Starting phenix.real_space_refine on Tue Feb 3 21:44:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9udv_64072/02_2026/9udv_64072.cif Found real_map, /net/cci-nas-00/data/ceres_data/9udv_64072/02_2026/9udv_64072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9udv_64072/02_2026/9udv_64072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9udv_64072/02_2026/9udv_64072.map" model { file = "/net/cci-nas-00/data/ceres_data/9udv_64072/02_2026/9udv_64072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9udv_64072/02_2026/9udv_64072.cif" } resolution = 3.6 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 49 5.16 5 C 4649 2.51 5 N 1139 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7066 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3562 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3487 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.61, per 1000 atoms: 0.23 Number of scatterers: 7066 At special positions: 0 Unit cell: (95.7, 71.5, 121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 1 15.00 O 1228 8.00 N 1139 7.00 C 4649 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 73 " distance=2.04 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: 0.81 Conformation dependent library (CDL) restraints added in 324.7 milliseconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 68.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 14 removed outlier: 3.843A pdb=" N ALA A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 41 removed outlier: 3.819A pdb=" N PHE A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 39 " --> pdb=" O CYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.950A pdb=" N VAL A 46 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS A 47 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 48 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.377A pdb=" N VAL A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.941A pdb=" N THR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 153 removed outlier: 3.515A pdb=" N VAL A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.561A pdb=" N ILE A 183 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.934A pdb=" N ASN A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 199 " --> pdb=" O GLY A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 228 Proline residue: A 214 - end of helix removed outlier: 3.875A pdb=" N ALA A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.598A pdb=" N VAL A 236 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 237 " --> pdb=" O GLU A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.823A pdb=" N LEU A 292 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 294 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 4.011A pdb=" N LEU A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.534A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 323' Processing helix chain 'A' and resid 332 through 357 removed outlier: 3.825A pdb=" N SER A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.505A pdb=" N CYS A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 372 through 383 removed outlier: 4.027A pdb=" N PHE A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 402 removed outlier: 3.892A pdb=" N VAL A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 396 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 removed outlier: 3.715A pdb=" N ILE A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 431 through 446 removed outlier: 4.007A pdb=" N GLY A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 463 through 475 removed outlier: 3.771A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 492 removed outlier: 3.900A pdb=" N LEU A 486 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 16 through 38 removed outlier: 4.066A pdb=" N ILE B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Proline residue: B 42 - end of helix No H-bonds generated for 'chain 'B' and resid 39 through 44' Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.562A pdb=" N LEU B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.728A pdb=" N GLY B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.744A pdb=" N VAL B 148 " --> pdb=" O TRP B 144 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 