Starting phenix.real_space_refine on Wed Aug 5 22:57:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vi1_65075/08_2026/9vi1_65075_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vi1_65075/08_2026/9vi1_65075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vi1_65075/08_2026/9vi1_65075_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vi1_65075/08_2026/9vi1_65075_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vi1_65075/08_2026/9vi1_65075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vi1_65075/08_2026/9vi1_65075.map" } resolution = 3.33 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= 0.001 sd= 0.010 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 7845 2.51 5 N 1866 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11802 Number of models: 1 Model: "" Number of chains: 3 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} Time building chain proxies: 2.42, per 1000 atoms: 0.21 Number of scatterers: 11802 At special positions: 0 Unit cell: (116.802, 113.967, 83.916, 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 2034 8.00 N 1866 7.00 C 7845 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: 0.57 Conformation dependent library (CDL) restraints added in 477.1 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: 88 helices and 1 sheets defined 83.7% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 16 through 35 removed outlier: 3.536A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 removed outlier: 3.511A pdb=" N SER A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.988A pdb=" N LEU A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.893A pdb=" N SER A 79 " --> pdb=" O ARG A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.608A pdb=" N ALA A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 105 removed outlier: 4.008A pdb=" N ILE A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.575A pdb=" N MET A 110 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.805A pdb=" N VAL A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 137 through 146 removed outlier: 4.015A pdb=" N HIS A 145 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 164 removed outlier: 3.505A pdb=" N TRP A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 157 " --> pdb=" O MET A 153 " (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: 3.679A pdb=" N SER A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 251 removed outlier: 3.622A pdb=" N LYS A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 279 removed outlier: 3.546A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.719A pdb=" N LEU A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.531A pdb=" N ASN A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.650A pdb=" N PHE A 323 " --> pdb=" O TRP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 Proline residue: A 332 - end of helix removed outlier: 3.553A pdb=" N ILE A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 356 removed outlier: 3.726A pdb=" N ILE A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 379 removed outlier: 3.775A pdb=" N THR A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.518A pdb=" N GLU A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.868A pdb=" N LEU A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 405 through 435 removed outlier: 3.766A pdb=" N VAL A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 469 removed outlier: 3.613A pdb=" N PHE A 453 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 482 removed outlier: 3.538A pdb=" N LEU A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.506A pdb=" N SER A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 487' Processing helix chain 'A' and resid 487 through 512 removed outlier: 3.826A pdb=" N PHE A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 497 " --> pdb=" O MET A 493 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 29 removed outlier: 3.702A pdb=" N THR B 20 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 removed outlier: 3.645A pdb=" N SER B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 75 removed outlier: 3.585A pdb=" N TYR B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.946A pdb=" N SER B 79 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.997A pdb=" N ALA B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.506A pdb=" N TYR B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 removed outlier: 4.453A pdb=" N MET B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 145 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 164 removed outlier: 3.617A pdb=" N TRP B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.525A pdb=" N SER B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 225 removed outlier: 4.019A pdb=" N THR B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 251 removed outlier: 4.096A pdb=" N ILE B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 279 removed outlier: 3.643A pdb=" N VAL B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.711A pdb=" N VAL B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.578A pdb=" N ASN B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 342 removed outlier: 3.747A