Starting phenix.real_space_refine on Fri Jul 3 04:57:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vcp_64960/07_2026/9vcp_64960_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vcp_64960/07_2026/9vcp_64960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vcp_64960/07_2026/9vcp_64960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vcp_64960/07_2026/9vcp_64960.map" model { file = "/net/cci-nas-00/data/ceres_data/9vcp_64960/07_2026/9vcp_64960_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vcp_64960/07_2026/9vcp_64960_neut_trim.cif" } resolution = 3.29 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= 0.013 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 7860 2.51 5 N 1869 2.21 5 O 2037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11823 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" 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: "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: 2.74, per 1000 atoms: 0.23 Number of scatterers: 11823 At special positions: 0 Unit cell: (83.349, 116.235, 109.431, 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 2037 8.00 N 1869 7.00 C 7860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 558.8 milliseconds 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 1 sheets defined 85.3% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 35 removed outlier: 3.838A pdb=" N THR A 20 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 74 removed outlier: 5.895A pdb=" N TRP A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 4.116A pdb=" N SER A 79 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 80 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 4.208A pdb=" N LEU A 100 " --> pdb=" O TRP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 133 through 146 removed outlier: 4.485A pdb=" N MET A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 163 removed outlier: 3.538A pdb=" N TRP A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 188 through 225 removed outlier: 3.599A pdb=" N VAL A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 251 removed outlier: 3.923A pdb=" N THR A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 278 removed outlier: 4.430A pdb=" N LEU A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 298 Processing helix chain 'A' and resid 299 through 304 removed outlier: 4.621A pdb=" N LEU A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.513A pdb=" N ASN A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 330 removed outlier: 4.207A pdb=" N VAL A 328 " --> pdb=" O TRP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 removed outlier: 3.613A pdb=" N ILE A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.808A pdb=" N PHE A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 removed outlier: 4.175A pdb=" N GLU A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.897A pdb=" N GLU A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.788A pdb=" N TYR A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 436 removed outlier: 3.590A pdb=" N SER A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 482 removed outlier: 3.591A pdb=" N VAL A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 458 " --> pdb=" O TRP A 454 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ILE A 471 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N SER A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 510 removed outlier: 3.982A pdb=" N PHE A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 35 Processing helix chain 'B' and resid 35 through 54 removed outlier: 3.500A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 74 removed outlier: 3.675A pdb=" N TYR B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.782A pdb=" N SER B 79 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 80 " --> pdb=" O PHE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 101 removed outlier: 3.690A pdb=" N LEU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 132 through 146 removed outlier: 4.018A pdb=" N MET B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 167 removed outlier: 3.545A pdb=" N TRP B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.664A pdb=" N ILE B 186 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 187 " --> pdb=" O LYS B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 187' Processing helix chain 'B' and resid 188 through 225 removed outlier: 3.712A pdb=" N VAL B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.648A 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 removed outlier: 3.596A