149 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN B 150 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 156 " --> pdb=" O CYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 removed outlier: 4.545A pdb=" N TRP B 161 " --> pdb=" O THR B 158 " (cutoff:3.500A) Proline residue: B 162 - end of helix No H-bonds generated for 'chain 'B' and resid 158 through 163' Processing helix chain 'B' and resid 164 through 172 removed outlier: 4.109A pdb=" N ASN B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TRP B 171 " --> pdb=" O CYS B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 186 through 198 removed outlier: 4.027A pdb=" N ASN B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 229 removed outlier: 4.045A pdb=" N VAL B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Proline residue: B 214 - end of helix removed outlier: 3.682A pdb=" N ALA B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B 225 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 removed outlier: 4.462A pdb=" N LEU B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N CYS B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 326 removed outlier: 3.808A pdb=" N THR B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Proline residue: B 319 - end of helix removed outlier: 3.807A pdb=" N ALA B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.189A pdb=" N GLY B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 371 through 382 removed outlier: 3.687A pdb=" N MET B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 400 removed outlier: 3.681A pdb=" N ILE B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 396 " --> pdb=" O VAL B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 416 removed outlier: 4.052A pdb=" N VAL B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 413 " --> pdb=" O THR B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 446 removed outlier: 3.677A pdb=" N SER B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 removed outlier: 3.552A pdb=" N LEU B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 461 through 469 removed outlier: 4.123A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 476 removed outlier: 3.562A pdb=" N LEU B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.675A pdb=" N LYS B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 486 " --> pdb=" O TYR B 482 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 1.00 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: 2125 1.34 - 1.46: 1850 1.46 - 1.58: 3208 1.58 - 1.70: 1 1.70 - 1.82: 73 Bond restraints: 7257 Sorted by residual: bond pdb=" O6 G6P B 601 " pdb=" P G6P B 601 " ideal model delta sigma weight residual 1.722 1.591 0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" C LEU B 318 " pdb=" N PRO B 319 " ideal model delta sigma weight residual 1.337 1.384 -0.047 9.80e-03 1.04e+04 2.31e+01 bond pdb=" C LYS A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.08e-02 8.57e+03 2.17e+01 bond pdb=" C ALA B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.331 1.366 -0.035 7.90e-03 1.60e+04 1.91e+01 bond pdb=" C LYS B 41 " pdb=" N PRO B 42 " ideal model delta sigma weight residual 1.337 1.360 -0.024 9.80e-03 1.04e+04 5.89e+00 ... (remaining 7252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 9508 2.43 - 4.85: 312 4.85 - 7.28: 46 7.28 - 9.70: 12 9.70 - 12.13: 4 Bond angle restraints: 9882 Sorted by residual: angle pdb=" C TRP B 138 " pdb=" N ASN B 139 " pdb=" CA ASN B 139 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" N ILE A 104 " pdb=" CA ILE A 104 " pdb=" C ILE A 104 " ideal model delta sigma weight residual 112.96 108.01 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" N PRO A 42 " pdb=" CA PRO A 42 " pdb=" C PRO A 42 " ideal model delta sigma weight residual 113.98 119.77 -5.79 1.29e+00 6.01e-01 2.01e+01 angle pdb=" C SER A 66 " pdb=" N LEU A 67 " pdb=" CA LEU A 67 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C ALA B 291 " pdb=" N LEU B 292 " pdb=" CA LEU B 292 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 ... (remaining 9877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.17: 3845 15.17 - 30.34: 241 30.34 - 45.51: 43 45.51 - 60.68: 3 60.68 - 75.85: 5 Dihedral angle