Starting phenix.real_space_refine on Fri Jul 3 04:55:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vbn_64928/07_2026/9vbn_64928_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vbn_64928/07_2026/9vbn_64928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vbn_64928/07_2026/9vbn_64928_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vbn_64928/07_2026/9vbn_64928_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vbn_64928/07_2026/9vbn_64928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vbn_64928/07_2026/9vbn_64928.map" } resolution = 3.23 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7866 2.51 5 N 1873 2.21 5 O 2038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 11834 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3945 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 17, 'TRANS': 487} Chain: "B" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3934 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 17, 'TRANS': 486} Chain: "C" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3934 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 17, 'TRANS': 486} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.19 Number of scatterers: 11834 At special positions: 0 Unit cell: (111.132, 115.101, 82.215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2038 8.00 N 1873 7.00 C 7866 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: 0.78 Conformation dependent library (CDL) restraints added in 524.6 milliseconds 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 1 sheets defined 86.2% alpha, 0.1% 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 14 through 35 removed outlier: 3.543A pdb=" N TYR A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 removed outlier: 3.660A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 4.101A pdb=" N LEU A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 97 through 105 removed outlier: 4.218A pdb=" N PHE A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 118 through 123 removed outlier: 4.089A pdb=" N MET A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 4.655A pdb=" N MET A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 145 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 167 removed outlier: 3.687A pdb=" N TRP A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 184 through 187 removed outlier: 3.642A pdb=" N ASN A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 187' Processing helix chain 'A' and resid 188 through 225 removed outlier: 4.190A pdb=" N SER A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 251 Processing helix chain 'A' and resid 253 through 278 removed outlier: 3.687A pdb=" N ARG A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.865A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 removed outlier: 4.702A pdb=" N LEU A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 319 through 340 removed outlier: 3.767A pdb=" N PHE A 323 " --> pdb=" O TRP A 319 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 328 " --> pdb=" O TRP A 324 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP A 330 " --> pdb=" O TRP A 326 " (cutoff:3.500A) Proline residue: A 332 - end of helix removed outlier: 3.518A pdb=" N LEU A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 356 through 379 removed outlier: 3.954A pdb=" N PHE A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.576A pdb=" N MET A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.597A pdb=" N GLY A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 396' Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.745A pdb=" N SER A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 removed outlier: 3.665A pdb=" N LEU A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 469 removed outlier: 3.759A pdb=" N MET A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 482 removed outlier: 3.751A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 512 removed outlier: 3.763A pdb=" N PHE A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 35 removed outlier: 4.073A pdb=" N TYR B 19 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 32 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 removed outlier: 3.621A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 74 removed outlier: 4.095A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.730A pdb=" N SER B 79 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 removed outlier: 4.346A pdb=" N ALA B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.573A pdb=" N PHE B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 131 through 146 