Starting phenix.real_space_refine on Tue Apr 7 07:58:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d9u_46680/04_2026/9d9u_46680.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d9u_46680/04_2026/9d9u_46680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d9u_46680/04_2026/9d9u_46680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d9u_46680/04_2026/9d9u_46680.map" model { file = "/net/cci-nas-00/data/ceres_data/9d9u_46680/04_2026/9d9u_46680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d9u_46680/04_2026/9d9u_46680.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Fe 14 7.16 5 S 50 5.16 5 C 8101 2.51 5 N 2194 2.21 5 O 2342 1.98 5 H 12520 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25221 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 5912 Classifications: {'peptide': 380} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 361} Chain breaks: 2 Chain: "B" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5915 Classifications: {'peptide': 379} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 360} Chain breaks: 2 Chain: "C" Number of atoms: 6694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 6694 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 415} Chain breaks: 1 Chain: "D" Number of atoms: 6672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6672 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 414} Chain breaks: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13134 SG CYS C 121 90.874 31.213 51.783 1.00121.51 S ATOM 350 SG CYS A 91 88.127 33.438 47.642 1.00 86.47 S ATOM 12025 SG CYS C 32 84.996 33.150 53.352 1.00 95.68 S ATOM 12314 SG CYS C 52 90.972 36.316 52.750 1.00130.56 S ATOM 12314 SG CYS C 52 90.972 36.316 52.750 1.00130.56 S ATOM 1419 SG CYS A 158 94.809 36.540 47.644 1.00110.70 S ATOM 12352 SG CYS C 56 90.673 40.067 46.900 1.00161.17 S ATOM 19806 SG CYS D 121 21.838 59.828 51.773 1.00118.05 S ATOM 6236 SG CYS B 91 24.409 57.686 47.576 1.00 86.96 S ATOM 18697 SG CYS D 32 27.715 57.902 53.226 1.00 97.43 S ATOM 18986 SG CYS D 52 21.839 54.919 52.971 1.00125.08 S ATOM 18986 SG CYS D 52 21.839 54.919 52.971 1.00125.08 S ATOM 7305 SG CYS B 158 17.636 54.526 47.870 1.00110.41 S ATOM 19024 SG CYS D 56 21.793 50.307 47.917 1.00149.77 S Time building chain proxies: 4.87, per 1000 atoms: 0.19 Number of scatterers: 25221 At special positions: 0 Unit cell: (113.025, 91.575, 103.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 14 26.01 S 50 16.00 O 2342 8.00 N 2194 7.00 C 8101 6.00 H 12520 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 759.9 milliseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2950 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 14 sheets defined 59.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 93 through 110 removed outlier: 4.383A pdb=" N ILE A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 157 through 163 removed outlier: 3.684A pdb=" N ILE A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.332A pdb=" N VAL A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 270 through 286 removed outlier: 5.324A pdb=" N TYR A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N MET A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 removed outlier: 3.699A pdb=" N GLY A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 341 Proline residue: A 331 - end of helix removed outlier: 3.942A pdb=" N GLU A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 335 " --> pdb=" O PRO A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.652A pdb=" N GLY A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 431 through 439 removed outlier: 3.923A pdb=" N LEU A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 removed outlier: 4.361A pdb=" N ALA A 452 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 453 " --> pdb=" O HIS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 471 removed outlier: 3.572A pdb=" N ILE A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 481 removed outlier: 3.624A pdb=" N HIS A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 93 through 110 removed outlier: 4.369A pdb=" N ILE B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 132 through 148 Processing helix chain 'B' and resid 157 through 163 removed outlier: 3.600A pdb=" N ILE B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 179 removed outlier: 4.219A pdb=" N VAL B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 296 through 313 removed outlier: 3.685A pdb=" N GLY B 300 " --> pdb=" O TYR B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 340 Proline residue: B 331 - end of helix removed outlier: 3.603A pdb=" N GLU