restraints: 4137 sinusoidal: 1546 harmonic: 2591 Sorted by residual: dihedral pdb=" CA LYS A 41 " pdb=" C LYS A 41 " pdb=" N PRO A 42 " pdb=" CA PRO A 42 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 73 " pdb=" CB CYS B 73 " ideal model delta sinusoidal sigma weight residual -86.00 -135.67 49.67 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA ASP B 341 " pdb=" C ASP B 341 " pdb=" N VAL B 342 " pdb=" CA VAL B 342 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 4134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 867 0.067 - 0.133: 230 0.133 - 0.200: 30 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 1131 Sorted by residual: chirality pdb=" C1 G6P B 601 " pdb=" C2 G6P B 601 " pdb=" O1 G6P B 601 " pdb=" O5 G6P B 601 " both_signs ideal model delta sigma weight residual False -2.03 -2.36 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ASN B 139 " pdb=" N ASN B 139 " pdb=" C ASN B 139 " pdb=" CB ASN B 139 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE B 140 " pdb=" CA ILE B 140 " pdb=" CG1 ILE B 140 " pdb=" CG2 ILE B 140 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1128 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 373 " 0.049 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO A 374 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 455 " -0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 456 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 76 " 0.047 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO A 77 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.040 5.00e-02 4.00e+02 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2271 2.83 - 3.35: 6362 3.35 - 3.86: 10634 3.86 - 4.38: 12533 4.38 - 4.90: 20946 Nonbonded interactions: 52746 Sorted by model distance: nonbonded pdb=" OG1 THR A 166 " pdb=" OG SER A 430 " model vdw 2.311 3.040 nonbonded pdb=" OG SER B 119 " pdb=" O GLY B 222 " model vdw 2.329 3.040 nonbonded pdb=" O ILE A 454 " pdb=" OG1 THR A 457 " model vdw 2.341 3.040 nonbonded pdb=" NH1 ARG A 49 " pdb=" O VAL A 203 " model vdw 2.356 3.120 nonbonded pdb=" OG SER B 55 " pdb=" OE1 GLU B 56 " model vdw 2.359 3.040 ... (remaining 52741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 244 or (resid 286 and (name N or name CA or name \ C or name O or name CB )) or resid 287 through 495)) selection = (chain 'B' and resid 1 through 495) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.007 0.131 7259 Z= 0.319 Angle : 1.058 12.130 9886 Z= 0.578 Chirality : 0.060 0.333 1131 Planarity : 0.008 0.073 1208 Dihedral : 10.513 75.854 2489 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.57 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -6.14 (0.18), residues: 910 helix: -4.14 (0.10), residues: 616 sheet: None (None), residues: 0 loop : -3.37 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 115 TYR 0.028 0.003 TYR B 36 PHE 0.018 0.002 PHE B 146 TRP 0.022 0.002 TRP A 10 HIS 0.014 0.003 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 7257) covalent geometry : angle 1.05771 ( 9882) SS BOND : bond 0.00500 ( 2) SS BOND : angle 1.14831 ( 4) hydrogen bonds : bond 0.21192 ( 269) hydrogen bonds : angle 7.93230 ( 792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4927 (ttp) cc_final: 0.4026 (ttt) REVERT: A 13 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.6034 (tpt170) REVERT: A 84 LYS cc_start: 0.8715 (mttm) cc_final: 0.8513 (mtmt) REVERT: A 153 ASN cc_start: 0.8722 (t0) cc_final: 0.8476 (t0) REVERT: A 437 ASP cc_start: 0.8839 (t0) cc_final: 0.8612 (t70) REVERT: A 454 ILE cc_start: 0.7939 (tt) cc_final: 0.7671 (tp) REVERT: A 475 LEU cc_start: 0.8954 (mp) cc_final: 0.8726 (tt) REVERT: B 38 MET cc_start: 0.8506 (ptt) cc_final: 0.8284 (ptt) REVERT: B 193 ILE cc_start: 0.8961 (tt) cc_final: 0.8680 (tt) REVERT: B 341 ASP cc_start: 0.8713 (m-30) cc_final: 0.8472 (m-30) REVERT: B 475 LEU cc_start: 0.8836 (mt) cc_final: 0.8527 (tt) REVERT: B 484 GLU cc_start: 0.7787 (tp30) cc_final: 0.7264 (tp30) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.0767 time to fit residues: 21.2940 Evaluate side-chains 108 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 HIS B 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.153581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117056 restraints weight = 10261.