removed outlier: 4.620A pdb=" N MET B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS B 145 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 167 removed outlier: 3.738A pdb=" N TRP B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.772A pdb=" N ASN B 187 " --> pdb=" O LYS B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 188 through 226 removed outlier: 3.952A pdb=" N SER B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 252 Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.553A pdb=" N LEU B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 299 removed outlier: 3.904A pdb=" N VAL B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.659A pdb=" N LEU B 304 " --> pdb=" O MET B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.567A pdb=" N MET B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 340 removed outlier: 4.001A pdb=" N PHE B 323 " --> pdb=" O TRP B 319 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 328 " --> pdb=" O TRP B 324 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP B 330 " --> pdb=" O TRP B 326 " (cutoff:3.500A) Proline residue: B 332 - end of helix removed outlier: 3.594A pdb=" N LEU B 336 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 356 through 379 removed outlier: 3.887A pdb=" N PHE B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.572A pdb=" N VAL B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 405 through 421 removed outlier: 4.434A pdb=" N TYR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 removed outlier: 3.799A pdb=" N LEU B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 469 removed outlier: 3.793A pdb=" N MET B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 removed outlier: 3.758A pdb=" N THR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 512 removed outlier: 3.800A pdb=" N PHE B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 488 " --> pdb=" O PRO B 484 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 505 " --> pdb=" O LYS B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 35 removed outlier: 3.677A pdb=" N THR C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.617A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 74 removed outlier: 4.103A pdb=" N LEU C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.771A pdb=" N SER C 79 " --> pdb=" O ARG C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 97 through 105 removed outlier: 3.906A pdb=" N PHE C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.570A pdb=" N PHE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 131 through 146 removed outlier: 4.651A pdb=" N MET C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS C 145 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 146 " --> pdb=" O THR C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 167 removed outlier: 3.678A pdb=" N TRP C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 187 removed outlier: 3.599A pdb=" N ASN C 187 " --> pdb=" O LYS C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 187' Processing helix chain 'C' and resid 188 through 226 removed outlier: 4.041A pdb=" N VAL C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 204 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 251 Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.854A pdb=" N ARG C 258 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 277 removed outlier: 4.296A pdb=" N VAL C 265 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.947A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 removed outlier: 4.688A pdb=" N LEU C 304 " --> pdb=" O MET C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 319 through 341 removed outlier: 3.770A pdb=" N PHE C 323 " --> pdb=" O TRP C 319 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 328 " --> pdb=" O TRP C 324 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP C 330 " --> pdb=" O TRP C 326 " (cutoff:3.500A) Proline residue: C 332 - end of helix removed outlier: 3.644A pdb=" N LEU C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 356 through 379 removed outlier: 3.861A pdb=" N PHE C 361 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 376 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.703A pdb=" N ALA C 401 " --> pdb=" O TYR C 397 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 422 Processing helix chain 'C' and resid 423 through 436 removed outlier: 4.180A pdb=" N SER C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 469 removed outlier: 3.531A pdb=" N ILE C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN C 469 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 removed outlier: 3.759A pdb=" N THR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 512 removed outlier: 3.801A pdb=" N PHE C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE C 490 " --> pdb=" O SER C 486 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13 removed outlier: 4.034A pdb=" N LYS B 12 " --> pdb=" O GLN B 438 " (cutoff:3.500A) 794 hydrogen bonds defined for protein. 