Starting phenix.real_space_refine on Wed Aug 5 21:19:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21fk_67628/08_2026/21fk_67628.cif Found real_map, /net/cci-nas-00/data/ceres_data/21fk_67628/08_2026/21fk_67628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21fk_67628/08_2026/21fk_67628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21fk_67628/08_2026/21fk_67628.map" model { file = "/net/cci-nas-00/data/ceres_data/21fk_67628/08_2026/21fk_67628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21fk_67628/08_2026/21fk_67628.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7770 2.51 5 N 1749 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11574 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3858 Classifications: {'peptide': 499} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C Time building chain proxies: 2.69, per 1000 atoms: 0.23 Number of scatterers: 11574 At special positions: 0 Unit cell: (121.573, 115.107, 80.1867, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1992 8.00 N 1749 7.00 C 7770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 467.4 milliseconds 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 0 sheets defined 84.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 7 through 28 removed outlier: 3.814A pdb=" N PHE A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Proline residue: A 24 - end of helix Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.607A pdb=" N GLU A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 68 removed outlier: 4.430A pdb=" N PHE A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.757A pdb=" N LYS A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 73 " --> pdb=" O HIS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 73' Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 98 through 109 removed outlier: 4.375A pdb=" N VAL A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.891A pdb=" N TYR A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 116 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.987A pdb=" N ALA A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.546A pdb=" N VAL A 149 " --> pdb=" O TRP A 145 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 150' Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.991A pdb=" N ILE A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.766A pdb=" N CYS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 179 through 182 removed outlier: 3.748A pdb=" N ASP A 182 " --> pdb=" O LYS A 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 183 through 220 removed outlier: 3.791A pdb=" N LYS A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 225 through 243 removed outlier: 3.648A pdb=" N SER A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 273 removed outlier: 4.178A pdb=" N LEU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 removed outlier: 4.223A pdb=" N THR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.655A pdb=" N LEU A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 373 removed outlier: 3.508A pdb=" N LEU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TRP A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 360 " --> pdb=" O CYS A 356 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 369 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.658A pdb=" N MET A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 432 removed outlier: 3.575A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.725A pdb=" N GLY A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 removed outlier: 3.694A pdb=" N LEU A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.723A pdb=" N VAL A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 497 " --> pdb=" O MET A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 3.814A pdb=" N PHE B 11 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Proline residue: B 24 - end of helix Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.607A pdb=" N GLU B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 68 removed outlier: 4.430A pdb=" N PHE B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.757A pdb=" N LYS B 72 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 73 " --> pdb=" O HIS B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 98 through 109 removed outlier: 4.375A pdb=" N VAL B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.891A pdb=" N TYR B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 116 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 140 removed outlier: 3.987A pdb=" N ALA B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 removed outlier: 3.546A pdb=" N VAL B 149 " --> pdb=" O TRP B 145 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 145 through 150' Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.991A pdb=" N ILE B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.766A pdb=" N CYS B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 182 removed outlier: 3.748A pdb=" N ASP B 182 " --> pdb=" O LYS B 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 182' Processing helix chain 'B' and resid 183 through 220 removed outlier: 3.791A pdb=" N LYS B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 225 through 243 removed outlier: 3.649A pdb=" N SER B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 273 removed outlier: 4.178A pdb=" N