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120799 restraints weight = 5228.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123340 restraints weight = 3547.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124738 restraints weight = 2841.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125318 restraints weight = 2518.646| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7259 Z= 0.139 Angle : 0.656 10.821 9886 Z= 0.339 Chirality : 0.043 0.145 1131 Planarity : 0.005 0.057 1208 Dihedral : 5.699 28.251 998 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.15 % Favored : 93.74 % Rotamer: Outliers : 1.87 % Allowed : 10.29 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.22), residues: 910 helix: -3.06 (0.15), residues: 633 sheet: None (None), residues: 0 loop : -2.85 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 115 TYR 0.022 0.001 TYR B 36 PHE 0.022 0.001 PHE A 78 TRP 0.025 0.001 TRP A 75 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7257) covalent geometry : angle 0.65593 ( 9882) SS BOND : bond 0.00337 ( 2) SS BOND : angle 1.42883 ( 4) hydrogen bonds : bond 0.05079 ( 269) hydrogen bonds : angle 4.95669 ( 792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4739 (ttp) cc_final: 0.4093 (ttt) REVERT: A 378 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7345 (tt) REVERT: A 454 ILE cc_start: 0.8047 (tt) cc_final: 0.7830 (mm) REVERT: A 475 LEU cc_start: 0.9077 (mp) cc_final: 0.8803 (tt) REVERT: B 193 ILE cc_start: 0.8796 (tt) cc_final: 0.8585 (tt) REVERT: B 475 LEU cc_start: 0.8715 (mt) cc_final: 0.8459 (tt) REVERT: B 478 CYS cc_start: 0.8928 (m) cc_final: 0.8618 (m) REVERT: B 484 GLU cc_start: 0.7637 (tp30) cc_final: 0.7227 (tp30) outliers start: 14 outliers final: 6 residues processed: 128 average time/residue: 0.0714 time to fit residues: 13.1149 Evaluate side-chains 105 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 412 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 6 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 0.0670 chunk 70 optimal weight: 9.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114462 restraints weight = 10374.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118233 restraints weight = 5298.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120746 restraints weight = 3604.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122028 restraints weight = 2898.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123055 restraints weight = 2589.577| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7259 Z= 0.124 Angle : 0.614 10.232 9886 Z= 0.315 Chirality : 0.042 0.183 1131 Planarity : 0.005 0.053 1208 Dihedral : 5.079 25.485 998 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.88 % Allowed : 11.10 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.24), residues: 910 helix: -2.44 (0.17), residues: 623 sheet: None (None), residues: 0 loop : -2.74 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.015 0.001 TYR B 36 PHE 0.017 0.001 PHE B 377 TRP 0.013 0.001 TRP A 75 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7257) covalent geometry : angle 0.60971 ( 9882) SS BOND : bond 0.00393 ( 2) SS BOND : angle 3.81517 ( 4) hydrogen bonds : bond 0.04033 ( 269) hydrogen bonds : angle 4.44110 ( 792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4799 (ttp) cc_final: 0.4140 (ttt) REVERT: A 71 MET cc_start: 0.7612 (mmm) cc_final: 0.7274 (mmm) REVERT: A 378 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7542 (tt) REVERT: A 475 LEU cc_start: 0.9113 (mp) cc_final: 0.8799 (tt) REVERT: B 36 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: B 122 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8267 (ttp) REVERT: B 193 ILE cc_start: 0.8909 (tt) cc_final: 0.8708 (tt) REVERT: B 315 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8263 (tt) REVERT: B 418 THR cc_start: 0.9056 (p) cc_final: 0.8817 (t) REVERT: B 484 GLU cc_start: 0.7600 (tp30) cc_final: 0.7273 (tp30) outliers start: 29 outliers final: 15 residues processed: 140 average time/residue: 0.0672 time to fit residues: 13.7842 Evaluate side-chains 121 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 422 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.0050 chunk 73 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.155664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117965 restraints weight = 10334.