pdb=" N GLY B 256 " --> pdb=" O VAL B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 257 through 279 removed outlier: 3.688A pdb=" N SER B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 299 removed outlier: 3.740A pdb=" N LEU B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 319 through 342 removed outlier: 3.504A pdb=" N PHE B 323 " --> pdb=" O TRP B 319 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 328 " --> pdb=" O TRP B 324 " (cutoff:3.500A) Proline residue: B 332 - end of helix Processing helix chain 'B' and resid 346 through 356 Processing helix chain 'B' and resid 356 through 370 removed outlier: 4.043A pdb=" N PHE B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.825A pdb=" N GLU B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 399 removed outlier: 4.714A pdb=" N PHE B 396 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 397 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 399 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 437 removed outlier: 3.758A pdb=" N TYR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 469 removed outlier: 3.610A pdb=" N ARG B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 453 " --> pdb=" O TRP B 449 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 481 removed outlier: 3.668A pdb=" N LEU B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 512 removed outlier: 3.738A pdb=" N PHE B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 488 " --> pdb=" O PRO B 484 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 35 removed outlier: 3.501A pdb=" N LEU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 75 removed outlier: 5.676A pdb=" N TRP C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.920A pdb=" N SER C 79 " --> pdb=" O ARG C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.584A pdb=" N ALA C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.825A pdb=" N LEU C 109 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 123 removed outlier: 3.962A pdb=" N VAL C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.518A pdb=" N ALA C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 146 " --> pdb=" O THR C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 167 removed outlier: 3.532A pdb=" N TRP C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N MET C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET C 157 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 158 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.993A pdb=" N ALA C 177 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 187 Processing helix chain 'C' and resid 188 through 225 removed outlier: 3.568A pdb=" N GLY C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 252 removed outlier: 4.111A pdb=" N THR C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 259 through 277 removed outlier: 4.254A pdb=" N VAL C 265 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 removed outlier: 4.098A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 removed outlier: 4.491A pdb=" N LEU C 304 " --> pdb=" O MET C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 319 through 330 removed outlier: 3.908A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 removed outlier: 3.711A pdb=" N ILE C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 356 Processing helix chain 'C' and resid 356 through 379 removed outlier: 4.040A pdb=" N PHE C 361 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.734A pdb=" N GLU C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) 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 400 Processing helix chain 'C' and resid 401 through 403 No H-bonds generated for 'chain 'C' and resid 401 through 403' Processing helix chain 'C' and resid 405 through 436 removed outlier: 3.622A pdb=" N PHE C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 469 removed outlier: 3.542A pdb=" N ARG C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE C 453 " --> pdb=" O TRP C 449 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 469 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 removed outlier: 3.505A pdb=" N LEU C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 512 removed outlier: 3.981A pdb=" N PHE C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE C 490 " --> pdb=" O SER C 486 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 12 through 13 removed outlier: 4.461A pdb=" N LYS C 12 " --> pdb=" O GLN C 438 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2379 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: 1.78 