2334 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: 1.63 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3549 1.34 - 1.46: 2648 1.46 - 1.58: 5856 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12161 Sorted by residual: bond pdb=" N ILE A 107 " pdb=" CA ILE A 107 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.89e+00 bond pdb=" N ILE B 107 " pdb=" CA ILE B 107 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.84e+00 bond pdb=" N ILE C 107 " pdb=" CA ILE C 107 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.79e+00 bond pdb=" N VAL C 114 " pdb=" CA VAL C 114 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.41e-02 5.03e+03 6.44e+00 bond pdb=" N ASP A 108 " pdb=" CA ASP A 108 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.33e-02 5.65e+03 5.12e+00 ... (remaining 12156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 16350 1.93 - 3.86: 186 3.86 - 5.79: 32 5.79 - 7.72: 1 7.72 - 9.65: 2 Bond angle restraints: 16571 Sorted by residual: angle pdb=" N VAL C 114 " pdb=" CA VAL C 114 " pdb=" C VAL C 114 " ideal model delta sigma weight residual 111.77 107.43 4.34 1.04e+00 9.25e-01 1.74e+01 angle pdb=" N VAL B 114 " pdb=" CA VAL B 114 " pdb=" C VAL B 114 " ideal model delta sigma weight residual 111.77 107.63 4.14 1.04e+00 9.25e-01 1.58e+01 angle pdb=" N ASP C 108 " pdb=" CA ASP C 108 " pdb=" C ASP C 108 " ideal model delta sigma weight residual 112.89 107.98 4.91 1.24e+00 6.50e-01 1.57e+01 angle pdb=" N ASP B 108 " pdb=" CA ASP B 108 " pdb=" C ASP B 108 " ideal model delta sigma weight residual 112.89 108.16 4.73 1.24e+00 6.50e-01 1.46e+01 angle pdb=" N TYR B 166 " pdb=" CA TYR B 166 " pdb=" C TYR B 166 " ideal model delta sigma weight residual 113.97 109.45 4.52 1.28e+00 6.10e-01 1.25e+01 ... (remaining 16566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 6085 16.32 - 32.64: 579 32.64 - 48.96: 173 48.96 - 65.28: 54 65.28 - 81.60: 5 Dihedral angle restraints: 6896 sinusoidal: 2561 harmonic: 4335 Sorted by residual: dihedral pdb=" CG ARG B 343 " pdb=" CD ARG B 343 " pdb=" NE ARG B 343 " pdb=" CZ ARG B 343 " ideal model delta sinusoidal sigma weight residual 180.00 137.17 42.83 2 1.50e+01 4.44e-03 9.86e+00 dihedral pdb=" N ARG A 36 " pdb=" CA ARG A 36 " pdb=" CB ARG A 36 " pdb=" CG ARG A 36 " ideal model delta sinusoidal sigma weight residual -180.00 -121.12 -58.88 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG A 311 " pdb=" C ARG A 311 " pdb=" N PRO A 312 " pdb=" CA PRO A 312 " ideal model delta harmonic sigma weight residual 180.00 164.66 15.34 0 5.00e+00 4.00e-02 9.42e+00 ... (remaining 6893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1664 0.055 - 0.109: 225 0.109 - 0.164: 9 0.164 - 0.218: 3 0.218 - 0.273: 2 Chirality restraints: 1903 Sorted by residual: chirality pdb=" CB VAL C 114 " pdb=" CA VAL C 114 " pdb=" CG1 VAL C 114 " pdb=" CG2 VAL C 114 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE B 107 " pdb=" N ILE B 107 " pdb=" C ILE B 107 " pdb=" CB ILE B 107 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE C 107 " pdb=" N ILE C 107 " pdb=" C ILE C 107 " pdb=" CB ILE C 107 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1900 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 170 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 171 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 14 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO B 15 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 170 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO C 171 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 171 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 171 " -0.015 5.00e-02 4.00e+02 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1255 2.75 - 3.28: 11790 3.28 - 3.82: 19230 3.82 - 4.36: 23044 4.36 - 4.90: 40620 Nonbonded interactions: 95939 Sorted by model distance: nonbonded pdb=" O PHE B 91 " pdb=" NH2 ARG B 345 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASN A 286 " pdb=" OG SER C 306 " model vdw 2.237 3.040 nonbonded pdb=" CE2 TRP B 327 " pdb=" C8 CHT B 601 " model vdw 2.295 3.680 nonbonded pdb=" OG SER B 306 " pdb=" OD1 ASN C 286 " model vdw 2.297 3.040 nonbonded