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121940 restraints weight = 5194.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124557 restraints weight = 3520.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126138 restraints weight = 2837.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126772 restraints weight = 2507.782| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7259 Z= 0.103 Angle : 0.576 9.352 9886 Z= 0.292 Chirality : 0.042 0.230 1131 Planarity : 0.004 0.049 1208 Dihedral : 4.681 24.358 998 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.41 % Allowed : 12.17 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.25), residues: 910 helix: -2.01 (0.18), residues: 631 sheet: None (None), residues: 0 loop : -2.76 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.015 0.001 TYR A 381 PHE 0.018 0.001 PHE B 377 TRP 0.011 0.001 TRP A 459 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7257) covalent geometry : angle 0.57168 ( 9882) SS BOND : bond 0.00350 ( 2) SS BOND : angle 3.40420 ( 4) hydrogen bonds : bond 0.03323 ( 269) hydrogen bonds : angle 4.12014 ( 792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.275 Fit side-chains REVERT: A 1 MET cc_start: 0.4654 (ttp) cc_final: 0.3998 (ttt) REVERT: A 71 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7677 (mmm) REVERT: A 117 TYR cc_start: 0.8764 (t80) cc_final: 0.8459 (t80) REVERT: A 475 LEU cc_start: 0.9104 (mp) cc_final: 0.8740 (tt) REVERT: B 4 SER cc_start: 0.8349 (t) cc_final: 0.8069 (p) REVERT: B 36 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: B 393 MET cc_start: 0.7276 (tpp) cc_final: 0.6968 (tpp) REVERT: B 418 THR cc_start: 0.9089 (p) cc_final: 0.8848 (t) REVERT: B 419 HIS cc_start: 0.8215 (t70) cc_final: 0.7822 (t70) REVERT: B 479 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7236 (ttp-170) REVERT: B 484 GLU cc_start: 0.7594 (tp30) cc_final: 0.7186 (tp30) outliers start: 33 outliers final: 16 residues processed: 140 average time/residue: 0.0693 time to fit residues: 13.9951 Evaluate side-chains 121 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118702 restraints weight = 9965.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122675 restraints weight = 4968.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125313 restraints weight = 3344.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126677 restraints weight = 2668.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127606 restraints weight = 2373.079| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7259 Z= 0.106 Angle : 0.571 8.109 9886 Z= 0.290 Chirality : 0.041 0.174 1131 Planarity : 0.004 0.046 1208 Dihedral : 4.486 23.898 998 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.61 % Allowed : 13.90 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.26), residues: 910 helix: -1.69 (0.19), residues: 631 sheet: None (None), residues: 0 loop : -2.71 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 177 TYR 0.015 0.001 TYR A 381 PHE 0.018 0.001 PHE B 377 TRP 0.013 0.001 TRP A 75 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7257) covalent geometry : angle 0.56915 ( 9882) SS BOND : bond 0.00373 ( 2) SS BOND : angle 2.26669 ( 4) hydrogen bonds : bond 0.03225 ( 269) hydrogen bonds : angle 3.97243 ( 792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.261 Fit side-chains REVERT: A 1 MET cc_start: 0.4852 (ttp) cc_final: 0.4186 (ttt) REVERT: A 71 MET cc_start: 0.8243 (mmm) cc_final: 0.7972 (mmm) REVERT: A 117 TYR cc_start: 0.8819 (t80) cc_final: 0.8519 (t80) REVERT: A 475 LEU cc_start: 0.9126 (mp) cc_final: 0.8765 (tt) REVERT: B 4 SER cc_start: 0.8376 (t) cc_final: 0.8095 (p) REVERT: B 36 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: B 122 MET cc_start: 0.8823 (ttp) cc_final: 0.8464 (ttp) REVERT: B 299 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 315 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8182 (tt) REVERT: B 418 THR cc_start: 0.9028 (p) cc_final: 0.8779 (t) REVERT: B 419 HIS cc_start: 0.8132 (t70) cc_final: 0.7768 (t70) REVERT: B 484 GLU cc_start: 0.7599 (tp30) cc_final: 0.7246 (tp30) outliers start: 27 outliers final: 20 residues processed: 130 average time/residue: 0.0613 time to fit residues: 11.6093 Evaluate side-chains 130 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 24 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.154552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116906 restraints weight = 10099.