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3540 1.34 - 1.46: 2397 1.46 - 1.58: 6105 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12150 Sorted by residual: bond pdb=" N VAL A 114 " pdb=" CA VAL A 114 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.09e-02 8.42e+03 1.10e+01 bond pdb=" N PHE A 91 " pdb=" CA PHE A 91 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.14e-02 7.69e+03 9.92e+00 bond pdb=" N VAL C 328 " pdb=" CA VAL C 328 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.59e+00 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.57e+00 bond pdb=" N SER C 331 " pdb=" CA SER C 331 " ideal model delta sigma weight residual 1.462 1.488 -0.026 8.50e-03 1.38e+04 9.43e+00 ... (remaining 12145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 16284 1.84 - 3.69: 229 3.69 - 5.53: 39 5.53 - 7.38: 3 7.38 - 9.22: 2 Bond angle restraints: 16557 Sorted by residual: angle pdb=" N LEU A 109 " pdb=" CA LEU A 109 " pdb=" C LEU A 109 " ideal model delta sigma weight residual 113.20 107.60 5.60 1.21e+00 6.83e-01 2.14e+01 angle pdb=" N MET A 110 " pdb=" CA MET A 110 " pdb=" C MET A 110 " ideal model delta sigma weight residual 113.97 108.91 5.06 1.28e+00 6.10e-01 1.56e+01 angle pdb=" N ASN C 469 " pdb=" CA ASN C 469 " pdb=" C ASN C 469 " ideal model delta sigma weight residual 112.72 108.10 4.62 1.28e+00 6.10e-01 1.30e+01 angle pdb=" N ALA A 115 " pdb=" CA ALA A 115 " pdb=" C ALA A 115 " ideal model delta sigma weight residual 114.56 110.02 4.54 1.27e+00 6.20e-01 1.28e+01 angle pdb=" N LEU C 109 " pdb=" CA LEU C 109 " pdb=" C LEU C 109 " ideal model delta sigma weight residual 112.54 108.23 4.31 1.22e+00 6.72e-01 1.25e+01 ... (remaining 16552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 6078 14.74 - 29.47: 564 29.47 - 44.21: 174 44.21 - 58.95: 49 58.95 - 73.68: 23 Dihedral angle restraints: 6888 sinusoidal: 2556 harmonic: 4332 Sorted by residual: dihedral pdb=" CA TRP C 324 " pdb=" CB TRP C 324 " pdb=" CG TRP C 324 " pdb=" CD1 TRP C 324 " ideal model delta sinusoidal sigma weight residual -90.00 -162.94 72.94 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB MET C 110 " pdb=" CG MET C 110 " pdb=" SD MET C 110 " pdb=" CE MET C 110 " ideal model delta sinusoidal sigma weight residual 60.00 3.80 56.20 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CA ASN C 218 " pdb=" CB ASN C 218 " pdb=" CG ASN C 218 " pdb=" OD1 ASN C 218 " ideal model delta sinusoidal sigma weight residual 120.00 -179.29 -60.71 2 2.00e+01 2.50e-03 9.13e+00 ... (remaining 6885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1410 0.040 - 0.081: 418 0.081 - 0.121: 59 0.121 - 0.161: 9 0.161 - 0.202: 6 Chirality restraints: 1902 Sorted by residual: 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 2.63 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA VAL A 114 " pdb=" N VAL A 114 " pdb=" C VAL A 114 " pdb=" CB VAL A 114 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 1899 not shown) Planarity restraints: 2022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 28 " 0.009 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE A 28 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 28 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 28 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 28 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 28 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 28 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 118 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.14e+00 pdb=" C VAL B 118 " 0.018 2.00e-02 2.50e+03 pdb=" O VAL B 118 " -0.007 2.00e-02 2.50e+03 pdb=" N THR B 119 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 88 " 0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO A 89 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.014 5.00e-02 4.00e+02 ... (remaining 2019 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 6923 3.02 - 3.49: 12112 3.49 - 3.96: 18379 3.96 - 4.43: 21944 4.43 - 4.90: 34955 Nonbonded interactions: 94313 Sorted by model distance: nonbonded pdb=" N GLN B 123 " pdb=" OE1 GLN B 123 " model vdw 2.555 3.120 nonbonded pdb=" N LEU A 109 " pdb=" N MET A 110 " model vdw 2.602 2.560 nonbonded pdb=" N VAL A 118 " pdb=" N THR A 119 " model vdw 2.617 2.560 nonbonded pdb=" N GLY C 104 " pdb=" N ILE C 105 " model vdw 2.621 2.560 nonbonded pdb=" C SER A 95 " pdb=" OG SER A 95 " model vdw 2.630 2.616 ... (remaining 94308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 0.003 0.037 12150 Z= 0.196 Angle : 0.557 9.223 16557 Z= 0.335 Chirality : 0.038 0.202 1902 Planarity : 0.003 0.026 2022 Dihedral : 13.919 73.685 4122 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.13 % Allowed : 12.94 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.21), residues: 1506 helix: -0.24 (0.15), residues: 1111 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 258 TYR 0.010 0.001 TYR B 421 PHE 0.025 0.001 PHE A 28 TRP 0.010 0.001 TRP C 326 HIS 0.009 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.20 (12150) covalent geometry : angle 0.55731 / 0.33 (16557) hydrogen bonds : bond 0.28108 / 18.33 ( 816) hydrogen bonds : angle 7.90136 / 5.53 ( 2379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.406 Fit side-chains REVERT: B 148 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8126 (tt) REVERT: B 324 TRP cc_start: 0.7515 (m-10) cc_final: 0.6520 (m-10) outliers start: 14 outliers final: 11 residues processed: 195 average time/residue: 0.0805 time to fit residues: 24.2833 Evaluate side-chains 182 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 324 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN A 291 ASN A 371 ASN B 349 GLN C 379 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116188 restraints weight = 15096.232| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.78 r_work: 0.3121 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12150 Z= 0.166 Angle : 0.584 11.208 16557 Z= 0.312 Chirality : 0.040 0.163 1902 Planarity : 0.004 0.024 2022 Dihedral : 5.539 76.207 1647 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.51 % Allowed : 14.08 % Favored : 83.41 % 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: 0.67 (0.22), residues: 1506 helix: 0.94 (0.16), residues: 1142 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 512 TYR 0.020 0.001 TYR A 375 PHE 0.017 0.002 PHE C 420 TRP 0.015 0.001 TRP A 42 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (12150) covalent geometry : angle 0.58440 / 0.31 (16557) hydrogen bonds : bond 0.07213 / 4.68 ( 816) hydrogen bonds : angle 4.53133 / 3.19 ( 2379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.308 Fit side-chains REVERT: A 203 ILE cc_start: 0.7859 (mt) cc_final: 0.7364 (pt) REVERT: B 148 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7224 (mt) REVERT: B 187 ASN cc_start: 0.7829 (t0) cc_final: 0.7629 (p0) REVERT: C 184 LYS cc_start: 0.8541 (mptt) cc_final: 0.7991 (tptm) REVERT: C 210 LEU cc_start: 0.7717 (tp) cc_final: 0.6932 (mp) outliers start: 31 outliers final: 21 residues processed: 190 average time/residue: 0.0854 time to fit residues: 25.1616 Evaluate side-chains 186 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 135 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117805 restraints weight = 15215.638| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.72 r_work: 0.3168 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12150 Z= 0.126 Angle : 0.504 11.522 16557 Z= 0.266 Chirality : 0.038 0.148 1902 Planarity : 0.003 0.029 2022 Dihedral : 5.065 73.846 1639 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.59 % Allowed : 14.64 % Favored : 82.77 % 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: 0.99 (0.23), residues: 1506 helix: 1.22 (0.16), residues: 1147 sheet: None (None), residues: 0 loop : -1.09 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 507 TYR 0.018 0.001 TYR A 219 PHE 0.017 0.001 PHE C 420 TRP 0.014 0.001 TRP A 42 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (12150) covalent geometry : angle 0.50405 / 0.27 (16557) hydrogen bonds : bond 0.05689 / 3.68 ( 816) hydrogen bonds : angle 4.08765 / 2.86 ( 2379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.293 Fit side-chains REVERT: A 203 ILE cc_start: 0.7861 (mt) cc_final: 0.7338 (pt) REVERT: A 209 THR cc_start: 0.6987 (OUTLIER) cc_final: 0.6657 (m) REVERT: B 148 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7330 (mt) REVERT: B 324 TRP cc_start: 0.7312 (m-10) cc_final: 0.6843 (m-10) REVERT: B 506 ARG cc_start: 0.6694 (ttt180) cc_final: 0.6169 (ttp80) REVERT: C 210 LEU cc_start: 0.7801 (tp) cc_final: 0.6981 (mp) REVERT: C 436 THR cc_start: 0.8685 (t) cc_final: 0.8436 (t) outliers start: 32 outliers final: 17 residues processed: 192 average time/residue: 0.0747 time to fit residues: 22.7135 Evaluate side-chains 181 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN A 291 ASN A 371 ASN C 379 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117349 restraints weight = 15121.134| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.81 r_work: 0.3147 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12150 Z= 0.130 Angle : 0.513 