B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 335 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 removed outlier: 3.566A pdb=" N HIS B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 431 through 439 removed outlier: 3.560A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 removed outlier: 4.202A pdb=" N ALA B 452 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 453 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 471 removed outlier: 3.612A pdb=" N ILE B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 459 " --> pdb=" O TYR B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 removed outlier: 3.612A pdb=" N HIS B 475 " --> pdb=" O HIS B 471 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'C' and resid 32 through 35 Processing helix chain 'C' and resid 36 through 42 Processing helix chain 'C' and resid 58 through 65 removed outlier: 4.385A pdb=" N MET C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 95 through 110 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.518A pdb=" N ASP C 124 " --> pdb=" O GLY C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.532A pdb=" N VAL C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.883A pdb=" N GLY C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 171 Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.510A pdb=" N ILE C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 235 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 274 through 290 Processing helix chain 'C' and resid 292 through 321 removed outlier: 4.160A pdb=" N ASP C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 348 Processing helix chain 'C' and resid 366 through 376 Processing helix chain 'C' and resid 390 through 401 Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 445 through 463 removed outlier: 3.592A pdb=" N ALA C 450 " --> pdb=" O GLY C 446 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 451 " --> pdb=" O TYR C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'D' and resid 32 through 35 Processing helix chain 'D' and resid 36 through 42 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.585A pdb=" N MET D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.828A pdb=" N VAL D 80 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.615A pdb=" N ASP D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Proline residue: D 136 - end of helix Processing helix chain 'D' and resid 150 through 154 removed outlier: 3.556A pdb=" N GLY D 154 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 171 Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 200 through 215 removed outlier: 3.514A pdb=" N ILE D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 274 through 290 Processing helix chain 'D' and resid 292 through 321 removed outlier: 4.150A pdb=" N ASP D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 348 Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 390 through 401 Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 416 through 424 Processing helix chain 'D' and resid 445 through 463 Processing helix chain 'D' and resid 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.540A pdb=" N ILE A 152 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 82 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA A 155 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 84 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 249 removed outlier: 7.775A pdb=" N ARG A 244 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 221 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN A 246 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 223 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL A 248 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL A 225 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA A 264 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU A 222 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR A 266 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN A 224 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 290 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR A 266 " --> pdb=" O VAL A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA4, first strand: chain 'A' and resid 425 through 426 removed outlier: 7.315A pdb=" N ILE A 425 " --> pdb=" O ILE A 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.492A pdb=" N ILE B 152 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 244 through 249 removed outlier: 7.708A pdb=" N ARG B 244 " --> pdb=" O GLN B 219 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP B 221 " --> pdb=" O ARG B 244 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN B 246 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 223 " --> pdb=" O ASN B 246 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL B 248 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL B 225 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA B 264 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 222 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR B 266 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN B 224 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B 268 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 226 " --> pdb=" O GLY B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.959A pdb=" N ASP B 369 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B 347 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 371 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 425 through 426 removed outlier: 7.428A pdb=" N ILE B 425 " --> pdb=" O ILE B 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.194A pdb=" N PHE C 115 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA C 147 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 117 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 218 through 220 removed outlier: 7.742A pdb=" N LYS C 218 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N HIS C 186 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASN C 220 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 188 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA C 239 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR C 187 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 241 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU C 266 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASN C 242 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 385 through 387 removed outlier: 7.010A pdb=" N PHE C 329 " --> pdb=" O GLY C 354 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLN C 356 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 331 " --> pdb=" O GLN C 356 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE C 358 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY C 333 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 410 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.193A pdb=" N PHE D 115 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA D 147 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL D 117 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 218 through 220 removed outlier: 7.740A pdb=" N LYS D 218 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS D 186 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASN D 220 " --> pdb=" O HIS D 186 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D 188 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA D 239 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR D 187 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU D 266 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASN D 242 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 385 through 387 removed outlier: 6.983A pdb=" N PHE D 329 " --> pdb=" O GLY D 354 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLN D 356 " --> pdb=" O PHE D 329 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 331 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE D 358 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY D 333 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU D 410 " --> pdb=" O VAL D 428 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1821 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: 6.12 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.26: 14655 1.26 - 1.68: 10774 1.68 - 2.11: 54 2.11 - 2.53: 45 2.53 - 2.95: 17 Bond restraints: 25545 Sorted by residual: bond pdb=" S1 CLF D 501 " pdb="FE6 CLF D 501 " ideal model delta sigma weight residual 2.200 2.952 -0.752 2.00e-02 2.50e+03 1.42e+03 bond pdb=" S1 CLF C 501 " pdb="FE6 CLF C 501 " ideal model delta sigma weight residual 2.200 2.867 -0.667 2.00e-02 2.50e+03 1.11e+03 bond pdb="FE4 CLF C 501 " pdb="FE5 CLF C 501 " ideal model delta sigma weight residual 2.200 2.859 -0.659 2.00e-02 2.50e+03 1.09e+03 bond pdb="FE4 CLF D 501 " pdb="FE5 CLF D 501 " ideal model delta sigma weight residual 2.200 2.804 -0.604 2.00e-02 2.50e+03 9.11e+02 bond pdb="FE5 CLF D 501 " pdb="FE6 CLF D 501 " ideal model delta sigma weight residual 2.200 2.712 -0.512 2.00e-02 2.50e+03 6.55e+02 ... (remaining 25540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.78: 46035 6.78 - 13.56: 1 13.56 - 20.34: 2 20.34 - 27.13: 0 27.13 - 33.91: 4 Bond angle restraints: 46042 Sorted by residual: angle pdb=" S1 CLF C 501 " pdb="FE2 CLF C 501 " pdb="FE4 