LEU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 removed outlier: 4.223A pdb=" N THR B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.655A pdb=" N LEU B 330 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 336 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 373 removed outlier: 3.508A pdb=" N LEU B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TRP B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE B 360 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 369 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 370 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 386 through 397 removed outlier: 3.658A pdb=" N MET B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 432 removed outlier: 3.575A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 454 through 464 removed outlier: 3.725A pdb=" N GLY B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 478 removed outlier: 3.694A pdb=" N LEU B 470 " --> pdb=" O ASP B 466 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 497 removed outlier: 3.723A pdb=" N VAL B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 497 " --> pdb=" O MET B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 28 removed outlier: 3.814A pdb=" N PHE C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE C 15 " --> pdb=" O PHE C 11 " (cutoff:3.500A) Proline residue: C 24 - end of helix Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.607A pdb=" N GLU C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 68 removed outlier: 4.431A pdb=" N PHE C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.757A pdb=" N LYS C 72 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 73 " --> pdb=" O HIS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 73' Processing helix chain 'C' and resid 85 through 98 Processing helix chain 'C' and resid 98 through 109 removed outlier: 4.375A pdb=" N VAL C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE C 108 " --> pdb=" O TYR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 116 removed outlier: 3.892A pdb=" N TYR C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C 116 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 140 removed outlier: 3.988A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.546A pdb=" N VAL C 149 " --> pdb=" O TRP C 145 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 145 through 150' Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.991A pdb=" N ILE C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 removed outlier: 3.766A pdb=" N CYS C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 179 through 182 removed outlier: 3.748A pdb=" N ASP C 182 " --> pdb=" O LYS C 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 182' Processing helix chain 'C' and resid 183 through 220 removed outlier: 3.790A pdb=" N LYS C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Proline residue: C 210 - end of helix Processing helix chain 'C' and resid 225 through 243 removed outlier: 3.649A pdb=" N SER C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 273 removed outlier: 4.178A pdb=" N LEU C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 293 removed outlier: 4.222A pdb=" N THR C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.655A pdb=" N LEU C 330 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 336 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 373 removed outlier: 3.508A pdb=" N LEU C 346 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TRP C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY C 355 " --> pdb=" O TRP C 351 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE C 360 " --> pdb=" O CYS C 356 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS C 369 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 370 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.659A pdb=" N MET C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 432 removed outlier: 3.575A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 454 through 464 removed outlier: 3.726A pdb=" N GLY C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 478 removed outlier: 3.694A pdb=" N LEU C 470 " --> pdb=" O ASP C 466 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 497 removed outlier: 3.723A pdb=" N VAL C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS C 497 " --> pdb=" O MET C 493 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 2151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1719 1.31 - 1.43: 3373 1.43 - 1.56: 6713 1.56 - 1.68: 0 1.68 - 1.81: 108 Bond restraints: 11913 Sorted by residual: bond pdb=" C ILE C 322 " pdb=" O ILE C 322 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.23e-02 6.61e+03 2.11e+01 bond pdb=" C ILE B 322 " pdb=" O ILE B 322 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.23e-02 6.61e+03 2.10e+01 bond pdb=" C ILE A 322 " pdb=" O ILE A 322 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.23e-02 6.61e+03 2.09e+01 bond pdb=" CA PHE A 94 " pdb=" C PHE A 94 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.30e-02 5.92e+03 1.99e+01 bond pdb=" CA PHE C 94 " pdb=" C PHE C 94 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.30e-02 5.92e+03 1.98e+01 ... (remaining 11908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 15676 2.05 - 4.09: 425 4.09 - 6.14: 105 6.14 - 8.19: 33 8.19 - 10.24: 12 Bond angle restraints: 16251 Sorted by residual: angle pdb=" N