12.336 16557 Z= 0.266 Chirality : 0.038 0.223 1902 Planarity : 0.003 0.025 2022 Dihedral : 4.957 74.433 1637 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.18 % Allowed : 15.53 % Favored : 82.28 % 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 (0.23), residues: 1506 helix: 1.32 (0.16), residues: 1150 sheet: None (None), residues: 0 loop : -1.14 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.028 0.001 TYR A 219 PHE 0.014 0.001 PHE C 420 TRP 0.014 0.001 TRP A 42 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (12150) covalent geometry : angle 0.51285 / 0.27 (16557) hydrogen bonds : bond 0.05231 / 3.40 ( 816) hydrogen bonds : angle 3.92947 / 2.75 ( 2379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.476 Fit side-chains REVERT: A 203 ILE cc_start: 0.7860 (mt) cc_final: 0.7312 (pt) REVERT: A 209 THR cc_start: 0.6980 (OUTLIER) cc_final: 0.6692 (m) REVERT: A 237 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6239 (mm) REVERT: B 148 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7328 (mt) REVERT: B 324 TRP cc_start: 0.7339 (m-10) cc_final: 0.6876 (m-10) REVERT: C 210 LEU cc_start: 0.7805 (tp) cc_final: 0.6937 (mp) REVERT: C 436 THR cc_start: 0.8670 (t) cc_final: 0.8425 (t) outliers start: 27 outliers final: 18 residues processed: 181 average time/residue: 0.0781 time to fit residues: 22.1202 Evaluate side-chains 182 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 456 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 70 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 128 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 291 ASN C 371 ASN C 379 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118523 restraints weight = 15080.054| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.80 r_work: 0.3173 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12150 Z= 0.118 Angle : 0.495 12.612 16557 Z= 0.255 Chirality : 0.038 0.297 1902 Planarity : 0.003 0.026 2022 Dihedral : 4.884 73.212 1635 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.83 % Allowed : 16.10 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1506 helix: 1.45 (0.16), residues: 1155 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 506 TYR 0.019 0.001 TYR A 219 PHE 0.011 0.001 PHE C 38 TRP 0.012 0.001 TRP A 42 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (12150) covalent geometry : angle 0.49524 / 0.26 (16557) hydrogen bonds : bond 0.04767 / 3.09 ( 816) hydrogen bonds : angle 3.81298 / 2.67 ( 2379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.465 Fit side-chains REVERT: A 203 ILE cc_start: 0.7832 (mt) cc_final: 0.7270 (pt) REVERT: B 30 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7497 (mp) REVERT: B 148 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 324 TRP cc_start: 0.7335 (m-10) cc_final: 0.6881 (m-10) REVERT: C 210 LEU cc_start: 0.7730 (tp) cc_final: 0.6839 (mp) REVERT: C 436 THR cc_start: 0.8632 (t) cc_final: 0.8386 (t) outliers start: 35 outliers final: 23 residues processed: 190 average time/residue: 0.0765 time to fit residues: 23.1465 Evaluate side-chains 179 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 456 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 95 optimal weight: 6.9990 chunk 143 optimal weight: 0.0970 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121767 restraints weight = 15056.386| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.72 r_work: 0.3217 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12150 Z= 0.103 Angle : 0.485 12.297 16557 Z= 0.247 Chirality : 0.037 0.365 1902 Planarity : 0.003 0.026 2022 Dihedral : 4.790 69.634 1635 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.07 % Allowed : 15.86 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.23), residues: 1506 helix: 1.56 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -1.10 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 506 TYR 0.015 0.001 TYR A 375 PHE 0.012 0.001 PHE B 337 TRP 0.012 0.001 TRP B 365 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (12150) covalent geometry : angle 0.48493 / 0.25 (16557) hydrogen bonds : bond 0.04187 / 2.73 ( 816) hydrogen bonds : angle 3.71227 / 2.60 ( 2379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.547 Fit side-chains REVERT: A 110 MET cc_start: 0.8317 (ttm) cc_final: 0.8002 (mtp) REVERT: A 203 ILE cc_start: 0.7848 (mt) cc_final: 0.7283 (pt) REVERT: B 30 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7537 (mp) REVERT: B 148 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7443 (mt) REVERT: B 300 MET cc_start: 0.8985 (mmm) cc_final: 