pdb=" O SER B 367 " pdb=" ND2 ASN B 371 " model vdw 2.300 3.120 ... (remaining 95934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 601) 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: 7.380 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.680 Find NCS groups from input model: 0.140 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12161 Z= 0.131 Angle : 0.527 9.646 16571 Z= 0.313 Chirality : 0.037 0.273 1903 Planarity : 0.003 0.027 2024 Dihedral : 14.720 81.598 4128 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.73 % Allowed : 15.76 % Favored : 83.51 % 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: -0.48 (0.21), residues: 1507 helix: 0.05 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 36 TYR 0.013 0.001 TYR C 421 PHE 0.018 0.001 PHE B 277 TRP 0.012 0.001 TRP B 96 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (12161) covalent geometry : angle 0.52707 / 0.31 (16571) hydrogen bonds : bond 0.27783 / 18.18 ( 794) hydrogen bonds : angle 7.68286 / 5.39 ( 2334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7479 (pm20) cc_final: 0.7131 (pt0) REVERT: B 210 LEU cc_start: 0.8802 (tp) cc_final: 0.8484 (mm) REVERT: B 506 ARG cc_start: 0.6990 (mtm-85) cc_final: 0.6395 (mmt-90) REVERT: C 469 ASN cc_start: 0.8897 (t0) cc_final: 0.8675 (t0) REVERT: C 506 ARG cc_start: 0.7022 (tpp80) cc_final: 0.6686 (mtm-85) outliers start: 9 outliers final: 8 residues processed: 161 average time/residue: 0.0658 time to fit residues: 16.6696 Evaluate side-chains 149 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 407 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 291 ASN C 371 ASN C 443 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.153122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123159 restraints weight = 13380.841| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.62 r_work: 0.2971 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12161 Z= 0.174 Angle : 0.576 9.131 16571 Z= 0.308 Chirality : 0.040 0.142 1903 Planarity : 0.004 0.033 2024 Dihedral : 5.249 58.493 1643 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.48 % Allowed : 13.58 % Favored : 82.94 % 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: 0.49 (0.22), residues: 1507 helix: 0.87 (0.16), residues: 1132 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 345 TYR 0.016 0.001 TYR C 421 PHE 0.019 0.002 PHE C 299 TRP 0.015 0.002 TRP A 315 HIS 0.002 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (12161) covalent geometry : angle 0.57610 / 0.31 (16571) hydrogen bonds : bond 0.06511 / 4.26 ( 794) hydrogen bonds : angle 4.65877 / 3.31 ( 2334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.413 Fit side-chains REVERT: A 126 GLU cc_start: 0.7325 (pm20) cc_final: 0.6906 (pt0) REVERT: B 506 ARG cc_start: 0.6392 (mtm-85) cc_final: 0.5981 (mmp80) REVERT: C 460 LEU cc_start: 0.6985 (tp) cc_final: 0.6669 (tp) REVERT: C 469 ASN cc_start: 0.8606 (t0) cc_final: 0.8238 (t0) REVERT: C 506 ARG cc_start: 0.6540 (tpp80) cc_final: 0.6100 (mtm-85) outliers start: 43 outliers final: 26 residues processed: 194 average time/residue: 0.0751 time to fit residues: 22.5340 Evaluate side-chains 181 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 104 optimal weight: 0.0060 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 291 ASN C 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.157836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.125719 restraints weight = 13368.361| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.85 r_work: 0.3195 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12161 Z= 0.106 Angle : 0.452 7.407 16571 Z= 0.239 Chirality : 0.037 0.141 1903 Planarity : 0.003 0.030 2024 Dihedral : 4.761 51.437 1640 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.26 % Allowed : 16.33 % Favored : 81.41 % 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: 1.17 (0.23), residues: 1507 helix: 1.36 (0.16), residues: 1145 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 345 TYR 0.012 0.001 TYR C 421 PHE 0.021 0.001 PHE B 277 TRP 0.014 0.001 TRP C 42 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (12161) covalent geometry : angle 0.45212 / 0.24 (16571) hydrogen bonds : bond 0.04340 / 2.85 ( 794) hydrogen bonds : angle 4.11874 / 2.94 ( 2334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.419 Fit side-chains REVERT: A 126 GLU cc_start: 0.7521 (pm20) cc_final: 0.7147 (pt0) REVERT: A 174 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7461 (mm) REVERT: B 182 PHE cc_start: 0.7756 (m-10) cc_final: 0.7495 (m-80) REVERT: B 280 