVERT: D 351 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.6352 (m-80) REVERT: E 156 GLU cc_start: 0.8512 (tt0) cc_final: 0.7942 (tm-30) REVERT: F 363 ILE cc_start: 0.8139 (mm) cc_final: 0.7770 (mm) REVERT: G 17 PHE cc_start: 0.7070 (m-80) cc_final: 0.6730 (m-80) REVERT: G 18 ARG cc_start: 0.7787 (ppt170) cc_final: 0.7495 (ppt170) REVERT: G 108 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: G 377 ILE cc_start: 0.9025 (tp) cc_final: 0.8745 (tp) outliers start: 58 outliers final: 47 residues processed: 318 average time/residue: 0.3083 time to fit residues: 148.2682 Evaluate side-chains 320 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 2.053 ------------------------------------------------------------------------------- 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 295 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 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 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 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 126 TYR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 334 CYS 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 243 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 273 PHE 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 133 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 10 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.182429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143064 restraints weight = 25727.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.141081 restraints weight = 17793.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.142291 restraints weight = 19501.663| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17983 Z= 0.123 Angle : 0.522 8.409 24286 Z= 0.278 Chirality : 0.038 0.163 2647 Planarity : 0.003 0.054 2955 Dihedral : 3.965 29.011 2283 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.09 % Allowed : 21.29 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 2059 helix: 1.73 (0.15), residues: 1376 sheet: -0.31 (0.46), residues: 141 loop : -2.58 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 170 HIS 0.009 0.001 HIS C 251 PHE 0.037 0.001 PHE F 41 TYR 0.026 0.001 TYR A 279 ARG 0.006 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 1049) hydrogen bonds : angle 3.71237 ( 3117) SS BOND : bond 0.00175 ( 14) SS BOND : angle 0.37426 ( 28) covalent geometry : bond 0.00278 (17969) covalent geometry : angle 0.52190 (24258) ********************** 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 330 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 270 time to evaluate : 2.032 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7097 (t80) REVERT: B 145 TRP cc_start: 0.6649 (t60) cc_final: 0.6164 (t60) REVERT: C 248 PHE cc_start: 0.6975 (t80) cc_final: 0.6645 (t80) REVERT: C 273 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7887 (t80) REVERT: D 37 MET cc_start: 0.7489 (tpt) cc_final: 0.7067 (tmm) REVERT: D 143 ASN cc_start: 0.8300 (t0) cc_final: 0.7941 (t0) REVERT: D 158 PHE cc_start: 0.7162 (t80) cc_final: 0.6902 (t80) REVERT: D 347 ARG cc_start: 0.7618 (ttm170) cc_final: 0.6384 (mpp-170) REVERT: D 351 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.6363 (m-80) REVERT: E 156 GLU cc_start: 0.8527 (tt0) cc_final: 0.7988 (tm-30) REVERT: F 363 ILE cc_start: 0.8187 (mm) cc_final: 0.7807 (mm) REVERT: G 17 PHE cc_start: 0.7020 (m-80) cc_final: 0.6645 (m-80) REVERT: G 108 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: G 377 ILE cc_start: 0.8980 (tp) cc_final: 0.8684 (tp) outliers start: 60 outliers final: 54 residues processed: 307 average time/residue: 0.2979 time to fit residues: 137.0241 Evaluate side-chains 324 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 1.885 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 295 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 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 277 ILE 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 351 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU 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 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 243 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 159 ILE 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 8 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 157 optimal weight: 0.5980 chunk 192 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.182167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.142769 restraints weight = 25674.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140516 restraints weight = 18067.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141925 restraints weight = 19292.028| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2747 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= 0.129 Angle : 0.530 8.303 24286 Z= 0.283 Chirality : 0.038 0.161 2647 Planarity : 0.003 0.054 2955 Dihedral : 3.981 29.032 2283 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.20 % Allowed : 21.49 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 2059 helix: 1.75 (0.15), residues: 1367 sheet: -0.26 (0.46), residues: 139 loop : -2.56 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 23 HIS 0.010 0.001 HIS C 251 PHE 0.042 0.001 PHE C 391 TYR 0.026 0.001 TYR A 279 ARG 0.006 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 1049) hydrogen bonds : angle 3.73327 ( 3117) SS BOND : bond 0.00179 ( 14) SS BOND : angle 0.36677 ( 28) covalent geometry : bond 0.00296 (17969) covalent geometry : angle 0.53035 (24258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5402.38 seconds wall clock time: 96 minutes 36.75 seconds (5796.75 seconds total)