CLF C 501 " ideal model delta sigma weight residual 90.00 56.09 33.91 3.00e+00 1.11e-01 1.28e+02 angle pdb=" S1 CLF D 501 " pdb="FE2 CLF D 501 " pdb="FE4 CLF D 501 " ideal model delta sigma weight residual 90.00 56.10 33.90 3.00e+00 1.11e-01 1.28e+02 angle pdb=" S1 CLF D 501 " pdb="FE2 CLF D 501 " pdb="FE1 CLF D 501 " ideal model delta sigma weight residual 90.00 58.45 31.55 3.00e+00 1.11e-01 1.11e+02 angle pdb=" S1 CLF C 501 " pdb="FE2 CLF C 501 " pdb="FE1 CLF C 501 " ideal model delta sigma weight residual 90.00 58.53 31.47 3.00e+00 1.11e-01 1.10e+02 angle pdb=" S1 CLF C 501 " pdb="FE2 CLF C 501 " pdb="FE3 CLF C 501 " ideal model delta sigma weight residual 90.00 105.77 -15.77 3.00e+00 1.11e-01 2.76e+01 ... (remaining 46037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 10527 17.61 - 35.22: 914 35.22 - 52.83: 356 52.83 - 70.44: 128 70.44 - 88.05: 36 Dihedral angle restraints: 11961 sinusoidal: 6453 harmonic: 5508 Sorted by residual: dihedral pdb=" CA TYR D 67 " pdb=" C TYR D 67 " pdb=" N ASN D 68 " pdb=" CA ASN D 68 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ALA D 57 " pdb=" C ALA D 57 " pdb=" N ASP D 58 " pdb=" CA ASP D 58 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TRP D 191 " pdb=" C TRP D 191 " pdb=" N SER D 192 " pdb=" CA SER D 192 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 11958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1137 0.028 - 0.056: 523 0.056 - 0.084: 144 0.084 - 0.112: 113 0.112 - 0.140: 39 Chirality restraints: 1956 Sorted by residual: chirality pdb=" CA TYR D 458 " pdb=" N TYR D 458 " pdb=" C TYR D 458 " pdb=" CB TYR D 458 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA PRO D 269 " pdb=" N PRO D 269 " pdb=" C PRO D 269 " pdb=" CB PRO D 269 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 180 " pdb=" N ILE A 180 " pdb=" C ILE A 180 " pdb=" CB ILE A 180 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1953 not shown) Planarity restraints: 3846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 432 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO D 433 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 433 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 433 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 432 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO C 433 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 433 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 433 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 122 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO C 123 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " 0.022 5.00e-02 4.00e+02 ... (remaining 3843 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 773 2.13 - 2.75: 47406 2.75 - 3.36: 77072 3.36 - 3.98: 102246 3.98 - 4.60: 160444 Nonbonded interactions: 387941 Sorted by model distance: nonbonded pdb=" OE1 GLU B 72 " pdb=" H GLU B 72 " model vdw 1.512 2.450 nonbonded pdb=" OD1 ASP A 302 " pdb=" HH TYR A 455 " model vdw 1.558 2.450 nonbonded pdb=" O ASN D 68 " pdb=" H PHE D 70 " model vdw 1.570 2.450 nonbonded pdb=" OE1 GLU C 97 " pdb=" H GLU C 97 " model vdw 1.590 2.450 nonbonded pdb=" HH TYR C 75 " pdb=" O ASP C 111 " model vdw 1.594 2.450 ... (remaining 387936 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 69 through 187 or resid 199 through 494)) selection = (chain 'B' and (resid 69 through 371 or resid 410 through 494)) } ncs_group { reference = (chain 'C' and resid 22 through 501) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.090 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.022 0.752 13037 Z= 1.046 Angle : 0.738 33.908 17621 Z= 0.328 Chirality : 0.042 0.140 1956 Planarity : 0.004 0.040 2300 Dihedral : 16.345 88.047 4665 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.83 % Allowed : 13.96 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1612 helix: 1.21 (0.19), residues: 818 sheet: -0.87 (0.44), residues: 145 loop : -0.79 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 126 TYR 0.017 0.001 TYR D 67 PHE 0.013 0.001 PHE D 200 TRP 0.021 0.001 TRP B 229 HIS 0.004 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.02083 (13025) covalent geometry : angle 0.73822 (17621) hydrogen bonds : bond 0.14707 ( 629) hydrogen bonds : angle 7.16666 ( 1821) Misc. bond : bond 0.25581 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 SER cc_start: 0.8198 (p) cc_final: 0.7959 (p) REVERT: B 217 ARG cc_start: 0.8235 (mmm-85) cc_final: 0.8027 (ttp80) REVERT: C 107 LEU cc_start: 0.8856 (mp) cc_final: 0.8649 (mp) REVERT: D 148 GLU cc_start: 0.8214 (mt-10) cc_final: 0.8012 (mt-10) REVERT: D 178 GLU cc_start: 0.8178 (mp0) cc_final: 