Starting phenix.real_space_refine on Thu Jul 2 11:14:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsc_65300/07_2026/9vsc_65300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsc_65300/07_2026/9vsc_65300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vsc_65300/07_2026/9vsc_65300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsc_65300/07_2026/9vsc_65300.map" model { file = "/net/cci-nas-00/data/ceres_data/9vsc_65300/07_2026/9vsc_65300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsc_65300/07_2026/9vsc_65300.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.049 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 39 5.16 5 C 5454 2.51 5 N 1281 2.21 5 O 1428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8205 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2734 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 9, 'TRANS': 348} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 1.57, per 1000 atoms: 0.19 Number of scatterers: 8205 At special positions: 0 Unit cell: (113.3, 113.3, 70.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 39 16.00 O 1428 8.00 N 1281 7.00 C 5454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 381.4 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.893A pdb=" N ILE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.859A pdb=" N ILE A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.605A pdb=" N VAL A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 removed outlier: 3.660A pdb=" N THR A 124 " --> pdb=" O ALA A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 127 through 135 removed outlier: 5.200A pdb=" N LEU A 132 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN A 133 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 135 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 153 through 161 removed outlier: 3.912A pdb=" N VAL A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.844A pdb=" N ASN A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.508A pdb=" N SER A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.893A pdb=" N ALA A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.813A pdb=" N LEU A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Proline residue: A 213 - end of helix removed outlier: 3.717A pdb=" N GLY A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 250 removed outlier: 3.571A pdb=" N LEU A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.737A pdb=" N GLY A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.911A pdb=" N GLU A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.825A pdb=" N ILE A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.695A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.614A pdb=" N ALA A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 367 removed outlier: 3.753A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.697A pdb=" N ILE A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 removed outlier: 3.768A pdb=" N CYS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.751A pdb=" N VAL A 418 " --> pdb=" O MET A 414 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 433 removed outlier: 3.626A pdb=" N ILE A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 428 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 433 " --> pdb=" O CYS A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.893A pdb=" N ILE B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.858A pdb=" N ILE B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.606A pdb=" N VAL B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 124 removed outlier: 3.661A pdb=" N THR B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 124' Processing helix chain 'B' and resid 127 through 135 removed outlier: 5.200A pdb=" N LEU B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR B 135 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.912A pdb=" N VAL B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 removed outlier: 3.844A pdb=" N ASN B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.508A pdb=" N SER B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.893A pdb=" N ALA B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 196 Processing helix chain 'B' and resid 197 through 217 removed outlier: 3.813A pdb=" N LEU B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Proline residue: B 213 - end of helix removed outlier: 3.717A pdb=" N GLY B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 250 removed outlier: 3.571A pdb=" N LEU B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.737A pdb=" N GLY B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 289 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 290 " --> pdb=" O TRP B 286 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.912A pdb=" N GLU B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 309 " --> pdb=" O TYR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 327 through 334 removed outlier: 3.825A pdb=" N ILE B 331 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.695A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.614A