pdb=" N ALA B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Proline residue: B 332 - end of helix removed outlier: 3.558A pdb=" N LEU B 336 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 341 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 356 through 379 removed outlier: 4.067A pdb=" N PHE B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS B 379 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.774A pdb=" N ALA B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 395 Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.706A pdb=" N LEU B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 435 removed outlier: 3.560A pdb=" N SER B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 469 removed outlier: 3.718A pdb=" N GLY B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 removed outlier: 3.741A pdb=" N LEU B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 475 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 510 removed outlier: 3.719A pdb=" N PHE B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 488 " --> pdb=" O PRO B 484 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 510 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 29 removed outlier: 3.619A pdb=" N LEU C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 4.031A pdb=" N ILE C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.523A pdb=" N ARG C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C 48 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 75 removed outlier: 3.733A pdb=" N TYR C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.872A pdb=" N MET C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 132 through 146 removed outlier: 4.397A pdb=" N MET C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 146 " --> pdb=" O THR C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 removed outlier: 4.694A pdb=" N MET C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 187 removed outlier: 3.750A pdb=" N ASN C 187 " --> pdb=" O LYS C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 187' Processing helix chain 'C' and resid 188 through 225 removed outlier: 3.503A pdb=" N SER C 193 " --> pdb=" O PRO C 189 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 204 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 251 removed outlier: 3.634A pdb=" N LYS C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 279 removed outlier: 4.300A pdb=" N ARG C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 265 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.717A pdb=" N LEU C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 319 through 342 removed outlier: 3.996A pdb=" N VAL C 328 " --> pdb=" O TRP C 324 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Proline residue: C 332 - end of helix removed outlier: 3.785A pdb=" N ARG C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'C' and resid 356 through 370 removed outlier: 3.920A pdb=" N PHE C 361 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 removed outlier: 3.870A pdb=" N GLU C 376 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 379 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.512A pdb=" N SER C 398 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 400 " --> pdb=" O PHE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 437 removed outlier: 3.503A pdb=" N SER C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 412 " --> pdb=" O PHE C 408 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL C 431 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 470 removed outlier: 3.614A pdb=" N ARG C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C 453 " --> pdb=" O TRP C 449 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 469 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 removed outlier: 4.223A pdb=" N LEU C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN C 475 " --> pdb=" O ILE C 471 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 512 removed outlier: 3.502A pdb=" N PHE C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 512 " --> pdb=" O GLU C 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 4.124A pdb=" N LYS A 12 " --> pdb=" O GLN A 438 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1902 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: 1.82 Time building geometry restraints manager: 0.93 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: 3538 1.34 - 1.46: 2523 1.46 - 1.57: 5963 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12132 Sorted by residual: bond pdb=" N GLU C 116 " pdb=" CA GLU C 116 " ideal model delta sigma weight residual 1.462 1.490 -0.028 7.70e-03 1.69e+04 1.35e+01 bond pdb=" N VAL B 114 " pdb=" CA VAL B 114 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.17e+01 bond pdb=" N VAL C 114 " pdb=" CA VAL C 114 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" N VAL C 118 " pdb=" CA VAL C 118 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.28e+00 bond pdb=" N VAL B 118 " pdb=" CA VAL B 118 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.25e+00 ... (remaining 12127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 16222 1.74 - 3.47: 260 3.47 - 5.21: 39 5.21 - 6.95: 9 6.95 - 8.68: 3 Bond angle restraints: 16533 Sorted by residual: angle pdb=" N TYR B 121 " pdb=" CA TYR B 121 " pdb=" C TYR B 121 " ideal model delta sigma weight residual 113.55 108.35 5.20 1.26e+00 6.30e-01 1.70e+01 angle pdb=" N PRO C 125 " pdb=" CA PRO C 125 " pdb=" C PRO C 125 " ideal model delta sigma weight residual 113.47 108.52 4.95 1.43e+00 4.89e-01 1.20e+01 angle pdb=" CA THR B 119 " pdb=" CB THR B 119 " pdb=" OG1 THR B 119 " ideal model delta sigma weight residual 109.60 104.52 5.08 1.50e+00 4.44e-01 1.15e+01 angle pdb=" CA GLY C 127 " pdb=" C GLY C 127 " pdb=" O GLY C 127 " ideal model delta sigma weight residual 122.43 118.06 4.37 1.39e+00 5.18e-01 9.86e+00 angle pdb=" CA VAL C 118 " pdb=" C VAL C 118 " pdb=" O VAL C 118 " ideal model delta sigma weight residual 121.17 117.88 3.29 1.06e+00 8.90e-01 9.66e+00 ... (remaining 16528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 6105 17.62 - 35.23: 624 35.23 - 52.85: 123 52.85 - 70.46: 23 70.46 - 88.08: 7 Dihedral angle restraints: 6882 sinusoidal: 2550 harmonic: 4332 Sorted by residual: dihedral pdb=" CA ASP A 504 " pdb=" CB ASP A 504 " pdb=" CG ASP A 504 " pdb=" OD1 ASP A 504 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA TRP B 324 " pdb=" CB TRP B 324 " pdb=" CG TRP B 324 " pdb=" CD1 TRP B 324 " ideal model delta sinusoidal sigma weight residual 90.00 160.67 -70.67 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU C 503 " pdb=" CG GLU C 503 " pdb=" CD GLU C 503 " pdb=" OE1 GLU C 503 " ideal model delta sinusoidal sigma weight residual 0.00 88.08 -88.08 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1285 0.038 - 0.076: 552 0.076 - 0.115: 52 0.115 - 0.153: 9 0.153 - 0.191: 4 Chirality restraints: 1902 Sorted by residual: chirality pdb=" CA VAL C 140 " pdb=" N VAL C 140 " pdb=" C VAL C 140 " pdb=" CB VAL C 140 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA VAL B 114 " pdb=" N VAL B 114 " pdb=" C VAL B 114 " pdb=" CB VAL B 114 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA TYR C 146 " pdb=" N TYR C 146 " pdb=" C TYR C 146 " pdb=" CB TYR C 146 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 1899 not shown) Planarity restraints: 2022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 107 " 0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C ILE C 107 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE C 107 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP C 108 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 137 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C GLN C 137 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN C 137 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA C 138 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 179 " 0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO B 180 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " 0.016 5.00e-02 4.00e+02 ... (remaining 2019 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 6080 3.02 - 3.49: 11720 3.49 - 3.96: 17631 3.96 - 4.43: 21439 4.43 - 4.90: 34490 Nonbonded interactions: 91360 Sorted by model distance: nonbonded pdb=" N GLN B 86 " pdb=" OE1 GLN B 86 " model vdw 2.545 3.120 nonbonded pdb=" N THR C 149 " pdb=" OG1 THR C 149 " model vdw 2.546 2.496 nonbonded pdb=" O SER C 342 " pdb=" OG SER C 342 " model vdw 2.581 3.040 nonbonded pdb=" O SER B 342 " pdb=" OG SER B 342 " model vdw 2.596 3.040 nonbonded pdb=" O SER A 342 " pdb=" OG SER A 342 " model vdw 2.601 3.040 ... (remaining 91355 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: 19.720 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.630 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 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 0.039 12132 Z= 0.202 Angle : 0.571 8.684 16533 Z= 0.355 Chirality : 0.038 0.191 1902 Planarity : 0.003 0.028 2022 Dihedral : 14.634 88.080 4116 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.89 % Allowed : 12.54 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.19), residues: 1506 helix: -2.48 (0.13), residues: 1104 sheet: None (None), residues: 0 loop : -1.01 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 36 TYR 0.007 0.001 TYR B 121 PHE 0.009 0.001 PHE B 112 TRP 0.012 0.001 TRP C 327 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.20 (12132) covalent geometry : angle 0.57129 / 0.35 (16533) hydrogen bonds : bond 0.31515 / 20.24 ( 652) hydrogen bonds : angle 9.19802 / 6.34 ( 1902) *********************** 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 181 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.300 Fit side-chains REVERT: B 19 TYR cc_start: 0.8838 (m-10) cc_final: 0.8589 (m-80) REVERT: B 52 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7017 (tttm) REVERT: B 76 ARG cc_start: 0.6658 (ptt180) cc_final: 0.5198 (mpp-170) REVERT: B 123 GLN cc_start: 0.8701 (tt0) cc_final: 0.8451 (mt0) outliers start: 11 outliers final: 10 residues processed: 177 average time/residue: 0.0888 time to fit residues: 23.6232 Evaluate side-chains 153 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 32 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN C 379 HIS C 