0.7939 (pm20) REVERT: D 252 ASP cc_start: 0.7858 (t70) cc_final: 0.7576 (t0) REVERT: D 276 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7507 (tttm) REVERT: D 320 GLU cc_start: 0.8204 (tp30) cc_final: 0.7962 (tp30) outliers start: 24 outliers final: 8 residues processed: 179 average time/residue: 1.5113 time to fit residues: 292.9637 Evaluate side-chains 126 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 311 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.074991 restraints weight = 47308.845| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.03 r_work: 0.2801 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 13037 Z= 0.222 Angle : 0.732 30.078 17621 Z= 0.345 Chirality : 0.044 0.172 1956 Planarity : 0.004 0.040 2300 Dihedral : 5.455 52.604 1795 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.91 % Allowed : 14.65 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.21), residues: 1612 helix: 1.04 (0.18), residues: 837 sheet: -1.30 (0.41), residues: 151 loop : -0.74 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 126 TYR 0.021 0.002 TYR C 458 PHE 0.015 0.001 PHE C 61 TRP 0.015 0.001 TRP B 229 HIS 0.010 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00468 (13025) covalent geometry : angle 0.73183 (17621) hydrogen bonds : bond 0.04768 ( 629) hydrogen bonds : angle 5.75681 ( 1821) Misc. bond : bond 0.06452 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 ARG cc_start: 0.8761 (mtp85) cc_final: 0.8387 (ttm-80) REVERT: B 72 GLU cc_start: 0.6562 (mp0) cc_final: 0.6162 (mp0) REVERT: B 157 SER cc_start: 0.7609 (p) cc_final: 0.7316 (p) REVERT: B 217 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7581 (ttp80) REVERT: B 232 ASP cc_start: 0.8268 (t0) cc_final: 0.8066 (t0) REVERT: D 63 ASN cc_start: 0.7863 (m-40) cc_final: 0.7427 (t0) outliers start: 25 outliers final: 12 residues processed: 142 average time/residue: 1.3724 time to fit residues: 213.1757 Evaluate side-chains 130 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 337 TYR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 151 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.073397 restraints weight = 46690.350| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.09 r_work: 0.2745 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 13037 Z= 0.173 Angle : 0.701 29.577 17621 Z= 0.314 Chirality : 0.042 0.146 1956 Planarity : 0.004 0.041 2300 Dihedral : 5.111 46.725 1790 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.75 % Allowed : 14.57 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1612 helix: 1.27 (0.18), residues: 840 sheet: -1.34 (0.41), residues: 144 loop : -0.67 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 483 TYR 0.019 0.001 TYR C 458 PHE 0.011 0.001 PHE D 200 TRP 0.018 0.001 TRP B 229 HIS 0.004 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00367 (13025) covalent geometry : angle 0.70101 (17621) hydrogen bonds : bond 0.04845 ( 629) hydrogen bonds : angle 5.40585 ( 1821) Misc. bond : bond 0.06781 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 419 ARG cc_start: 0.8818 (mtp85) cc_final: 0.8546 (ttm-80) REVERT: B 72 GLU cc_start: 0.6397 (mp0) cc_final: 0.5992 (mp0) REVERT: B 157 SER cc_start: 0.7750 (p) cc_final: 0.7432 (p) REVERT: B 217 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7683 (ttp80) REVERT: C 337 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.9029 (t80) REVERT: D 63 ASN cc_start: 0.7952 (m-40) cc_final: 0.7512 (t0) REVERT: D 252 ASP cc_start: 0.8636 (t0) cc_final: 0.8233 (t0) outliers start: 23 outliers final: 10 residues processed: 141 average time/residue: 1.4453 time to fit residues: 221.2990 Evaluate side-chains 128 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 337 TYR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 94 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.116116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.074588 restraints weight = 46785.830| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.03 r_work: 0.2794 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13037 Z= 0.170 Angle : 0.696 29.205 17621 Z= 0.311 Chirality : 0.042 0.148 1956 Planarity : 0.004 0.038 2300 Dihedral : 4.775 46.944 1785 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.45 % Allowed : 15.71 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1612 helix: 1.34 (0.18), residues: 839 sheet: -1.37 (0.41), residues: 142 loop : -0.64 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.020 0.001 TYR C 458 PHE 0.011 0.001 PHE D 200 TRP 0.010 0.001 TRP C 323 HIS 0.004 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00374 (13025) covalent