0.8778 (tpt) REVERT: B 324 TRP cc_start: 0.7333 (m-10) cc_final: 0.6850 (m-10) REVERT: C 210 LEU cc_start: 0.7702 (tp) cc_final: 0.6823 (mp) REVERT: C 436 THR cc_start: 0.8590 (t) cc_final: 0.8349 (t) outliers start: 38 outliers final: 24 residues processed: 187 average time/residue: 0.0794 time to fit residues: 23.7227 Evaluate side-chains 180 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 456 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 133 optimal weight: 0.0010 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN A 218 ASN C 379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115002 restraints weight = 15140.552| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.71 r_work: 0.3137 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12150 Z= 0.169 Angle : 0.553 11.750 16557 Z= 0.285 Chirality : 0.040 0.363 1902 Planarity : 0.003 0.029 2022 Dihedral : 4.933 78.274 1635 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.32 % Allowed : 15.86 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.23), residues: 1506 helix: 1.41 (0.16), residues: 1175 sheet: None (None), residues: 0 loop : -1.17 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 506 TYR 0.017 0.001 TYR A 375 PHE 0.018 0.001 PHE B 333 TRP 0.013 0.001 TRP C 327 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (12150) covalent geometry : angle 0.55307 / 0.29 (16557) hydrogen bonds : bond 0.05449 / 3.53 ( 816) hydrogen bonds : angle 3.86488 / 2.71 ( 2379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.376 Fit side-chains REVERT: A 148 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7426 (tp) REVERT: A 203 ILE cc_start: 0.7923 (mt) cc_final: 0.7384 (pt) REVERT: A 420 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: B 30 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7526 (mp) REVERT: B 148 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7375 (mt) REVERT: B 300 MET cc_start: 0.9030 (mmm) cc_final: 0.8809 (tpt) REVERT: B 324 TRP cc_start: 0.7409 (m-10) cc_final: 0.6975 (m-10) REVERT: C 210 LEU cc_start: 0.7803 (tp) cc_final: 0.6877 (mp) REVERT: C 436 THR cc_start: 0.8635 (t) cc_final: 0.8383 (t) outliers start: 41 outliers final: 28 residues processed: 184 average time/residue: 0.0818 time to fit residues: 23.5756 Evaluate side-chains 189 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 456 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 117 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 116 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118717 restraints weight = 15196.942| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.80 r_work: 0.3172 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12150 Z= 0.113 Angle : 0.507 12.946 16557 Z= 0.257 Chirality : 0.038 0.386 1902 Planarity : 0.003 0.031 2022 Dihedral : 4.772 73.729 1635 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.59 % Allowed : 16.75 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.23), residues: 1506 helix: 1.55 (0.16), residues: 1174 sheet: None (None), residues: 0 loop : -1.15 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 506 TYR 0.015 0.001 TYR A 375 PHE 0.012 0.001 PHE C 38 TRP 0.012 0.001 TRP B 42 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (12150) covalent geometry : angle 0.50660 / 0.26 (16557) hydrogen bonds : bond 0.04527 / 2.94 ( 816) hydrogen bonds : angle 3.73780 / 2.62 ( 2379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.350 Fit side-chains REVERT: A 110 MET cc_start: 0.8347 (ttm) cc_final: 0.7971 (mtp) REVERT: A 153 MET cc_start: 0.8262 (mtt) cc_final: 0.8054 (mtt) REVERT: A 203 ILE cc_start: 0.7826 (mt) cc_final: 0.7259 (pt) REVERT: B 30 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7513 (mp) REVERT: B 148 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7344 (mt) REVERT: B 300 MET cc_start: 0.8996 (mmm) cc_final: 0.8793 (tpt) REVERT: B 324 TRP cc_start: 0.7326 (m-10) cc_final: 0.6884 (m-10) REVERT: C 210 LEU cc_start: 0.7708 (tp) cc_final: 0.6817 (mp) REVERT: C 436 THR cc_start: 0.8547 (t) cc_final: 0.8279 (t) outliers start: 32 outliers final: 27 residues processed: 180 average time/residue: 0.0816 time to fit residues: 23.1991 Evaluate side-chains 183 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 456 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.153053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117766 restraints weight = 15021.838| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.71 r_work: 0.3168 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12150 Z= 0.132 