GLY A 251 " pdb=" CA GLY A 251 " pdb=" C GLY A 251 " ideal model delta sigma weight residual 112.73 121.58 -8.85 1.20e+00 6.94e-01 5.44e+01 angle pdb=" N GLY B 251 " pdb=" CA GLY B 251 " pdb=" C GLY B 251 " ideal model delta sigma weight residual 112.73 121.57 -8.84 1.20e+00 6.94e-01 5.43e+01 angle pdb=" N GLY C 251 " pdb=" CA GLY C 251 " pdb=" C GLY C 251 " ideal model delta sigma weight residual 112.73 121.55 -8.82 1.20e+00 6.94e-01 5.40e+01 angle pdb=" N ALA C 156 " pdb=" CA ALA C 156 " pdb=" C ALA C 156 " ideal model delta sigma weight residual 111.36 119.29 -7.93 1.09e+00 8.42e-01 5.29e+01 angle pdb=" N ALA B 156 " pdb=" CA ALA B 156 " pdb=" C ALA B 156 " ideal model delta sigma weight residual 111.36 119.28 -7.92 1.09e+00 8.42e-01 5.27e+01 ... (remaining 16246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.59: 5540 11.59 - 23.18: 736 23.18 - 34.77: 317 34.77 - 46.36: 82 46.36 - 57.95: 45 Dihedral angle restraints: 6720 sinusoidal: 2466 harmonic: 4254 Sorted by residual: dihedral pdb=" N PHE C 420 " pdb=" C PHE C 420 " pdb=" CA PHE C 420 " pdb=" CB PHE C 420 " ideal model delta harmonic sigma weight residual 122.80 138.91 -16.11 0 2.50e+00 1.60e-01 4.15e+01 dihedral pdb=" N PHE A 420 " pdb=" C PHE A 420 " pdb=" CA PHE A 420 " pdb=" CB PHE A 420 " ideal model delta harmonic sigma weight residual 122.80 138.89 -16.09 0 2.50e+00 1.60e-01 4.14e+01 dihedral pdb=" N PHE B 420 " pdb=" C PHE B 420 " pdb=" CA PHE B 420 " pdb=" CB PHE B 420 " ideal model delta harmonic sigma weight residual 122.80 138.83 -16.03 0 2.50e+00 1.60e-01 4.11e+01 ... (remaining 6717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1818 0.139 - 0.278: 63 0.278 - 0.417: 15 0.417 - 0.556: 6 0.556 - 0.695: 3 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CA PHE C 420 " pdb=" N PHE C 420 " pdb=" C PHE C 420 " pdb=" CB PHE C 420 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA PHE A 420 " pdb=" N PHE A 420 " pdb=" C PHE A 420 " pdb=" CB PHE A 420 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA PHE B 420 " pdb=" N PHE B 420 " pdb=" C PHE B 420 " pdb=" CB PHE B 420 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 ... (remaining 1902 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 88 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C SER B 88 " 0.057 2.00e-02 2.50e+03 pdb=" O SER B 88 " -0.021 2.00e-02 2.50e+03 pdb=" N TRP B 89 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 88 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C SER C 88 " -0.057 2.00e-02 2.50e+03 pdb=" O SER C 88 " 0.021 2.00e-02 2.50e+03 pdb=" N TRP C 89 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 88 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C SER A 88 " -0.057 2.00e-02 2.50e+03 pdb=" O SER A 88 " 0.021 2.00e-02 2.50e+03 pdb=" N TRP A 89 " 0.019 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2241 2.76 - 3.30: 10806 3.30 - 3.83: 18279 3.83 - 4.37: 20352 4.37 - 4.90: 37299 Nonbonded interactions: 88977 Sorted by model distance: nonbonded pdb=" O PHE B 9 " pdb=" OG SER B 13 " model vdw 2.229 3.040 nonbonded pdb=" O PHE C 9 " pdb=" OG SER C 13 " model vdw 2.229 3.040 nonbonded pdb=" O PHE A 9 " pdb=" OG SER A 13 " model vdw 2.229 3.040 nonbonded pdb=" O GLY A 308 " pdb=" OG SER A 312 " model vdw 2.310 3.040 nonbonded pdb=" O GLY C 308 " pdb=" OG SER C 312 " model vdw 2.311 3.040 ... (remaining 88972 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.006 0.058 11913 Z= 0.453 Angle : 0.879 10.236 16251 Z= 0.584 Chirality : 0.073 0.695 1905 Planarity : 0.006 0.050 1944 Dihedral : 13.879 57.953 4014 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.46 % Allowed : 16.10 % Favored : 82.44 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1491 helix: 0.33 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -2.27 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 250 TYR 0.032 0.002 TYR A 157 PHE 0.037 0.002 PHE A 327 TRP 0.015 0.001 TRP C 140 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.45 (11913) covalent geometry : angle 0.87908 / 0.58 (16251) hydrogen bonds : bond 0.18797 / 12.16 ( 717) hydrogen bonds : angle 5.57812 / 3.96 ( 2151) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.287 Fit side-chains REVERT: A 56 MET cc_start: 0.8819 (tpt) cc_final: 0.8489 (tpt) REVERT: A 159 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.7228 (t80) REVERT: A 162 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 324 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.7473 (t80) REVERT: B 56 MET cc_start: 0.8689 (tpt) cc_final: 0.8167 (tpt) REVERT: B 92 MET cc_start: 0.5131 (mtm) cc_final: 0.4354 (mmp) REVERT: B 162 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8279 (mp) REVERT: B 194 MET cc_start: 0.7654 (mmm) cc_final: 0.7137 (mtp) REVERT: B 324 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.6608 (t80) REVERT: C 49 MET cc_start: 0.8546 (pmm) cc_final: 0.8300 (pmm) REVERT: C 81 LYS cc_start: 0.7368 (ttmt) cc_final: 0.6728 (tttp) REVERT: C 92 MET cc_start: 0.4726 (mtm) cc_final: 0.4265 (mmp) REVERT: C 159 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7103 (t80) REVERT: C 162 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8162 (mp) REVERT: C 194 MET cc_start: 0.7560 (mmm) cc_final: 0.7030 (mtp) REVERT: C 324 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7450 (t80) REVERT: C 330 LEU cc_start: 0.8190 (mp) cc_final: 0.7721 (tt) outliers start: 18 outliers final: 4 residues processed: 137 average time/residue: 0.0782 time to fit residues: 17.1867 Evaluate side-chains 137 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 326 PRO Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 326 PRO Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 328 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.165677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.156370 restraints weight = 12481.095| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 0.62 r_work: 0.3346 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.3192 rms_B_bonded: 2.67 restraints_weight: 0.1250 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11913 Z= 0.169 Angle : 0.571 5.790 16251 Z= 0.313 Chirality : 0.042 0.136 1905 Planarity : 0.004 0.039 1944 Dihedral : 5.890 59.601 1600 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.30 % Allowed : 14.63 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1491 helix: 0.77 (0.16), residues: 1164 sheet: None (None), residues: 0 loop : -2.45 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 337 TYR 0.015 0.001 TYR B 157 PHE 0.023 0.001 PHE A 420 TRP 0.022 0.001 TRP B 140 HIS 0.007 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (11913) covalent geometry : angle 0.57117 / 0.31 (16251) hydrogen bonds : bond 0.06507 / 4.26 ( 717) hydrogen bonds : angle 3.82673 / 2.72 ( 2151) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.389 Fit side-chains REVERT: A 324 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7153 (t80) REVERT: B 56 MET cc_start: 0.8461 (tpt) cc_final: 0.7813 (tpt) REVERT: B 135 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: B 162 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8265 (mp) REVERT: B 324 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6836 (t80) REVERT: C 81 LYS cc_start: 0.7003 (ttmt) cc_final: 0.6653 (tttp) REVERT: C 162 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8489 (mp) REVERT: C 194 MET cc_start: 0.7621 (mmm) cc_final: 0.7359 (mtp) outliers start: 16 outliers final: 4 residues processed: 135 average time/residue: 0.0599 time to fit residues: 13.0786 Evaluate side-chains 127 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 324 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 112 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.159632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140523 restraints weight = 12744.140| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 0.92 r_work: 0.3192 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work: 0.2942 rms_B_bonded: 4.37 restraints_weight: 0.1250 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11913 Z= 0.210 Angle : 0.618 6.399 16251 Z= 0.333 Chirality : 0.044 0.152 1905 Planarity : 0.004 0.042 1944 Dihedral : 5.581 59.430 1582 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.79 % Allowed : 14.47 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.23), residues: 1491 helix: 0.80 (0.16), residues: 1155 sheet: None (None), residues: 0 loop : -2.52 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 337 TYR 0.017 0.002 TYR A 160 PHE 0.018 0.002 PHE A 420 TRP 0.023 0.002 TRP A 140 HIS 0.008 0.002 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 (11913) covalent geometry : angle 0.61759 / 0.33 (16251) hydrogen bonds : bond 0.06664 / 4.37 ( 717) hydrogen bonds : angle 3.88317 / 2.76 ( 2151) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.409 Fit side-chains REVERT: A 324 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7207 (t80) REVERT: A 383 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: B 11 PHE cc_start: 0.7816 (t80) cc_final: 0.7478 (t80) REVERT: B 56 MET cc_start: 0.8527 (tpt) cc_final: 0.8014 (tpt) REVERT: B 92 MET cc_start: 0.5478 (mmp) cc_final: 0.4738 (mmt) REVERT: B 324 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7101 (t80) REVERT: B 420 PHE cc_start: 0.7447 (p90) cc_final: 0.7187 (p90) REVERT: C 56 MET cc_start: 0.8558 (tpt) cc_final: 0.7995 (tpt) REVERT: C 81 LYS cc_start: 0.7413 (ttmt) cc_final: 0.6872 (tttp) REVERT: C 194 MET cc_start: 0.7961 (mmm) cc_final: 0.7563 (mtp) REVERT: C 383 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7991 (mp0) outliers start: 22 outliers final: 12 residues processed: 151 average time/residue: 0.0661 time to fit residues: 15.9514 Evaluate side-chains 139 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 18 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.167638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.158398 restraints weight = 12583.948| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 0.67 r_work: 0.3518 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work: 0.3315 rms_B_bonded: 4.17 restraints_weight: 0.1250 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11913 Z= 0.125 Angle : 0.507 7.375 16251 Z= 0.269 Chirality : 0.039 0.135 1905 Planarity : 0.004 0.035 1944 Dihedral : 5.009 59.364 1578 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.46 % Allowed : 15.53 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1491 helix: 1.10 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -2.61 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 250 TYR 0.008 0.001 TYR C 157 PHE 0.018 0.001 PHE A 193 TRP 0.014 0.001 TRP A 140 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (11913) covalent