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6653 (t70) REVERT: B 506 ARG cc_start: 0.6525 (mtm-85) cc_final: 0.5951 (mmt-90) REVERT: C 237 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7692 (mp) REVERT: C 460 LEU cc_start: 0.7320 (tp) cc_final: 0.6980 (tp) REVERT: C 469 ASN cc_start: 0.8773 (t0) cc_final: 0.8445 (t0) REVERT: C 506 ARG cc_start: 0.6755 (tpp80) cc_final: 0.6305 (mtm-85) outliers start: 28 outliers final: 16 residues processed: 195 average time/residue: 0.0741 time to fit residues: 22.4991 Evaluate side-chains 180 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.154475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122480 restraints weight = 13307.726| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.81 r_work: 0.3058 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12161 Z= 0.141 Angle : 0.517 8.487 16571 Z= 0.268 Chirality : 0.039 0.139 1903 Planarity : 0.003 0.030 2024 Dihedral : 4.112 45.592 1634 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.37 % Allowed : 15.60 % Favored : 80.03 % 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: 1.09 (0.22), residues: 1507 helix: 1.31 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 345 TYR 0.017 0.001 TYR C 421 PHE 0.022 0.002 PHE B 277 TRP 0.012 0.001 TRP C 42 HIS 0.002 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (12161) covalent geometry : angle 0.51733 / 0.27 (16571) hydrogen bonds : bond 0.04898 / 3.20 ( 794) hydrogen bonds : angle 4.09482 / 2.91 ( 2334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.487 Fit side-chains REVERT: A 126 GLU cc_start: 0.7532 (pm20) cc_final: 0.7140 (pt0) REVERT: A 174 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7681 (mm) REVERT: A 394 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8417 (mtt180) REVERT: B 182 PHE cc_start: 0.7841 (m-80) cc_final: 0.7498 (m-80) REVERT: B 338 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6056 (mp) REVERT: C 469 ASN cc_start: 0.8798 (t0) cc_final: 0.8456 (t0) REVERT: C 506 ARG cc_start: 0.6648 (tpp80) cc_final: 0.6173 (mtm-85) outliers start: 54 outliers final: 36 residues processed: 205 average time/residue: 0.0821 time to fit residues: 25.9480 Evaluate side-chains 199 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 142 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.154068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121835 restraints weight = 13367.482| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.88 r_work: 0.3130 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12161 Z= 0.141 Angle : 0.506 8.682 16571 Z= 0.264 Chirality : 0.039 0.144 1903 Planarity : 0.003 0.029 2024 Dihedral : 4.237 50.107 1634 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.28 % Allowed : 15.93 % Favored : 79.79 % 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: 1.08 (0.22), residues: 1507 helix: 1.30 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.017 0.001 TYR C 421 PHE 0.023 0.002 PHE B 277 TRP 0.012 0.001 TRP C 42 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12161) covalent geometry : angle 0.50564 / 0.26 (16571) hydrogen bonds : bond 0.04763 / 3.11 ( 794) hydrogen bonds : angle 4.02865 / 2.85 ( 2334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 0.420 Fit side-chains REVERT: A 126 GLU cc_start: 0.7517 (pm20) cc_final: 0.7084 (pt0) REVERT: A 174 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7568 (mm) REVERT: A 394 ARG cc_start: 0.8625 (mtt180) cc_final: 0.8410 (mtt180) REVERT: B 182 PHE cc_start: 0.7801 (m-80) cc_final: 0.7452 (m-80) REVERT: B 338 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6093 (mp) REVERT: C 469 ASN cc_start: 0.8812 (t0) cc_final: 0.8461 (t0) REVERT: C 506 ARG cc_start: 0.6646 (tpp80) cc_final: 0.6190 (mtm-85) outliers start: 53 outliers final: 39 residues processed: 199 average time/residue: 0.0817 time to fit residues: 25.0657 Evaluate side-chains 199 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 67 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.155723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123508 restraints weight = 13395.115| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.87 r_work: 0.3221 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12161 Z= 0.110 Angle : 0.469 8.411 16571 Z= 0.244 Chirality : 0.038 0.151 1903 Planarity : 0.003 0.028 2024 Dihedral : 4.264 57.218 1634 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.31 % Allowed : 16.98 % Favored : 79.71 % 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: 1.36 (0.22), residues: 1507 helix: 1.48 (0.16), residues: 1142 