pdb=" N ALA B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 367 removed outlier: 3.753A pdb=" N ILE B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.696A pdb=" N ILE B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 374 " --> pdb=" O PRO B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.768A pdb=" N CYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.752A pdb=" N VAL B 418 " --> pdb=" O MET B 414 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 433 removed outlier: 3.626A pdb=" N ILE B 426 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 428 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP B 433 " --> pdb=" O CYS B 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 78 through 81 Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.894A pdb=" N ILE C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 107 removed outlier: 3.858A pdb=" N ILE C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.606A pdb=" N VAL C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C 119 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 124 removed outlier: 3.660A pdb=" N THR C 124 " --> pdb=" O ALA C 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 124' Processing helix chain 'C' and resid 127 through 135 removed outlier: 5.199A pdb=" N LEU C 132 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN C 133 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR C 135 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 150 Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.912A pdb=" N VAL C 157 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 removed outlier: 3.843A pdb=" N ASN C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.507A pdb=" N SER C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.893A pdb=" N ALA C 183 " --> pdb=" O CYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 197 through 217 removed outlier: 3.813A pdb=" N LEU C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Proline residue: C 213 - end of helix removed outlier: 3.716A pdb=" N GLY C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 250 removed outlier: 3.570A pdb=" N LEU C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C 235 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 284 through 295 removed outlier: 3.738A pdb=" N GLY C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 289 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 290 " --> pdb=" O TRP C 286 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 309 removed outlier: 3.912A pdb=" N GLU C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'C' and resid 327 through 334 removed outlier: 3.826A pdb=" N ILE C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 332 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.695A pdb=" N ILE C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.614A pdb=" N ALA C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 removed outlier: 3.753A pdb=" N ILE C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 380 removed outlier: 3.696A pdb=" N ILE C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 374 " --> pdb=" O PRO C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 406 removed outlier: 3.767A pdb=" N CYS C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 removed outlier: 3.752A pdb=" N VAL C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 433 removed outlier: 3.627A pdb=" N ILE C 426 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 428 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 433 " --> pdb=" O CYS C 429 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 882 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: 0.83 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2455 1.34 - 1.46: 1554 1.46 - 1.57: 4307 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 8370 Sorted by residual: bond pdb=" CB PRO C 370 " pdb=" CG PRO C 370 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.82e+00 bond pdb=" CB PRO A 370 " pdb=" CG PRO A 370 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.79e+00 bond pdb=" CB PRO B 370 " pdb=" CG PRO B 370 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO B 330 " pdb=" CG PRO B 330 " ideal model delta sigma weight residual 1.492 1.416 0.076 5.00e-02 4.00e+02 2.31e+00 bond pdb=" CB PRO A 330 " pdb=" CG PRO A 330 " ideal model delta sigma weight residual 1.492 1.416 0.076 5.00e-02 4.00e+02 2.29e+00 ... (remaining 8365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 10904 2.11 - 4.21: 430 4.21 - 6.32: 48 6.32 - 8.43: 18 8.43 - 10.54: 3 Bond angle restraints: 11403 Sorted by residual: angle pdb=" N GLN C 95 " pdb=" CA GLN C 95 " pdb=" C GLN C 95 " ideal model delta sigma weight residual 109.81 120.35 -10.54 2.21e+00 2.05e-01 2.27e+01 angle pdb=" N GLN B 95 " pdb=" CA GLN B 95 " pdb=" C GLN B 95 " ideal model delta sigma weight residual 109.81 120.33 -10.52 2.21e+00 2.05e-01 2.27e+01 angle pdb=" N GLN A 95 " pdb=" CA GLN A 95 " pdb=" C GLN A 95 " ideal model delta sigma weight residual 109.81 120.32 -10.51 2.21e+00 2.05e-01 