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.084529 restraints weight = 18005.008| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.31 r_work: 0.2788 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12132 Z= 0.164 Angle : 0.573 9.361 16533 Z= 0.298 Chirality : 0.039 0.143 1902 Planarity : 0.004 0.034 2022 Dihedral : 4.844 43.441 1640 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.78 % Allowed : 14.48 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.20), residues: 1506 helix: -1.33 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : -1.05 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 340 TYR 0.011 0.001 TYR C 219 PHE 0.016 0.001 PHE A 333 TRP 0.014 0.002 TRP C 42 HIS 0.007 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (12132) covalent geometry : angle 0.57335 / 0.30 (16533) hydrogen bonds : bond 0.05982 / 3.76 ( 652) hydrogen bonds : angle 4.64845 / 3.17 ( 1902) *********************** 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 174 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.310 Fit side-chains REVERT: B 24 LEU cc_start: 0.7636 (mt) cc_final: 0.7237 (tt) REVERT: B 76 ARG cc_start: 0.6310 (ptt180) cc_final: 0.4936 (mpp-170) outliers start: 22 outliers final: 18 residues processed: 168 average time/residue: 0.0822 time to fit residues: 21.3220 Evaluate side-chains 162 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN B 349 GLN C 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.085512 restraints weight = 18070.748| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.33 r_work: 0.2808 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12132 Z= 0.125 Angle : 0.486 8.196 16533 Z= 0.249 Chirality : 0.037 0.143 1902 Planarity : 0.003 0.032 2022 Dihedral : 4.192 47.658 1628 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.10 % Allowed : 15.94 % Favored : 81.96 % 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: -1.34 (0.21), residues: 1506 helix: -0.68 (0.15), residues: 1119 sheet: None (None), residues: 0 loop : -1.02 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 507 TYR 0.013 0.001 TYR B 421 PHE 0.010 0.001 PHE A 333 TRP 0.013 0.001 TRP C 151 HIS 0.001 0.000 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (12132) covalent geometry : angle 0.48622 / 0.25 (16533) hydrogen bonds : bond 0.05012 / 3.18 ( 652) hydrogen bonds : angle 4.03922 / 2.76 ( 1902) *********************** 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 185 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.347 Fit side-chains REVERT: B 24 LEU cc_start: 0.7651 (mt) cc_final: 0.7343 (tt) REVERT: B 76 ARG cc_start: 0.6300 (ptt180) cc_final: 0.4890 (mpp-170) REVERT: B 503 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7330 (tm-30) outliers start: 26 outliers final: 15 residues processed: 178 average time/residue: 0.0835 time to fit residues: 22.8973 Evaluate side-chains 158 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 324 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 125 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN C 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.086557 restraints weight = 17859.803| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.34 r_work: 0.2823 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12132 Z= 0.109 Angle : 0.473 8.913 16533 Z= 0.240 Chirality : 0.037 0.143 1902 Planarity : 0.003 0.031 2022 Dihedral : 4.069 51.917 1628 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.59 % Allowed : 16.42 % Favored : 80.99 % 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: -0.77 (0.22), residues: 1506 helix: -0.21 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -0.99 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 167 TYR 0.014 0.001 TYR B 421 PHE 0.014 0.001 PHE B 333 TRP 0.010 0.001 TRP C 42 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (12132) covalent geometry : angle 0.47252 / 0.24 (16533) hydrogen bonds : bond 0.04132 / 2.62 ( 652) hydrogen bonds : angle 3.76748 / 2.57 ( 1902) *********************** 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 185 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.382 Fit side-chains REVERT: B 24 LEU cc_start: 0.7626 (mt) cc_final: 0.7350 (tt) REVERT: B 76 ARG cc_start: 0.6129 (ptt180) cc_final: 0.4863 (mpp-170) REVERT: B 187 ASN cc_start: 0.8815 (t0) cc_final: 0.8512 (t0) REVERT: B 503 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7304 (tm-30) outliers start: 32 outliers final: 22 residues processed: 175 average time/residue: 0.0774 time to fit residues: 21.1891 Evaluate side-chains 166 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 341 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 HIS A 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.085184 restraints weight = 17922.013| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.36 r_work: 0.2809 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12132 Z= 0.127 Angle : 0.489 10.320 16533 Z= 0.247 Chirality : 0.038 0.161 1902 Planarity : 0.003 0.031 2022 Dihedral : 4.072 58.103 1628 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.51 % Allowed : 17.31 % Favored : 80.18 % 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: -0.46 (0.22), residues: 1506 helix: 0.02 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.89 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 507 TYR 0.013 0.001 TYR B 421 PHE 0.015 0.001 PHE B 333 TRP 0.009 0.001 TRP C 42 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12132) covalent geometry : angle 0.48863 / 0.25 (16533) hydrogen bonds : bond 0.04215 / 2.68 ( 652) hydrogen bonds : angle 3.73194 / 2.55 ( 1902) *********************** 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 182 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.435 Fit side-chains REVERT: B 24 LEU cc_start: 0.7670 (mt) cc_final: 0.7384 (tt) REVERT: B 76 ARG cc_start: 0.6169 (ptt180) cc_final: 0.4938 (mpp-170) REVERT: B 187 ASN cc_start: 0.8822 (t0) cc_final: 0.8422 (t0) outliers start: 31 outliers final: 25 residues processed: 174 average time/residue: 0.0751 time to fit residues: 20.4388 Evaluate side-chains 163 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 341 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 117 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 0.0670 chunk 41 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.086674 restraints weight = 17989.999| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.38 r_work: 0.2830 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12132 Z= 0.100 Angle : 0.463 9.481 16533 Z= 0.233 Chirality : 0.037 0.142 1902 Planarity : 0.003 0.030 2022 Dihedral : 3.842 50.740 1628 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.51 % Allowed : 17.96 % Favored : 79.53 % 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: -0.07 (0.22), residues: 1506 helix: 0.35 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.90 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 340 TYR 0.013 0.001 TYR B 421 PHE 0.012 0.001 PHE B 333 TRP 0.010 0.001 TRP C 151 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (12132) covalent geometry : angle 0.46339 / 0.23 (16533) hydrogen bonds : bond 0.03741 / 2.37 ( 652) hydrogen bonds : angle 3.57123 / 2.44 ( 1902) *********************** 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 181 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.271 Fit side-chains REVERT: B 24 LEU cc_start: 0.7671 (mt) cc_final: 0.7407 (tt) REVERT: B 76 ARG cc_start: 0.6180 (ptt180) cc_final: 0.4945 (mpp-170) REVERT: B 187 ASN cc_start: 0.8829 (t0) cc_final: 0.8413 (t0) REVERT: B 258 ARG cc_start: 0.5985 (tpt-90) cc_final: 0.5768 (tpp80) outliers start: 31 outliers final: 21 residues processed: 175 average time/residue: 0.0822 time to fit residues: 21.9986 Evaluate side-chains 161 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 341 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 4.9990 chunk 109 optimal weight: 0.0010 chunk 147 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 141 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 HIS A 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.087359 restraints weight = 17784.718| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.37 r_work: 0.2840 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12132 Z= 0.094 Angle : 0.458 9.598 16533 Z= 0.228 Chirality : 0.037 0.145 1902 Planarity : 0.003 0.029 2022 Dihedral : 3.704 41.037 1628 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.78 % Allowed : 18.69 % Favored : 79.53 % 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: 0.31 (0.22), residues: 1506 helix: 0.64 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -0.82 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 340 TYR 0.012 0.001 TYR B 421 PHE 0.012 0.001 PHE B 333 TRP 0.010 0.001 TRP C 151 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (12132) covalent geometry : angle 0.45758 / 0.23 (16533) hydrogen bonds : bond 0.03558 / 2.26 ( 652) hydrogen bonds : angle 3.50408 / 2.39 ( 1902) *********************** 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 169 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.316 Fit side-chains REVERT: B 24 LEU cc_start: 0.7650 (mt) cc_final: 0.7391 (tt) REVERT: B 76 ARG cc_start: 0.6196 (ptt180) cc_final: 0.5010 (mpp-170) REVERT: B 187 ASN cc_start: 0.8826 (t0) cc_final: 0.8399 (t0) outliers start: 22 outliers final: 19 residues processed: 163 average time/residue: 0.0817 time to fit residues: 20.9349 Evaluate side-chains 157 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 107 optimal weight: 0.0020 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 61 optimal weight: 0.0170 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.090026 restraints weight = 17637.613| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.36 r_work: 0.2880 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12132 Z= 0.082 Angle : 0.450 9.200 16533 Z= 0.221 Chirality : 0.036 0.142 1902 Planarity : 0.002 0.027 2022 Dihedral : 3.462 34.314 1628 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.05 % Allowed : 19.98 % Favored : 78.96 % 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: 0.88 (0.22), residues: 1506 helix: 1.08 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.69 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 