geometry : angle 0.69590 (17621) hydrogen bonds : bond 0.04296 ( 629) hydrogen bonds : angle 5.28685 ( 1821) Misc. bond : bond 0.03799 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 419 ARG cc_start: 0.8802 (mtp85) cc_final: 0.8543 (ttm-80) REVERT: B 72 GLU cc_start: 0.6376 (mp0) cc_final: 0.6000 (mp0) REVERT: B 157 SER cc_start: 0.7678 (p) cc_final: 0.7334 (p) REVERT: B 217 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7742 (ttp80) REVERT: B 281 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7461 (tt) REVERT: C 337 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.9053 (t80) REVERT: D 63 ASN cc_start: 0.7988 (m-40) cc_final: 0.7546 (t0) REVERT: D 252 ASP cc_start: 0.8691 (t0) cc_final: 0.8197 (t0) REVERT: D 293 SER cc_start: 0.8876 (t) cc_final: 0.8610 (p) outliers start: 19 outliers final: 11 residues processed: 132 average time/residue: 1.3824 time to fit residues: 199.3332 Evaluate side-chains 127 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 337 TYR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.072004 restraints weight = 46193.687| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.05 r_work: 0.2756 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 13037 Z= 0.219 Angle : 0.718 29.021 17621 Z= 0.325 Chirality : 0.043 0.160 1956 Planarity : 0.004 0.040 2300 Dihedral : 4.865 47.111 1785 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.98 % Allowed : 14.95 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.21), residues: 1612 helix: 1.30 (0.18), residues: 841 sheet: -1.41 (0.41), residues: 143 loop : -0.67 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 483 TYR 0.020 0.002 TYR C 458 PHE 0.020 0.001 PHE C 61 TRP 0.014 0.001 TRP B 229 HIS 0.006 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00489 (13025) covalent geometry : angle 0.71763 (17621) hydrogen bonds : bond 0.04712 ( 629) hydrogen bonds : angle 5.28408 ( 1821) Misc. bond : bond 0.04478 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8056 (tttt) REVERT: A 419 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8371 (ttm-80) REVERT: B 72 GLU cc_start: 0.6518 (mp0) cc_final: 0.6168 (mp0) REVERT: B 217 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7732 (ttp80) REVERT: B 281 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7502 (tt) REVERT: C 61 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: C 293 SER cc_start: 0.8899 (m) cc_final: 0.8613 (t) REVERT: C 337 TYR cc_start: 0.9357 (OUTLIER) cc_final: 0.8993 (t80) REVERT: D 63 ASN cc_start: 0.8078 (m-40) cc_final: 0.7661 (t0) REVERT: D 108 GLN cc_start: 0.8739 (pt0) cc_final: 0.8496 (pt0) outliers start: 26 outliers final: 11 residues processed: 138 average time/residue: 1.4116 time to fit residues: 212.6318 Evaluate side-chains 131 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 337 TYR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.115933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.073442 restraints weight = 46259.139| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.07 r_work: 0.2778 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 13037 Z= 0.156 Angle : 0.693 29.069 17621 Z= 0.309 Chirality : 0.042 0.149 1956 Planarity : 0.004 0.076 2300 Dihedral : 4.806 46.906 1785 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.37 % Allowed : 16.09 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1612 helix: 1.39 (0.18), residues: 840 sheet: -1.44 (0.41), residues: 142 loop : -0.63 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 153 TYR 0.020 0.001 TYR C 458 PHE 0.016 0.001 PHE C 61 TRP 0.011 0.001 TRP C 323 HIS 0.004 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00334 (13025) covalent geometry : angle 0.69295 (17621) hydrogen bonds : bond 0.04257 ( 629) hydrogen bonds : angle 5.18761 ( 1821) Misc. bond : bond 0.05560 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8331 (ttpp) cc_final: 0.8070 (tttt) REVERT: A 419 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8414 (ttm-80) REVERT: B 72 GLU cc_start: 0.6502 (mp0) cc_final: 0.6155 (mp0) REVERT: B 157 SER cc_start: 0.7530 (p) cc_final: 0.7181 (p) REVERT: B 217 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7718 (ttp80) REVERT: B 281 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7498 (tt) REVERT: B 341 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8577 (mtmm) REVERT: C 61 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6090 (m-80) REVERT: C 293 SER cc_start: 0.8890 (m) cc_final: 0.8594 (t) REVERT: C 337 TYR cc_start: 0.9341 (OUTLIER) cc_final: 0.9000 (t80) REVERT: D 63 ASN cc_start: 0.8016 (m-40) cc_final: 0.7611 (m-40) REVERT: D 108 GLN