Angle : 0.530 13.416 16557 Z= 0.269 Chirality : 0.039 0.390 1902 Planarity : 0.003 0.032 2022 Dihedral : 4.816 75.057 1635 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.83 % Allowed : 16.75 % Favored : 80.42 % 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: 1.42 (0.23), residues: 1506 helix: 1.56 (0.16), residues: 1165 sheet: None (None), residues: 0 loop : -1.18 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 258 TYR 0.016 0.001 TYR A 375 PHE 0.014 0.001 PHE B 77 TRP 0.011 0.001 TRP A 42 HIS 0.004 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12150) covalent geometry : angle 0.52987 / 0.27 (16557) hydrogen bonds : bond 0.04791 / 3.11 ( 816) hydrogen bonds : angle 3.78246 / 2.65 ( 2379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.287 Fit side-chains REVERT: A 110 MET cc_start: 0.8453 (ttm) cc_final: 0.8064 (mtp) REVERT: A 148 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7310 (tp) REVERT: A 203 ILE cc_start: 0.7880 (mt) cc_final: 0.7330 (pt) REVERT: A 209 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6657 (m) REVERT: A 420 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6604 (m-10) REVERT: B 30 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7546 (mp) REVERT: B 148 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7365 (mt) REVERT: B 324 TRP cc_start: 0.7399 (m-10) cc_final: 0.6961 (m-10) REVERT: C 210 LEU cc_start: 0.7774 (tp) cc_final: 0.6863 (mp) REVERT: C 436 THR cc_start: 0.8568 (t) cc_final: 0.8294 (t) outliers start: 35 outliers final: 27 residues processed: 179 average time/residue: 0.0803 time to fit residues: 22.1974 Evaluate side-chains 188 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118063 restraints weight = 15171.122| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.71 r_work: 0.3171 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12150 Z= 0.126 Angle : 0.528 11.637 16557 Z= 0.270 Chirality : 0.038 0.164 1902 Planarity : 0.003 0.031 2022 Dihedral : 4.820 74.442 1635 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.67 % Allowed : 17.23 % Favored : 80.10 % 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: 1.48 (0.23), residues: 1506 helix: 1.59 (0.16), residues: 1169 sheet: None (None), residues: 0 loop : -1.12 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 258 TYR 0.016 0.001 TYR A 375 PHE 0.021 0.001 PHE A 28 TRP 0.011 0.001 TRP B 42 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (12150) covalent geometry : angle 0.52797 / 0.27 (16557) hydrogen bonds : bond 0.04661 / 3.02 ( 816) hydrogen bonds : angle 3.75773 / 2.63 ( 2379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.442 Fit side-chains REVERT: A 110 MET cc_start: 0.8452 (ttm) cc_final: 0.8133 (mtp) REVERT: A 148 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7314 (tp) REVERT: A 203 ILE cc_start: 0.7867 (mt) cc_final: 0.7309 (pt) REVERT: A 209 THR cc_start: 0.6959 (OUTLIER) cc_final: 0.6635 (m) REVERT: A 420 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6638 (m-10) REVERT: B 30 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7562 (mp) REVERT: B 148 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7376 (mt) REVERT: B 324 TRP cc_start: 0.7391 (m-10) cc_final: 0.6947 (m-10) REVERT: C 210 LEU cc_start: 0.7768 (tp) cc_final: 0.6845 (mp) REVERT: C 436 THR cc_start: 0.8556 (t) cc_final: 0.8261 (t) outliers start: 33 outliers final: 25 residues processed: 181 average time/residue: 0.0755 time to fit residues: 21.4695 Evaluate side-chains 188 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119313 restraints weight = 15103.419| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.81 r_work: 0.3183 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12150 Z= 0.111 Angle : 0.509 11.700 16557 Z= 0.261 Chirality : 0.037 0.249 1902 Planarity : 0.003 0.030 2022 Dihedral : 4.729 71.819 1635 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.43 % Allowed : 17.48 % Favored : 80.10 % 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 (0.23), residues: 1506 helix: 1.68 (0.16), residues: 1167 sheet: None (None), residues: 0 loop : -1.11 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 258 TYR 0.016 0.001 TYR A 375 PHE 0.012 0.001 PHE C 38 TRP 0.010 0.001 TRP B 42 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (12150) covalent geometry : angle 0.50935 / 0.26 (16557) hydrogen bonds : bond 0.04277 / 2.78 ( 816) hydrogen bonds : angle 3.69039 / 2.58 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.35 seconds wall clock time: 49 minutes 37.52 seconds (2977.52 seconds total)