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 345 TYR 0.013 0.001 TYR C 421 PHE 0.023 0.001 PHE B 277 TRP 0.012 0.001 TRP C 42 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (12161) covalent geometry : angle 0.46881 / 0.24 (16571) hydrogen bonds : bond 0.04160 / 2.73 ( 794) hydrogen bonds : angle 3.88602 / 2.76 ( 2334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.407 Fit side-chains REVERT: A 126 GLU cc_start: 0.7435 (pm20) cc_final: 0.7008 (pt0) REVERT: A 174 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7525 (mm) REVERT: A 386 GLU cc_start: 0.7755 (tp30) cc_final: 0.7421 (tp30) REVERT: A 394 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8245 (mtt180) REVERT: B 280 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6781 (t70) REVERT: B 338 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5897 (mp) REVERT: C 469 ASN cc_start: 0.8740 (t0) cc_final: 0.8402 (t0) REVERT: C 506 ARG cc_start: 0.6505 (tpp80) cc_final: 0.6019 (mtm-85) outliers start: 41 outliers final: 31 residues processed: 190 average time/residue: 0.0832 time to fit residues: 24.3252 Evaluate side-chains 187 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 27 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 291 ASN C 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119288 restraints weight = 13382.328| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.82 r_work: 0.3055 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12161 Z= 0.213 Angle : 0.591 9.871 16571 Z= 0.307 Chirality : 0.042 0.169 1903 Planarity : 0.004 0.033 2024 Dihedral : 4.282 53.288 1632 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.69 % Allowed : 15.44 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.22), residues: 1507 helix: 0.95 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.10 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 136 TYR 0.021 0.001 TYR C 421 PHE 0.024 0.002 PHE B 277 TRP 0.011 0.002 TRP B 42 HIS 0.008 0.002 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (12161) covalent geometry : angle 0.59138 / 0.31 (16571) hydrogen bonds : bond 0.05592 / 3.63 ( 794) hydrogen bonds : angle 4.17148 / 2.95 ( 2334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 0.371 Fit side-chains REVERT: A 126 GLU cc_start: 0.7568 (pm20) cc_final: 0.7109 (pt0) REVERT: A 174 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7701 (mm) REVERT: A 386 GLU cc_start: 0.7895 (tp30) cc_final: 0.7584 (tp30) REVERT: A 394 ARG cc_start: 0.8695 (mtt180) cc_final: 0.8477 (mtt180) REVERT: B 338 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6135 (mp) REVERT: C 469 ASN cc_start: 0.8833 (t0) cc_final: 0.8484 (t0) REVERT: C 506 ARG cc_start: 0.6616 (tpp80) cc_final: 0.6104 (mtm-85) outliers start: 58 outliers final: 47 residues processed: 201 average time/residue: 0.0810 time to fit residues: 25.0735 Evaluate side-chains 204 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122371 restraints weight = 13312.867| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.87 r_work: 0.3148 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12161 Z= 0.123 Angle : 0.494 9.073 16571 Z= 0.256 Chirality : 0.038 0.160 1903 Planarity : 0.003 0.030 2024 Dihedral : 4.004 52.402 1632 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.72 % Allowed : 16.73 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.22), residues: 1507 helix: 1.27 (0.15), residues: 1159 sheet: None (None), residues: 0 loop : -0.95 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 507 TYR 0.015 0.001 TYR C 421 PHE 0.025 0.001 PHE B 277 TRP 0.013 0.001 TRP C 42 HIS 0.006 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12161) covalent geometry : angle 0.49379 / 0.26 (16571) hydrogen bonds : bond 0.04462 / 2.92 ( 794) hydrogen bonds : angle 3.94219 / 2.79 ( 2334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 0.430 Fit side-chains REVERT: A 126 GLU cc_start: 0.7512 (pm20) cc_final: 0.7051 (pt0) REVERT: A 174 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7636 (mm) REVERT: A 386 GLU cc_start: 0.7846 (tp30) cc_final: 0.7542 (tp30) REVERT: A 394 ARG cc_start: 0.8616 (mtt180) cc_final: 0.8282 (mtt180) REVERT: C 469 ASN cc_start: 0.8804 (t0) cc_final: 0.8459 (t0) REVERT: C 506 ARG cc_start: 0.6596 (tpp80) cc_final: 0.6097 (mtm-85) outliers start: 46 outliers final: 36 residues processed: 193 average time/residue: 0.0813 time to fit residues: 23.9142 Evaluate side-chains 190 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 0.3980 chunk 145 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123979 restraints weight = 