2.26e+01 angle pdb=" CA GLN A 95 " pdb=" C GLN A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 118.44 123.30 -4.86 1.59e+00 3.96e-01 9.33e+00 angle pdb=" CA GLN B 95 " pdb=" C GLN B 95 " pdb=" N PRO B 96 " ideal model delta sigma weight residual 118.44 123.29 -4.85 1.59e+00 3.96e-01 9.30e+00 ... (remaining 11398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.36: 4028 8.36 - 16.72: 634 16.72 - 25.08: 138 25.08 - 33.43: 39 33.43 - 41.79: 6 Dihedral angle restraints: 4845 sinusoidal: 1770 harmonic: 3075 Sorted by residual: dihedral pdb=" CA LEU B 292 " pdb=" C LEU B 292 " pdb=" N VAL B 293 " pdb=" CA VAL B 293 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA LEU C 292 " pdb=" C LEU C 292 " pdb=" N VAL C 293 " pdb=" CA VAL C 293 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA LEU A 292 " pdb=" C LEU A 292 " pdb=" N VAL A 293 " pdb=" CA VAL A 293 " ideal model delta harmonic sigma weight residual 180.00 155.00 25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 4842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 782 0.043 - 0.086: 530 0.086 - 0.129: 87 0.129 - 0.172: 23 0.172 - 0.215: 3 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CA GLN B 95 " pdb=" N GLN B 95 " pdb=" C GLN B 95 " pdb=" CB GLN B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLN C 95 " pdb=" N GLN C 95 " pdb=" C GLN C 95 " pdb=" CB GLN C 95 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLN A 95 " pdb=" N GLN A 95 " pdb=" C GLN A 95 " pdb=" CB GLN A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1422 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 79 " 0.040 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO C 80 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 79 " -0.040 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO A 80 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 79 " -0.040 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO B 80 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.033 5.00e-02 4.00e+02 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2599 2.81 - 3.34: 6931 3.34 - 3.86: 12426 3.86 - 4.38: 15401 4.38 - 4.90: 26220 Nonbonded interactions: 63577 Sorted by model distance: nonbonded pdb=" O TYR A 305 " pdb=" OG1 THR A 309 " model vdw 2.293 3.040 nonbonded pdb=" O TYR B 305 " pdb=" OG1 THR B 309 " model vdw 2.294 3.040 nonbonded pdb=" O TYR C 305 " pdb=" OG1 THR C 309 " model vdw 2.294 3.040 nonbonded pdb=" O SER C 398 " pdb=" OG1 THR C 402 " model vdw 2.390 3.040 nonbonded pdb=" O SER B 398 " pdb=" OG1 THR B 402 " model vdw 2.390 3.040 ... (remaining 63572 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.560 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.008 0.084 8370 Z= 0.319 Angle : 0.968 10.537 11403 Z= 0.510 Chirality : 0.053 0.215 1425 Planarity : 0.007 0.059 1377 Dihedral : 8.687 41.793 2865 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.34 (0.13), residues: 1062 helix: -4.93 (0.05), residues: 810 sheet: None (None), residues: 0 loop : -3.45 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 186 TYR 0.034 0.003 TYR B 159 PHE 0.015 0.002 PHE B 62 TRP 0.013 0.002 TRP B 286 HIS 0.009 0.003 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.32 ( 8370) covalent geometry : angle 0.96795 / 0.51 (11403) hydrogen bonds : bond 0.35238 / 23.18 ( 315) hydrogen bonds : angle 10.30348 / 6.98 ( 882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 128 LEU cc_start: 0.7501 (tp) cc_final: 0.7158 (mp) REVERT: C 338 HIS cc_start: 0.8435 (t-170) cc_final: 0.8200 (t70) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0836 time to fit residues: 13.7724 Evaluate side-chains 79 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.0060 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 ASN B 318 ASN C 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120505 restraints weight = 9675.967| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.16 r_work: 0.3111 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8370 Z= 0.108 Angle : 0.559 7.496 11403 Z= 0.291 Chirality : 0.038 0.115 1425 Planarity : 0.005 0.038 1377 Dihedral : 5.306 16.440 1116 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.74 (0.18), residues: 1062 helix: -3.72 (0.11), residues: 834 sheet: None (None), residues: 0 loop : -2.92 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.017 0.001 TYR A 413 PHE 0.008 0.001 PHE A 430 TRP 0.007 0.001 TRP A 291 HIS 0.002 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8370) covalent geometry : angle 0.55948 / 0.29 (11403) hydrogen bonds : bond 0.03889 / 2.50 ( 315) hydrogen bonds : angle 5.18835 / 3.42 ( 882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.266 Fit side-chains REVERT: A 186 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7004 (mmm160) REVERT: A 194 LYS cc_start: 0.8575 (mttp) cc_final: 0.7834 (pttp) REVERT: B 186 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7030 (mmm160) REVERT: C 186 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.7208 (mmp-170) REVERT: C 338 HIS cc_start: 0.8484 (t-170) cc_final: 0.8250 (t70) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.0834 time to fit residues: 11.4788 Evaluate side-chains 84 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 chunk 86 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 0.0670 chunk 102 optimal weight: 1.