Starting phenix.real_space_refine on Wed Feb 4 02:01:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsc_65300/02_2026/9vsc_65300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsc_65300/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9vsc_65300/02_2026/9vsc_65300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsc_65300/02_2026/9vsc_65300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vsc_65300/02_2026/9vsc_65300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsc_65300/02_2026/9vsc_65300.map" } 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-2.0-5952/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C Time building chain proxies: 2.14, per 1000 atoms: 0.26 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: 0.86 Conformation dependent library (CDL) restraints added in 361.7 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: 0.24 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: 1.02 Time building geometry restraints manager: 1.09 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: 0.02 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: 1.230 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.260 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 covalent geometry : bond 0.00806 ( 8370) covalent geometry : angle 0.96795 (11403) hydrogen bonds : bond 0.35238 ( 315) hydrogen bonds : angle 10.30348 ( 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 : 0.214 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: 0.1088 time to fit residues: 17.7087 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 : 0.285 ------------------------------------------------------------------------------- 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: 0.4980 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.165244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120509 restraints weight = 9663.435| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.15 r_work: 0.3112 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8370 Z= 0.106 Angle : 0.560 7.634 11403 Z= 0.291 Chirality : 0.038 0.114 1425 Planarity : 0.005 0.037 1377 Dihedral : 5.308 16.624 1116 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.22 % Allowed : 3.70 % 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: -5.75 (0.18), residues: 1062 helix: -3.73 (0.11), residues: 834 sheet: None (None), residues: 0 loop : -2.91 (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 0.006 0.001 TRP B 291 HIS 0.002 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8370) covalent geometry : angle 0.56003 (11403) hydrogen bonds : bond 0.04018 ( 315) hydrogen bonds : angle 5.19100 ( 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 102 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.299 Fit side-chains REVERT: A 186 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.6979 (mmm160) REVERT: A 194 LYS cc_start: 0.8573 (mttp) cc_final: 0.7838 (pttp) REVERT: B 186 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.7009 (mmm160) REVERT: C 186 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7202 (mmp-170) REVERT: C 301 LEU cc_start: 0.7759 (tp) cc_final: 0.7545 (tt) REVERT: C 338 HIS cc_start: 0.8483 (t-170) cc_final: 0.8247 (t70) outliers start: 2 outliers final: 1 residues processed: 102 average time/residue: 0.0958 time to fit residues: 13.3035 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 70 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 86 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3914 r_free = 0.3914 target = 0.162848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116478 restraints weight = 9569.997| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.19 r_work: 0.3010 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2546 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= 0.133 Angle : 0.547 5.374 11403 Z= 0.282 Chirality : 0.039 0.136 1425 Planarity : 0.004 0.039 1377 Dihedral : 4.912 15.574 1116 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.45 % Allowed : 5.72 % 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: -4.48 (0.22), residues: 1062 helix: -2.84 (0.14), residues: 843 sheet: None (None), residues: 0 loop : -2.36 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.015 0.001 TYR C 159 PHE 0.010 0.001 PHE A 430 TRP 0.006 0.001 TRP A 291 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8370) covalent geometry : angle 0.54739 (11403) hydrogen bonds : bond 0.04069 ( 315) hydrogen bonds : angle 4.77480 ( 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 95 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.296 Fit side-chains REVERT: A 186 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7167 (mmp-170) REVERT: A 194 LYS cc_start: 0.8600 (mttp) cc_final: 0.7964 (pttp) REVERT: A 295 MET cc_start: 0.6518 (mtt) cc_final: 0.6315 (mtm) REVERT: B 186 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7155 (mmm160) REVERT: C 186 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7256 (mmp-170) REVERT: C 338 HIS cc_start: 0.8357 (t-170) cc_final: 0.8144 (t70) outliers start: 4 outliers final: 1 residues processed: 94 average time/residue: 0.1099 time to fit residues: 13.6686 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 : 0.279 ------------------------------------------------------------------------------- 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: 0.9980 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN B 318 ASN B 338 HIS C 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.163980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117463 restraints weight = 9726.529| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.17 r_work: 0.3059 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8370 Z= 0.096 Angle : 0.493 8.858 11403 Z= 0.251 Chirality : 0.038 0.139 1425 Planarity : 0.004 0.032 1377 Dihedral : 4.373 12.907 1116 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.56 % Allowed : 6.06 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.23), residues: 1062 helix: -2.25 (0.16), residues: 834 sheet: None (None), residues: 0 loop : -2.37 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 187 TYR 0.011 0.001 