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120743 restraints weight = 5204.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123286 restraints weight = 3573.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124619 restraints weight = 2891.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125161 restraints weight = 2588.455| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7259 Z= 0.108 Angle : 0.555 7.057 9886 Z= 0.281 Chirality : 0.041 0.141 1131 Planarity : 0.004 0.069 1208 Dihedral : 4.397 22.970 998 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.48 % Allowed : 15.11 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.26), residues: 910 helix: -1.46 (0.19), residues: 633 sheet: None (None), residues: 0 loop : -2.65 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 479 TYR 0.016 0.001 TYR A 381 PHE 0.016 0.001 PHE B 377 TRP 0.014 0.001 TRP A 75 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7257) covalent geometry : angle 0.55423 ( 9882) SS BOND : bond 0.00181 ( 2) SS BOND : angle 1.64852 ( 4) hydrogen bonds : bond 0.03246 ( 269) hydrogen bonds : angle 3.91914 ( 792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.271 Fit side-chains REVERT: A 1 MET cc_start: 0.4706 (ttp) cc_final: 0.4071 (ttt) REVERT: A 71 MET cc_start: 0.8001 (mmm) cc_final: 0.7652 (mmt) REVERT: A 117 TYR cc_start: 0.8776 (t80) cc_final: 0.8467 (t80) REVERT: A 475 LEU cc_start: 0.9129 (mp) cc_final: 0.8767 (tt) REVERT: B 4 SER cc_start: 0.8357 (t) cc_final: 0.8065 (p) REVERT: B 36 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: B 122 MET cc_start: 0.8851 (ttp) cc_final: 0.8423 (ttt) REVERT: B 418 THR cc_start: 0.9040 (p) cc_final: 0.8805 (t) REVERT: B 419 HIS cc_start: 0.8233 (t70) cc_final: 0.7840 (t70) REVERT: B 484 GLU cc_start: 0.7531 (tp30) cc_final: 0.7165 (tp30) outliers start: 26 outliers final: 19 residues processed: 129 average time/residue: 0.0572 time to fit residues: 10.9963 Evaluate side-chains 130 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116385 restraints weight = 10010.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120202 restraints weight = 5249.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122699 restraints weight = 3639.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124026 restraints weight = 2968.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124465 restraints weight = 2663.991| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7259 Z= 0.113 Angle : 0.562 7.602 9886 Z= 0.281 Chirality : 0.041 0.141 1131 Planarity : 0.004 0.042 1208 Dihedral : 4.344 22.443 998 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.01 % Allowed : 14.97 % Favored : 81.02 % 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: -2.59 (0.27), residues: 910 helix: -1.22 (0.20), residues: 629 sheet: None (None), residues: 0 loop : -2.60 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 479 TYR 0.016 0.001 TYR A 381 PHE 0.010 0.001 PHE B 300 TRP 0.015 0.001 TRP A 75 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7257) covalent geometry : angle 0.56138 ( 9882) SS BOND : bond 0.00196 ( 2) SS BOND : angle 1.44262 ( 4) hydrogen bonds : bond 0.03248 ( 269) hydrogen bonds : angle 3.87466 ( 792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.259 Fit side-chains REVERT: A 1 MET cc_start: 0.4675 (ttp) cc_final: 0.4069 (ttt) REVERT: A 71 MET cc_start: 0.8028 (mmm) cc_final: 0.7817 (mmt) REVERT: A 117 TYR cc_start: 0.8778 (t80) cc_final: 0.8457 (t80) REVERT: A 339 LEU cc_start: 0.8353 (tp) cc_final: 0.8147 (tt) REVERT: A 475 LEU cc_start: 0.9084 (mp) cc_final: 0.8718 (tt) REVERT: B 4 SER cc_start: 0.8386 (t) cc_final: 0.8082 (p) REVERT: B 36 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: B 122 MET cc_start: 0.8829 (ttp) cc_final: 0.8542 (ttt) REVERT: B 299 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 368 MET cc_start: 0.7354 (mmt) cc_final: 0.6612 (mtt) REVERT: B 418 THR cc_start: 0.9038 (p) cc_final: 0.8821 (t) REVERT: B 419 HIS cc_start: 0.8323 (t70) cc_final: 0.7938 (t70) REVERT: B 484 GLU cc_start: 0.7557 (tp30) cc_final: 0.7194 (tp30) outliers start: 30 outliers final: 21 residues processed: 133 average time/residue: 0.0553 time to fit residues: 11.0683 Evaluate side-chains 132 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 0.1980 chunk 52 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118649 restraints weight = 10096.