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 HIS B 318 ASN C 138 ASN C 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.166311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120623 restraints weight = 9536.314| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.16 r_work: 0.3256 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8370 Z= 0.090 Angle : 0.501 8.185 11403 Z= 0.257 Chirality : 0.038 0.128 1425 Planarity : 0.004 0.035 1377 Dihedral : 4.572 13.173 1116 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.11 % Allowed : 6.06 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.22), residues: 1062 helix: -2.70 (0.14), residues: 864 sheet: None (None), residues: 0 loop : -2.15 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.013 0.001 TYR A 413 PHE 0.007 0.001 PHE C 178 TRP 0.005 0.000 TRP A 291 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 8370) covalent geometry : angle 0.50059 / 0.26 (11403) hydrogen bonds : bond 0.03211 / 2.07 ( 315) hydrogen bonds : angle 4.48808 / 2.99 ( 882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.205 Fit side-chains REVERT: A 186 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7386 (mmp-170) REVERT: A 194 LYS cc_start: 0.8651 (mttp) cc_final: 0.8124 (pttp) REVERT: B 186 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.7329 (mmm160) REVERT: C 186 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.7455 (mmp-170) REVERT: C 295 MET cc_start: 0.6538 (mtt) cc_final: 0.6238 (ttm) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.0974 time to fit residues: 12.1362 Evaluate side-chains 91 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 68 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN B 318 ASN B 338 HIS C 318 ASN C 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118721 restraints weight = 9692.185| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.20 r_work: 0.3047 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8370 Z= 0.096 Angle : 0.491 5.476 11403 Z= 0.251 Chirality : 0.038 0.144 1425 Planarity : 0.003 0.032 1377 Dihedral : 4.300 12.374 1116 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.79 % Allowed : 5.72 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.24), residues: 1062 helix: -2.23 (0.16), residues: 870 sheet: None (None), residues: 0 loop : -2.05 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.011 0.001 TYR A 413 PHE 0.008 0.001 PHE A 430 TRP 0.005 0.000 TRP A 291 HIS 0.003 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 8370) covalent geometry : angle 0.49084 / 0.25 (11403) hydrogen bonds : bond 0.03059 / 1.97 ( 315) hydrogen bonds : angle 4.32469 / 2.88 ( 882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.177 Fit side-chains REVERT: A 186 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7249 (mmp-170) REVERT: A 194 LYS cc_start: 0.8544 (mttp) cc_final: 0.7897 (pttp) REVERT: B 186 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.7847 (mmm160) REVERT: C 186 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7226 (mmp-170) REVERT: C 360 SER cc_start: 0.9017 (t) cc_final: 0.8779 (m) outliers start: 7 outliers final: 1 residues processed: 97 average time/residue: 0.0904 time to fit residues: 11.6121 Evaluate side-chains 91 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 62 optimal weight: 0.4980 chunk 20 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 46 optimal weight: 0.0370 chunk 21 optimal weight: 0.0010 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN C 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117973 restraints weight = 9788.197| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.19 r_work: 0.3089 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8370 Z= 0.089 Angle : 0.492 8.822 11403 Z= 0.244 Chirality : 0.037 0.145 1425 Planarity : 0.003 0.030 1377 Dihedral : 4.056 11.483 1116 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.22 % Allowed : 6.17 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.25), residues: 1062 helix: -1.88 (0.16), residues: 873 sheet: None (None), residues: 0 loop : -1.89 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.010 0.001 TYR A 413 PHE 0.007 0.001 PHE C 178 TRP 0.004 0.000 TRP A 291 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 ( 8370) covalent geometry : angle 0.49234 / 0.24 (11403) hydrogen bonds : bond 0.02797 / 1.80 ( 315) hydrogen bonds : angle 4.20170 / 2.80 ( 882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.283 Fit side-chains REVERT: A 186 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7312 (mmp-170) REVERT: A 194 LYS cc_start: 0.8572 (mttp) cc_final: 0.7990 (pttp) REVERT: B 186 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7958 (mmm160) REVERT: B 338 HIS cc_start: 0.8195 (t-170) cc_final: 0.7974 (t-170) REVERT: C 186 