13226.830| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.86 r_work: 0.3226 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12161 Z= 0.106 Angle : 0.472 8.967 16571 Z= 0.243 Chirality : 0.038 0.168 1903 Planarity : 0.003 0.029 2024 Dihedral : 3.806 53.036 1632 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.23 % Allowed : 17.30 % Favored : 79.47 % 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: 1.46 (0.22), residues: 1507 helix: 1.51 (0.16), residues: 1160 sheet: None (None), residues: 0 loop : -0.78 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 507 TYR 0.013 0.001 TYR C 421 PHE 0.026 0.001 PHE B 277 TRP 0.011 0.001 TRP C 42 HIS 0.007 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (12161) covalent geometry : angle 0.47154 / 0.24 (16571) hydrogen bonds : bond 0.03948 / 2.59 ( 794) hydrogen bonds : angle 3.81483 / 2.71 ( 2334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.405 Fit side-chains REVERT: A 126 GLU cc_start: 0.7457 (pm20) cc_final: 0.6987 (pt0) REVERT: A 174 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7588 (mm) REVERT: A 386 GLU cc_start: 0.7728 (tp30) cc_final: 0.7410 (tp30) REVERT: B 181 ILE cc_start: 0.7134 (mt) cc_final: 0.6881 (mt) REVERT: C 469 ASN cc_start: 0.8786 (t0) cc_final: 0.8448 (t0) REVERT: C 506 ARG cc_start: 0.6408 (tpp80) cc_final: 0.5910 (mtm-85) outliers start: 40 outliers final: 30 residues processed: 184 average time/residue: 0.0830 time to fit residues: 23.2443 Evaluate side-chains 182 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 99 optimal weight: 0.0040 chunk 115 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 66 optimal weight: 0.0060 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 overall best weight: 0.5608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 291 ASN C 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.156794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124066 restraints weight = 13333.107| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.85 r_work: 0.3224 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12161 Z= 0.103 Angle : 0.471 9.144 16571 Z= 0.242 Chirality : 0.037 0.166 1903 Planarity : 0.003 0.029 2024 Dihedral : 3.755 52.920 1632 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.43 % Allowed : 17.78 % Favored : 79.79 % 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: 1.59 (0.22), residues: 1507 helix: 1.63 (0.16), residues: 1152 sheet: None (None), residues: 0 loop : -0.78 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 394 TYR 0.013 0.001 TYR C 421 PHE 0.025 0.001 PHE B 277 TRP 0.010 0.001 TRP C 42 HIS 0.006 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (12161) covalent geometry : angle 0.47136 / 0.24 (16571) hydrogen bonds : bond 0.03847 / 2.53 ( 794) hydrogen bonds : angle 3.76524 / 2.67 ( 2334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.339 Fit side-chains REVERT: A 126 GLU cc_start: 0.7456 (pm20) cc_final: 0.6999 (pt0) REVERT: A 174 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 386 GLU cc_start: 0.7824 (tp30) cc_final: 0.7553 (tp30) REVERT: B 181 ILE cc_start: 0.7101 (mt) cc_final: 0.6876 (mt) REVERT: C 469 ASN cc_start: 0.8834 (t0) cc_final: 0.8500 (t0) REVERT: C 506 ARG cc_start: 0.6588 (tpp80) cc_final: 0.6086 (mtm-85) outliers start: 30 outliers final: 27 residues processed: 178 average time/residue: 0.0807 time to fit residues: 21.9720 Evaluate side-chains 180 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 391 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.156380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123682 restraints weight = 13269.520| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.89 r_work: 0.3214 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12161 Z= 0.111 Angle : 0.479 9.106 16571 Z= 0.246 Chirality : 0.038 0.167 1903 Planarity : 0.003 0.029 2024 Dihedral : 3.756 52.986 1632 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.67 % Allowed : 17.46 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.59 (0.22), residues: 1507 helix: 1.62 (0.16), residues: 1151 sheet: None (None), residues: 0 loop : -0.76 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 343 TYR 0.014 0.001 TYR C 421 PHE 0.025 0.001 PHE B 277 TRP 0.010 0.001 TRP C 42 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (12161) covalent geometry : angle 0.47948 / 0.25 (16571) hydrogen bonds : bond 0.03992 / 2.61 ( 794) hydrogen bonds : angle 3.76739 / 2.67 ( 2334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2593.18 seconds wall clock time: 45 minutes 7.00 seconds (2707.00 seconds total)