cc_start: 0.8694 (pt0) cc_final: 0.8455 (pt0) REVERT: D 268 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8798 (tmt170) outliers start: 18 outliers final: 11 residues processed: 134 average time/residue: 1.4015 time to fit residues: 205.1256 Evaluate side-chains 132 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 337 TYR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 18 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.072818 restraints weight = 45988.868| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.07 r_work: 0.2730 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 13037 Z= 0.171 Angle : 0.698 28.983 17621 Z= 0.311 Chirality : 0.042 0.152 1956 Planarity : 0.004 0.038 2300 Dihedral : 4.767 46.681 1785 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.68 % Allowed : 15.64 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1612 helix: 1.41 (0.18), residues: 841 sheet: -1.44 (0.41), residues: 142 loop : -0.59 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 483 TYR 0.020 0.001 TYR D 458 PHE 0.016 0.001 PHE C 61 TRP 0.014 0.001 TRP B 229 HIS 0.004 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00376 (13025) covalent geometry : angle 0.69752 (17621) hydrogen bonds : bond 0.04249 ( 629) hydrogen bonds : angle 5.14729 ( 1821) Misc. bond : bond 0.05184 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8388 (ttpp) cc_final: 0.8077 (tttt) REVERT: A 419 ARG cc_start: 0.8688 (mtp85) cc_final: 0.8402 (ttm-80) REVERT: B 72 GLU cc_start: 0.6530 (mp0) cc_final: 0.6180 (mp0) REVERT: B 157 SER cc_start: 0.7581 (p) cc_final: 0.7216 (p) REVERT: B 217 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7705 (ttp80) REVERT: C 61 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6067 (m-80) REVERT: C 337 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.9007 (t80) REVERT: D 63 ASN cc_start: 0.8066 (m-40) cc_final: 0.7676 (m-40) REVERT: D 108 GLN cc_start: 0.8675 (pt0) cc_final: 0.8467 (pt0) REVERT: D 268 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8855 (tmt170) outliers start: 22 outliers final: 11 residues processed: 137 average time/residue: 1.4446 time to fit residues: 215.5249 Evaluate side-chains 131 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 337 TYR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 113 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 0.0000 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 460 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.073321 restraints weight = 46334.568| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.08 r_work: 0.2739 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 13037 Z= 0.154 Angle : 0.692 28.977 17621 Z= 0.307 Chirality : 0.042 0.148 1956 Planarity : 0.004 0.038 2300 Dihedral : 4.727 46.267 1785 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.45 % Allowed : 15.94 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.21), residues: 1612 helix: 1.45 (0.18), residues: 842 sheet: -1.42 (0.41), residues: 142 loop : -0.59 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 483 TYR 0.020 0.001 TYR D 458 PHE 0.015 0.001 PHE C 61 TRP 0.019 0.001 TRP B 229 HIS 0.004 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00336 (13025) covalent geometry : angle 0.69232 (17621) hydrogen bonds : bond 0.04117 ( 629) hydrogen bonds : angle 5.08649 ( 1821) Misc. bond : bond 0.04406 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8073 (tttt) REVERT: A 419 ARG cc_start: 0.8657 (mtp85) cc_final: 0.8393 (ttm-80) REVERT: B 72 GLU cc_start: 0.6557 (mp0) cc_final: 0.6201 (mp0) REVERT: B 157 SER cc_start: 0.7581 (p) cc_final: 0.7202 (p) REVERT: B 217 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7737 (ttp80) REVERT: C 61 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.5969 (m-80) REVERT: C 337 TYR cc_start: 0.9340 (OUTLIER) cc_final: 0.8919 (t80) REVERT: D 63 ASN cc_start: 0.8126 (m-40) cc_final: 0.7718 (m-40) REVERT: D 268 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8840 (tmt170) outliers start: 19 outliers final: 10 residues processed: 132 average time/residue: 1.4539 time to fit residues: 208.6041 Evaluate side-chains 129 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 337 TYR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 36 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.072831 restraints weight = 46429.415| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.07 r_work: 0.2737 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13037 Z= 0.159 Angle : 0.696 28.980 17621 Z= 0.309 Chirality : 0.042 0.148 1956 Planarity : 0.004 0.108 2300 Dihedral : 4.739 46.041 1785 