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7258 (mmp-170) REVERT: C 295 MET cc_start: 0.6402 (mtt) cc_final: 0.5983 (ttm) outliers start: 2 outliers final: 2 residues processed: 89 average time/residue: 0.0996 time to fit residues: 11.7368 Evaluate side-chains 87 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 338 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN C 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119751 restraints weight = 9614.386| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.12 r_work: 0.3045 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8370 Z= 0.081 Angle : 0.473 7.964 11403 Z= 0.235 Chirality : 0.037 0.155 1425 Planarity : 0.003 0.029 1377 Dihedral : 3.817 10.999 1116 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.22 % Allowed : 6.62 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.25), residues: 1062 helix: -1.61 (0.17), residues: 879 sheet: None (None), residues: 0 loop : -1.69 (0.51), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 187 TYR 0.009 0.001 TYR A 413 PHE 0.006 0.001 PHE C 178 TRP 0.004 0.000 TRP C 291 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 ( 8370) covalent geometry : angle 0.47334 / 0.24 (11403) hydrogen bonds : bond 0.02497 / 1.60 ( 315) hydrogen bonds : angle 3.98250 / 2.65 ( 882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.215 Fit side-chains REVERT: A 186 ARG cc_start: 0.8306 (mmm-85) cc_final: 0.7385 (mmp-170) REVERT: A 434 LYS cc_start: 0.7938 (tttt) cc_final: 0.7452 (mmtp) REVERT: B 186 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.7360 (mmm160) REVERT: B 338 HIS cc_start: 0.8263 (t-170) cc_final: 0.8025 (t-170) REVERT: C 186 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7314 (mmp-170) REVERT: C 295 MET cc_start: 0.6403 (mtt) cc_final: 0.6009 (ttm) outliers start: 2 outliers final: 2 residues processed: 86 average time/residue: 0.0882 time to fit residues: 10.0455 Evaluate side-chains 84 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 338 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN C 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.162717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117269 restraints weight = 9766.693| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.08 r_work: 0.3005 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8370 Z= 0.109 Angle : 0.500 8.126 11403 Z= 0.248 Chirality : 0.038 0.165 1425 Planarity : 0.003 0.028 1377 Dihedral : 3.929 11.710 1116 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.22 % Allowed : 6.51 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.25), residues: 1062 helix: -1.48 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -2.02 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 187 TYR 0.011 0.001 TYR A 251 PHE 0.008 0.001 PHE C 178 TRP 0.006 0.001 TRP B 291 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 8370) covalent geometry : angle 0.50007 / 0.25 (11403) hydrogen bonds : bond 0.03032 / 1.96 ( 315) hydrogen bonds : angle 4.15232 / 2.76 ( 882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.296 Fit side-chains REVERT: A 186 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.7400 (mmp-170) REVERT: A 194 LYS cc_start: 0.8746 (mttp) cc_final: 0.8198 (mmtt) REVERT: A 434 LYS cc_start: 0.8082 (tttt) cc_final: 0.7512 (mmtp) REVERT: B 186 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.7368 (mmm160) REVERT: B 338 HIS cc_start: 0.8338 (t-170) cc_final: 0.8077 (t-170) REVERT: C 186 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7368 (mmp-170) REVERT: C 408 ASP cc_start: 0.8661 (t0) cc_final: 0.8329 (t0) outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.1135 time to fit residues: 13.4978 Evaluate side-chains 88 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 338 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.0000 chunk 88 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN C 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.162873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117188 restraints weight = 9641.756| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.08 r_work: 0.3035 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8370 Z= 0.087 Angle : 0.482 9.609 11403 Z= 0.237 Chirality : 0.037 0.166 1425 Planarity : 0.003 0.029 1377 Dihedral : 3.778 11.333 1116 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.22 % Allowed : 7.18 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.26), residues: 1062 helix: -1.32 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.97 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 187 TYR 0.008 0.001 TYR A 413 PHE 0.006 0.001 PHE A 178 TRP 0.004 0.000 TRP B 291 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 8370) covalent geometry : angle 0.48173 / 0.24 (11403) hydrogen bonds : bond 0.02608 / 1.68 ( 315) hydrogen bonds : angle 3.99218 / 2.66 ( 882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.289 Fit side-chains REVERT: A 186 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7330 (mmp-170) REVERT: A 434 LYS cc_start: 0.8089 (tttt) cc_final: 