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122568 restraints weight = 5229.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125198 restraints weight = 3601.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126449 restraints weight = 2919.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127297 restraints weight = 2624.957| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7259 Z= 0.097 Angle : 0.549 7.795 9886 Z= 0.273 Chirality : 0.041 0.142 1131 Planarity : 0.004 0.042 1208 Dihedral : 4.185 21.954 998 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.54 % Allowed : 16.31 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.27), residues: 910 helix: -0.97 (0.20), residues: 625 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 479 TYR 0.017 0.001 TYR A 381 PHE 0.012 0.001 PHE B 179 TRP 0.016 0.001 TRP A 75 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7257) covalent geometry : angle 0.54830 ( 9882) SS BOND : bond 0.00192 ( 2) SS BOND : angle 1.55957 ( 4) hydrogen bonds : bond 0.02940 ( 269) hydrogen bonds : angle 3.75608 ( 792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4851 (ttp) cc_final: 0.4259 (ttt) REVERT: A 71 MET cc_start: 0.7756 (mmm) cc_final: 0.7529 (mmt) REVERT: A 117 TYR cc_start: 0.8748 (t80) cc_final: 0.8419 (t80) REVERT: A 475 LEU cc_start: 0.9043 (mp) cc_final: 0.8683 (tt) REVERT: B 4 SER cc_start: 0.8391 (t) cc_final: 0.8082 (p) REVERT: B 36 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: B 122 MET cc_start: 0.8758 (ttp) cc_final: 0.8527 (ttt) REVERT: B 368 MET cc_start: 0.7292 (mmt) cc_final: 0.6593 (mtt) REVERT: B 418 THR cc_start: 0.9037 (p) cc_final: 0.8800 (t) REVERT: B 419 HIS cc_start: 0.8328 (t70) cc_final: 0.7967 (t70) REVERT: B 459 TRP cc_start: 0.7253 (t-100) cc_final: 0.6822 (t-100) REVERT: B 484 GLU cc_start: 0.7643 (tp30) cc_final: 0.7270 (tp30) outliers start: 19 outliers final: 15 residues processed: 131 average time/residue: 0.0535 time to fit residues: 10.2719 Evaluate side-chains 134 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.152318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114151 restraints weight = 10254.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117825 restraints weight = 5397.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120287 restraints weight = 3772.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121470 restraints weight = 3091.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122401 restraints weight = 2793.800| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7259 Z= 0.143 Angle : 0.596 7.300 9886 Z= 0.298 Chirality : 0.043 0.142 1131 Planarity : 0.004 0.040 1208 Dihedral : 4.374 21.825 998 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.07 % Allowed : 15.78 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.27), residues: 910 helix: -0.94 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 479 TYR 0.018 0.001 TYR A 381 PHE 0.010 0.001 PHE B 300 TRP 0.012 0.001 TRP A 75 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7257) covalent geometry : angle 0.59503 ( 9882) SS BOND : bond 0.00268 ( 2) SS BOND : angle 1.85732 ( 4) hydrogen bonds : bond 0.03568 ( 269) hydrogen bonds : angle 3.93251 ( 792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4813 (ttp) cc_final: 0.4236 (ttt) REVERT: A 117 TYR cc_start: 0.8789 (t80) cc_final: 0.8428 (t80) REVERT: A 393 MET cc_start: 0.6887 (mmm) cc_final: 0.6683 (mmt) REVERT: A 475 LEU cc_start: 0.9069 (mp) cc_final: 0.8703 (tt) REVERT: B 4 SER cc_start: 0.8493 (t) cc_final: 0.8187 (p) REVERT: B 36 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: B 92 ASN cc_start: 0.8221 (t0) cc_final: 