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.99 % Allowed : 16.40 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1612 helix: 1.48 (0.18), residues: 841 sheet: -1.40 (0.41), residues: 142 loop : -0.58 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 153 TYR 0.020 0.001 TYR D 458 PHE 0.014 0.001 PHE C 61 TRP 0.020 0.001 TRP B 229 HIS 0.004 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00350 (13025) covalent geometry : angle 0.69566 (17621) hydrogen bonds : bond 0.04123 ( 629) hydrogen bonds : angle 5.06955 ( 1821) Misc. bond : bond 0.04258 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8370 (ttpp) cc_final: 0.8071 (tttt) REVERT: A 419 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8395 (ttm-80) REVERT: B 72 GLU cc_start: 0.6524 (mp0) cc_final: 0.6182 (mp0) REVERT: B 157 SER cc_start: 0.7566 (p) cc_final: 0.7190 (p) REVERT: B 217 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7757 (ttp80) REVERT: B 229 TRP cc_start: 0.6661 (m100) cc_final: 0.6444 (m100) REVERT: C 61 PHE cc_start: 0.6601 (OUTLIER) cc_final: 0.5790 (m-80) REVERT: C 337 TYR cc_start: 0.9341 (OUTLIER) cc_final: 0.8992 (t80) REVERT: D 63 ASN cc_start: 0.8109 (m-40) cc_final: 0.7724 (m-40) REVERT: D 268 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8839 (tmt170) outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 1.5222 time to fit residues: 209.7678 Evaluate side-chains 127 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 337 TYR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 127 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 16 optimal weight: 0.0570 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073534 restraints weight = 46231.260| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.07 r_work: 0.2751 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 13037 Z= 0.136 Angle : 0.685 28.962 17621 Z= 0.302 Chirality : 0.041 0.142 1956 Planarity : 0.004 0.038 2300 Dihedral : 4.675 45.644 1785 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.92 % Allowed : 16.78 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1612 helix: 1.54 (0.18), residues: 844 sheet: -1.38 (0.41), residues: 142 loop : -0.55 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 483 TYR 0.020 0.001 TYR D 458 PHE 0.011 0.001 PHE B 102 TRP 0.019 0.001 TRP B 229 HIS 0.004 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00293 (13025) covalent geometry : angle 0.68502 (17621) hydrogen bonds : bond 0.03967 ( 629) hydrogen bonds : angle 5.02288 ( 1821) Misc. bond : bond 0.04110 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8085 (tttt) REVERT: A 419 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8394 (ttm-80) REVERT: B 72 GLU cc_start: 0.6522 (mp0) cc_final: 0.6179 (mp0) REVERT: B 157 SER cc_start: 0.7516 (p) cc_final: 0.7135 (p) REVERT: B 217 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7764 (ttp80) REVERT: C 61 PHE cc_start: 0.6592 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: C 337 TYR cc_start: 0.9334 (OUTLIER) cc_final: 0.8906 (t80) REVERT: D 63 ASN cc_start: 0.8094 (m-40) cc_final: 0.7684 (m-40) REVERT: D 268 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8824 (tmt170) outliers start: 12 outliers final: 10 residues processed: 128 average time/residue: 1.5387 time to fit residues: 213.6173 Evaluate side-chains 128 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 337 TYR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 127 optimal weight: 0.0050 chunk 77 optimal weight: 0.0870 chunk 111 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.116560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.073930 restraints weight = 46264.585| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.08 r_work: 0.2800 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 13037 Z= 0.127 Angle : 0.683 28.963 17621 Z= 0.300 Chirality : 0.041 0.139 1956 Planarity : 0.005 0.123 2300 Dihedral : 4.640 45.265 1785 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.14 % Allowed : 16.48 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.22), residues: 1612 helix: 1.57 (0.18), residues: 842 sheet: -1.36 (0.42), residues: 138 loop : -0.55 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 153 TYR 0.020 0.001 TYR D 458 PHE 0.011 0.001 PHE C 61 TRP 0.033 0.001 TRP B 229 HIS 0.003 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00272 (13025) covalent geometry : angle 0.68334 (17621) hydrogen bonds : bond 0.03871 ( 629) hydrogen bonds : angle 4.97216 ( 1821) Misc. bond : bond 0.04043 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9540.02 seconds wall clock time: 161 minutes 57.66 seconds (9717.66 seconds total)