0.7478 (mmtp) REVERT: B 186 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.7351 (mmm160) REVERT: B 338 HIS cc_start: 0.8312 (t-170) cc_final: 0.7998 (t-170) REVERT: C 186 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7357 (mmp-170) REVERT: C 295 MET cc_start: 0.6496 (mtt) cc_final: 0.6054 (ttm) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.1077 time to fit residues: 12.6507 Evaluate side-chains 85 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 338 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.161398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115724 restraints weight = 9645.400| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.06 r_work: 0.3001 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8370 Z= 0.132 Angle : 0.526 8.258 11403 Z= 0.259 Chirality : 0.039 0.160 1425 Planarity : 0.003 0.028 1377 Dihedral : 3.995 12.515 1116 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.45 % Allowed : 7.07 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.25), residues: 1062 helix: -1.39 (0.17), residues: 843 sheet: None (None), residues: 0 loop : -2.19 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 186 TYR 0.012 0.001 TYR A 251 PHE 0.010 0.001 PHE C 178 TRP 0.007 0.001 TRP A 291 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.13 ( 8370) covalent geometry : angle 0.52587 / 0.26 (11403) hydrogen bonds : bond 0.03355 / 2.18 ( 315) hydrogen bonds : angle 4.20490 / 2.80 ( 882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.253 Fit side-chains REVERT: A 186 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7376 (mmp-170) REVERT: A 434 LYS cc_start: 0.8098 (tttt) cc_final: 0.7482 (mmtp) REVERT: B 186 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.7321 (mmm160) REVERT: B 338 HIS cc_start: 0.8435 (t-170) cc_final: 0.8155 (t-170) REVERT: C 186 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.7351 (mmp-170) outliers start: 4 outliers final: 1 residues processed: 92 average time/residue: 0.0932 time to fit residues: 11.3477 Evaluate side-chains 89 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 59 optimal weight: 0.0980 chunk 85 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117225 restraints weight = 9708.721| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.07 r_work: 0.3008 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8370 Z= 0.100 Angle : 0.500 8.132 11403 Z= 0.248 Chirality : 0.038 0.165 1425 Planarity : 0.003 0.029 1377 Dihedral : 3.853 12.028 1116 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.11 % Allowed : 7.63 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.26), residues: 1062 helix: -1.18 (0.17), residues: 861 sheet: None (None), residues: 0 loop : -2.13 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.009 0.001 TYR A 251 PHE 0.007 0.001 PHE A 178 TRP 0.004 0.000 TRP A 291 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 ( 8370) covalent geometry : angle 0.49988 / 0.25 (11403) hydrogen bonds : bond 0.02871 / 1.85 ( 315) hydrogen bonds : angle 4.07282 / 2.72 ( 882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.292 Fit side-chains REVERT: A 186 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.7391 (mmp-170) REVERT: A 194 LYS cc_start: 0.8733 (mttp) cc_final: 0.8230 (mmtt) REVERT: A 434 LYS cc_start: 0.8109 (tttt) cc_final: 0.7486 (mmtp) REVERT: B 186 ARG cc_start: 0.8299 (mmm-85) cc_final: 0.7349 (mmm160) REVERT: B 338 HIS cc_start: 0.8416 (t-170) cc_final: 0.8102 (t-170) REVERT: C 186 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.7367 (mmp-170) REVERT: C 295 MET cc_start: 0.6537 (mtt) cc_final: 0.6148 (ttm) REVERT: C 408 ASP cc_start: 0.8640 (t0) cc_final: 0.8335 (t0) outliers start: 1 outliers final: 1 residues processed: 86 average time/residue: 0.1003 time to fit residues: 11.3869 Evaluate side-chains 85 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 54 optimal weight: 0.0000 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 60 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.162436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116322 restraints weight = 9714.035| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.12 r_work: 0.2990 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8370 Z= 0.112 Angle : 0.525 10.197 11403 Z= 0.258 Chirality : 0.038 0.167 1425 Planarity : 0.003 0.029 1377 Dihedral : 3.862 12.016 1116 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.11 % Allowed : 7.86 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.26), residues: 1062 helix: -1.12 (0.17), residues: 861 sheet: None (None), residues: 0 loop : -2.17 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.010 0.001 TYR A 251 PHE 0.008 0.001 PHE A 178 TRP 0.005 0.001 TRP A 291 HIS 0.002 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 ( 8370) covalent geometry : angle 0.52497 / 0.26 (11403) hydrogen bonds : bond 0.03019 / 1.95 ( 315) hydrogen bonds : angle 4.09765 / 2.73 ( 882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.32 seconds wall clock time: 30 minutes 52.76 seconds (1852.76 seconds total)