TYR A 413 PHE 0.008 0.001 PHE B 430 TRP 0.004 0.000 TRP B 291 HIS 0.002 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8370) covalent geometry : angle 0.49271 (11403) hydrogen bonds : bond 0.02968 ( 315) hydrogen bonds : angle 4.34043 ( 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 96 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.281 Fit side-chains REVERT: A 186 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7243 (mmp-170) REVERT: A 194 LYS cc_start: 0.8589 (mttp) cc_final: 0.7928 (pttp) REVERT: A 295 MET cc_start: 0.6338 (mtt) cc_final: 0.6053 (mtm) REVERT: B 186 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7866 (mmm160) REVERT: B 347 LYS cc_start: 0.8113 (mttp) cc_final: 0.7826 (mttm) REVERT: C 186 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7226 (mmp-170) REVERT: C 295 MET cc_start: 0.6507 (mtt) cc_final: 0.6101 (ttm) outliers start: 5 outliers final: 1 residues processed: 96 average time/residue: 0.1005 time to fit residues: 12.7853 Evaluate side-chains 87 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN C 318 ASN C 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114599 restraints weight = 9710.413| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.06 r_work: 0.3040 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8370 Z= 0.119 Angle : 0.525 8.275 11403 Z= 0.262 Chirality : 0.039 0.151 1425 Planarity : 0.003 0.030 1377 Dihedral : 4.338 12.575 1116 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.22 % Allowed : 6.96 % Favored : 92.82 % 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: -3.39 (0.24), residues: 1062 helix: -2.04 (0.16), residues: 840 sheet: None (None), residues: 0 loop : -2.11 (0.43), residues: 222 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 0.009 0.001 PHE C 178 TRP 0.005 0.001 TRP B 291 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8370) covalent geometry : angle 0.52476 (11403) hydrogen bonds : bond 0.03340 ( 315) hydrogen bonds : angle 4.39763 ( 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 : 0.230 Fit side-chains REVERT: A 186 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7308 (mmp-170) REVERT: A 194 LYS cc_start: 0.8643 (mttp) cc_final: 0.7985 (pttp) REVERT: A 408 ASP cc_start: 0.8419 (t0) cc_final: 0.8218 (t0) REVERT: B 186 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.7290 (mmm160) REVERT: C 186 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7306 (mmp-170) outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.1065 time to fit residues: 12.5165 Evaluate side-chains 88 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN C 318 ASN C 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118270 restraints weight = 9582.345| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.09 r_work: 0.3091 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8370 Z= 0.086 Angle : 0.486 9.474 11403 Z= 0.241 Chirality : 0.038 0.157 1425 Planarity : 0.003 0.029 1377 Dihedral : 4.039 11.941 1116 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: -3.02 (0.25), residues: 1062 helix: -1.80 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -1.82 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.009 0.001 TYR A 413 PHE 0.007 0.001 PHE C 178 TRP 0.003 0.000 TRP B 286 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 8370) covalent geometry : angle 0.48565 (11403) hydrogen bonds : bond 0.02690 ( 315) hydrogen bonds : angle 4.11733 ( 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 86 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.314 Fit side-chains REVERT: A 186 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7277 (mmp-170) REVERT: A 194 LYS cc_start: 0.8598 (mttp) cc_final: 0.7965 (pttp) REVERT: A 434 LYS cc_start: 0.8008 (tttt) cc_final: 0.7459 (mmtp) REVERT: B 186 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7327 (mmm160) REVERT: B 347 LYS cc_start: 0.8271 (mttp) cc_final: 0.8014 (mttm) REVERT: C 186 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7345 (mmp-170) REVERT: C 295 MET cc_start: 0.6540 (mtt) cc_final: 0.6077 (ttm) outliers start: 2 outliers final: 2 residues processed: 86 average time/residue: 0.0982 time to fit residues: 11.0680 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 : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain C residue 75 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN B 338 HIS C 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.159000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113446 restraints weight = 9762.245| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.06 r_work: 0.2987 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8370 Z= 0.180 Angle : 0.582 8.598 11403 Z= 0.289 Chirality : 0.041 0.165 1425 Planarity : 0.003 0.029 1377 Dihedral : 4.469 14.640 1116 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.34 % Allowed : 7.07 % 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: -3.16 (0.24), residues: 1062 helix: -1.87 (0.17), residues: 843 sheet: None (None), residues: 0 loop : -2.05 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.011 0.001 TYR C 251 PHE 0.012 0.001 PHE C 178 TRP 0.008 0.001 TRP C 257 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8370) covalent geometry : angle 0.58179 (11403) hydrogen bonds : bond 0.04047 ( 315) hydrogen bonds : angle 4.53652 ( 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: 3 poor density : 88 time to evaluate : 0.197 Fit side-chains REVERT: A 186 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7316 (mmp-170) REVERT: A 194 LYS cc_start: 0.8666 (mttp) cc_final: 0.8391 (mmtt) REVERT: A 434 LYS cc_start: 0.8115 (tttt) cc_final: 0.7524 (mttm) REVERT: B 186 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.7337 (mmm160) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.0965 time to fit residues: 11.3826 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 : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain C residue 75 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3910 r_free = 0.3910 target = 0.162280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116584 restraints weight = 9615.730| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.07 