340 TYR 0.011 0.001 TYR B 421 PHE 0.008 0.001 PHE C 38 TRP 0.016 0.001 TRP C 324 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.08 (12132) covalent geometry : angle 0.45043 / 0.22 (16533) hydrogen bonds : bond 0.03037 / 1.92 ( 652) hydrogen bonds : angle 3.34135 / 2.28 ( 1902) *********************** 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 166 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.447 Fit side-chains REVERT: B 24 LEU cc_start: 0.7621 (mt) cc_final: 0.7379 (tt) REVERT: B 76 ARG cc_start: 0.6094 (ptt180) cc_final: 0.4963 (mpp-170) REVERT: B 187 ASN cc_start: 0.8808 (t0) cc_final: 0.8396 (t0) REVERT: B 194 VAL cc_start: 0.8206 (t) cc_final: 0.7979 (p) outliers start: 13 outliers final: 11 residues processed: 161 average time/residue: 0.0915 time to fit residues: 22.9550 Evaluate side-chains 153 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 273 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 44 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 HIS A 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.086885 restraints weight = 17723.093| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.36 r_work: 0.2832 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12132 Z= 0.114 Angle : 0.484 9.149 16533 Z= 0.238 Chirality : 0.038 0.155 1902 Planarity : 0.003 0.028 2022 Dihedral : 3.419 36.593 1624 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.05 % Allowed : 20.23 % Favored : 78.72 % 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: 1.07 (0.22), residues: 1506 helix: 1.24 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : -0.61 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 TYR 0.011 0.001 TYR B 421 PHE 0.020 0.001 PHE C 182 TRP 0.008 0.001 TRP C 319 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (12132) covalent geometry : angle 0.48419 / 0.24 (16533) hydrogen bonds : bond 0.03577 / 2.28 ( 652) hydrogen bonds : angle 3.43565 / 2.35 ( 1902) *********************** 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 160 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.467 Fit side-chains REVERT: B 24 LEU cc_start: 0.7619 (mt) cc_final: 0.7375 (tt) REVERT: B 76 ARG cc_start: 0.6128 (ptt180) cc_final: 0.5009 (mpp-170) REVERT: B 187 ASN cc_start: 0.8805 (t0) cc_final: 0.8392 (t0) outliers start: 13 outliers final: 12 residues processed: 155 average time/residue: 0.0928 time to fit residues: 22.2494 Evaluate side-chains 158 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 60 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 128 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.087911 restraints weight = 17776.217| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.37 r_work: 0.2848 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12132 Z= 0.097 Angle : 0.479 9.226 16533 Z= 0.234 Chirality : 0.037 0.160 1902 Planarity : 0.003 0.027 2022 Dihedral : 3.408 36.703 1624 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.29 % Allowed : 20.31 % Favored : 78.40 % 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: 1.27 (0.22), residues: 1506 helix: 1.38 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -0.52 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 340 TYR 0.011 0.001 TYR B 421 PHE 0.025 0.001 PHE C 182 TRP 0.009 0.001 TRP C 151 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (12132) covalent geometry : angle 0.47946 / 0.23 (16533) hydrogen bonds : bond 0.03378 / 2.15 ( 652) hydrogen bonds : angle 3.38670 / 2.32 ( 1902) ********************** 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 166 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.466 Fit side-chains REVERT: B 24 LEU cc_start: 0.7619 (mt) cc_final: 0.7387 (tt) REVERT: B 52 LYS cc_start: 0.7423 (ttmt) cc_final: 0.6783 (tttm) REVERT: B 76 ARG cc_start: 0.6105 (ptt180) cc_final: 0.4998 (mpp-170) REVERT: B 187 ASN cc_start: 0.8798 (t0) cc_final: 0.8383 (t0) REVERT: C 508 GLU cc_start: 0.7119 (mm-30) cc_final: 0.5600 (tm-30) outliers start: 16 outliers final: 14 residues processed: 161 average time/residue: 0.0936 time to fit residues: 22.9934 Evaluate side-chains 161 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.087747 restraints weight = 17757.790| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.38 r_work: 0.2846 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12132 Z= 0.100 Angle : 0.487 9.401 16533 Z= 0.236 Chirality : 0.037 0.159 1902 Planarity : 0.003 0.028 2022 Dihedral : 3.454 42.627 1624 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.13 % Allowed : 20.31 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.22), residues: 1506 helix: 1.45 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -0.49 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 340 TYR 0.011 0.001 TYR B 421 PHE 0.018 0.001 PHE C 182 TRP 0.008 0.001 TRP C 151 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (12132) covalent geometry : angle 0.48651 / 0.24 (16533) hydrogen bonds : bond 0.03414 / 2.17 ( 652) hydrogen bonds : angle 3.40132 / 2.33 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2771.84 seconds wall clock time: 48 minutes 9.05 seconds (2889.05 seconds total)