0.7899 (t0) REVERT: B 122 MET cc_start: 0.8913 (ttp) cc_final: 0.8543 (ttt) REVERT: B 299 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8160 (tm-30) REVERT: B 418 THR cc_start: 0.8968 (p) cc_final: 0.8764 (t) REVERT: B 419 HIS cc_start: 0.8413 (t70) cc_final: 0.8060 (t70) REVERT: B 484 GLU cc_start: 0.7597 (tp30) cc_final: 0.7236 (tp30) outliers start: 23 outliers final: 19 residues processed: 126 average time/residue: 0.0603 time to fit residues: 11.0591 Evaluate side-chains 134 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 0.0070 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.155409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117709 restraints weight = 10067.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121598 restraints weight = 5226.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124123 restraints weight = 3614.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125430 restraints weight = 2942.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125945 restraints weight = 2644.794| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7259 Z= 0.101 Angle : 0.560 8.581 9886 Z= 0.277 Chirality : 0.041 0.141 1131 Planarity : 0.004 0.040 1208 Dihedral : 4.208 21.904 998 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.41 % Allowed : 16.44 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.28), residues: 910 helix: -0.71 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -2.46 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 479 TYR 0.025 0.001 TYR A 381 PHE 0.015 0.001 PHE B 179 TRP 0.015 0.001 TRP A 75 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7257) covalent geometry : angle 0.55900 ( 9882) SS BOND : bond 0.00211 ( 2) SS BOND : angle 1.82389 ( 4) hydrogen bonds : bond 0.02995 ( 269) hydrogen bonds : angle 3.77386 ( 792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4725 (ttp) cc_final: 0.4148 (ttt) REVERT: A 117 TYR cc_start: 0.8766 (t80) cc_final: 0.8397 (t80) REVERT: A 475 LEU cc_start: 0.9053 (mp) cc_final: 0.8716 (tt) REVERT: B 4 SER cc_start: 0.8492 (t) cc_final: 0.8181 (p) REVERT: B 36 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: B 92 ASN cc_start: 0.8101 (t0) cc_final: 0.7624 (t0) REVERT: B 122 MET cc_start: 0.8758 (ttp) cc_final: 0.8530 (ttt) REVERT: B 155 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7629 (tt) REVERT: B 299 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8124 (tm-30) REVERT: B 418 THR cc_start: 0.8986 (p) cc_final: 0.8769 (t) REVERT: B 419 HIS cc_start: 0.8526 (t70) cc_final: 0.8219 (t70) REVERT: B 459 TRP cc_start: 0.7259 (t-100) cc_final: 0.6844 (t-100) REVERT: B 484 GLU cc_start: 0.7654 (tp30) cc_final: 0.7292 (tp30) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 0.0547 time to fit residues: 10.4227 Evaluate side-chains 139 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 15 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115964 restraints weight = 10138.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119800 restraints weight = 5280.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122265 restraints weight = 3658.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123710 restraints weight = 2994.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124384 restraints weight = 2678.005| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7259 Z= 0.125 Angle : 0.576 7.648 9886 Z= 0.287 Chirality : 0.042 0.139 1131 Planarity : 0.004 0.039 1208 Dihedral : 4.249 21.719 998 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.94 % Allowed : 16.31 % Favored : 80.75 % 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: -1.94 (0.28), residues: 910 helix: -0.66 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -2.48 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 479 TYR 0.024 0.001 TYR A 381 PHE 0.014 0.001 PHE B 179 TRP 0.014 0.001 TRP A 75 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7257) covalent geometry : angle 0.57516 ( 9882) SS BOND : bond 0.00239 ( 2) SS BOND : angle 1.14103 ( 4) hydrogen bonds : bond 0.03252 ( 269) hydrogen bonds : angle 3.82958 ( 792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.73 seconds wall clock time: 21 minutes 9.55 seconds (1269.55 seconds total)