r_work: 0.3057 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8370 Z= 0.097 Angle : 0.492 8.327 11403 Z= 0.246 Chirality : 0.038 0.156 1425 Planarity : 0.003 0.030 1377 Dihedral : 4.080 11.485 1116 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.22 % Allowed : 7.07 % Favored : 92.70 % 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: -2.78 (0.25), residues: 1062 helix: -1.60 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -1.99 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.013 0.001 TYR A 251 PHE 0.007 0.001 PHE A 178 TRP 0.004 0.000 TRP B 286 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8370) covalent geometry : angle 0.49208 (11403) hydrogen bonds : bond 0.02857 ( 315) hydrogen bonds : angle 4.18908 ( 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 : 0.187 Fit side-chains REVERT: A 186 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7337 (mmp-170) REVERT: A 434 LYS cc_start: 0.8079 (tttt) cc_final: 0.7446 (mmtp) REVERT: B 186 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7423 (mmm160) REVERT: C 186 ARG cc_start: 0.8250 (mmt90) cc_final: 0.7242 (mmp-170) REVERT: C 295 MET cc_start: 0.6564 (mtt) cc_final: 0.6092 (ttm) outliers start: 2 outliers final: 2 residues processed: 89 average time/residue: 0.0976 time to fit residues: 11.3403 Evaluate side-chains 86 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain C residue 75 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3886 r_free = 0.3886 target = 0.159941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114297 restraints weight = 9633.986| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.05 r_work: 0.2982 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8370 Z= 0.152 Angle : 0.549 8.606 11403 Z= 0.275 Chirality : 0.040 0.169 1425 Planarity : 0.003 0.029 1377 Dihedral : 4.293 13.633 1116 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.22 % Allowed : 6.96 % Favored : 92.82 % 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: -2.90 (0.24), residues: 1062 helix: -1.67 (0.17), residues: 846 sheet: None (None), residues: 0 loop : -2.10 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 186 TYR 0.016 0.001 TYR A 251 PHE 0.011 0.001 PHE A 178 TRP 0.007 0.001 TRP C 257 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8370) covalent geometry : angle 0.54893 (11403) hydrogen bonds : bond 0.03674 ( 315) hydrogen bonds : angle 4.39661 ( 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 87 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.360 Fit side-chains REVERT: A 186 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.7316 (mmp-170) REVERT: A 188 GLU cc_start: 0.7963 (tt0) cc_final: 0.7738 (tp30) REVERT: A 194 LYS cc_start: 0.8637 (mttp) cc_final: 0.8362 (mmtt) REVERT: A 434 LYS cc_start: 0.8090 (tttt) cc_final: 0.7450 (mmtp) REVERT: B 186 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.7380 (mmm160) REVERT: C 186 ARG cc_start: 0.8283 (mmt90) cc_final: 0.7710 (mmm160) outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.1039 time to fit residues: 12.0600 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 : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain C residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3905 r_free = 0.3905 target = 0.161739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115915 restraints weight = 9689.944| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.10 r_work: 0.2998 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3303 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 : 0.501 8.458 11403 Z= 0.251 Chirality : 0.039 0.168 1425 Planarity : 0.003 0.030 1377 Dihedral : 4.067 11.928 1116 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.34 % Allowed : 6.96 % Favored : 92.70 % 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: -2.62 (0.25), residues: 1062 helix: -1.46 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -2.08 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.013 0.001 TYR A 251 PHE 0.008 0.001 PHE A 178 TRP 0.004 0.000 TRP B 286 HIS 0.002 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8370) covalent geometry : angle 0.50103 (11403) hydrogen bonds : bond 0.03021 ( 315) hydrogen bonds : angle 4.19762 ( 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 85 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.292 Fit side-chains REVERT: A 186 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.7328 (mmp-170) REVERT: A 434 LYS cc_start: 0.8064 (tttt) cc_final: 0.7424 (mmtp) REVERT: B 186 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7376 (mmm160) REVERT: C 186 ARG cc_start: 0.8373 (mmt90) cc_final: 0.7799 (mmm160) REVERT: C 295 MET cc_start: 0.6526 (mtt) cc_final: 0.6063 (ttm) outliers start: 3 outliers final: 3 residues processed: 85 average time/residue: 0.1008 time to fit residues: 11.3379 Evaluate side-chains 84 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain C residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 82 optimal weight: 0.0370 chunk 70 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3892 r_free = 0.3892 target = 0.160438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114469 restraints weight = 9712.256| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.10 r_work: 0.2981 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8370 Z= 0.142 Angle : 0.546 8.632 11403 Z= 0.273 Chirality : 0.040 0.171 1425 Planarity : 0.003 0.029 1377 Dihedral : 4.182 12.806 1116 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.34 % Allowed : 7.41 % 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: -2.68 (0.25), residues: 1062 helix: -1.47 (0.17), residues: 843 sheet: None (None), residues: 0 loop : -2.21 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.016 0.001 TYR A 251 PHE 0.010 0.001 PHE A 178 TRP 0.006 0.001 TRP C 257 HIS 0.002 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8370) covalent geometry : angle 0.54599 (11403) hydrogen bonds : bond 0.03495 ( 315) hydrogen bonds : angle 4.31923 ( 882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.92 seconds wall clock time: 35 minutes 30.26 seconds (2130.26 seconds total)