geometry : angle 0.50711 / 0.27 (16251) hydrogen bonds : bond 0.04798 / 3.15 ( 717) hydrogen bonds : angle 3.63070 / 2.56 ( 2151) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.402 Fit side-chains REVERT: A 92 MET cc_start: 0.4208 (mmp) cc_final: 0.3853 (mmt) REVERT: A 324 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6783 (t80) REVERT: B 56 MET cc_start: 0.8367 (tpt) cc_final: 0.7762 (tpt) REVERT: B 92 MET cc_start: 0.5812 (mmp) cc_final: 0.5112 (mmt) REVERT: B 108 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7972 (pp) REVERT: B 383 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: C 9 PHE cc_start: 0.7685 (t80) cc_final: 0.7430 (t80) REVERT: C 56 MET cc_start: 0.8600 (tpt) cc_final: 0.7925 (tpt) REVERT: C 81 LYS cc_start: 0.7124 (ttmt) cc_final: 0.6770 (tttp) REVERT: C 92 MET cc_start: 0.4924 (mmp) cc_final: 0.4221 (mmt) REVERT: C 108 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8122 (pp) REVERT: C 135 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8352 (m-80) outliers start: 18 outliers final: 5 residues processed: 143 average time/residue: 0.0755 time to fit residues: 17.1783 Evaluate side-chains 131 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 324 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 28 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.167052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.157686 restraints weight = 12608.577| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 0.63 r_work: 0.3372 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.3189 rms_B_bonded: 2.82 restraints_weight: 0.1250 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11913 Z= 0.109 Angle : 0.481 6.583 16251 Z= 0.253 Chirality : 0.038 0.135 1905 Planarity : 0.003 0.032 1944 Dihedral : 4.789 59.352 1578 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.63 % Allowed : 15.85 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.23), residues: 1491 helix: 1.36 (0.16), residues: 1149 sheet: None (None), residues: 0 loop : -2.27 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 337 TYR 0.007 0.001 TYR B 157 PHE 0.018 0.001 PHE A 193 TRP 0.013 0.001 TRP B 140 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (11913) covalent geometry : angle 0.48104 / 0.25 (16251) hydrogen bonds : bond 0.04140 / 2.73 ( 717) hydrogen bonds : angle 3.48554 / 2.46 ( 2151) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.415 Fit side-chains REVERT: A 92 MET cc_start: 0.4384 (mmp) cc_final: 0.4162 (mtm) REVERT: A 324 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6694 (t80) REVERT: A 383 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 56 MET cc_start: 0.8418 (tpt) cc_final: 0.7902 (tpt) REVERT: B 383 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: C 56 MET cc_start: 0.8549 (tpt) cc_final: 0.7924 (tpt) REVERT: C 81 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6725 (tttp) REVERT: C 92 MET cc_start: 0.4854 (mmp) cc_final: 0.4417 (mmt) REVERT: C 101 ASP cc_start: 0.7549 (m-30) cc_final: 0.7154 (m-30) REVERT: C 229 THR cc_start: 0.7798 (m) cc_final: 0.7577 (m) REVERT: C 383 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7894 (mp0) outliers start: 20 outliers final: 6 residues processed: 148 average time/residue: 0.0770 time to fit residues: 18.0877 Evaluate side-chains 135 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 383 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.166584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.146804 restraints weight = 12766.985| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.00 r_work: 0.3277 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11913 Z= 0.111 Angle : 0.486 6.607 16251 Z= 0.254 Chirality : 0.038 0.134 1905 Planarity : 0.003 0.031 1944 Dihedral : 4.498 59.511 1576 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.22 % Allowed : 16.67 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1491 helix: 1.40 (0.16), residues: 1152 sheet: None (None), residues: 0 loop : -2.24 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 337 TYR 0.015 0.001 TYR C 425 PHE 0.017 0.001 PHE C 193 TRP 0.012 0.001 TRP B 140 HIS 0.002 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (11913) covalent geometry : angle 0.48557 / 0.25 (16251) hydrogen bonds : bond 0.04126 / 2.72 ( 717) hydrogen bonds : angle 3.44772 / 2.43 ( 2151) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.421 Fit side-chains REVERT: A 324 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6747 (t80) REVERT: A 383 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: B 56 MET cc_start: 0.8412 (tpt) cc_final: 0.7922 (tpt) REVERT: B 92 MET cc_start: 0.5404 (mmp) cc_final: 0.4623 (mmt) REVERT: B 108 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7920 (pp) REVERT: B 383 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: C 56 MET cc_start: 0.8538 (tpt) cc_final: 0.7942 (tpt) REVERT: C 92 MET cc_start: 0.4696 (mmp) cc_final: 0.4323 (mmt) REVERT: C 229 THR cc_start: 0.7803 (m) cc_final: 0.7601 (m) REVERT: C 331 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: C 383 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7891 (mp0) outliers start: 15 outliers final: 8 residues processed: 141 average time/residue: 0.0843 time to fit residues: 18.9388 Evaluate side-chains 138 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 383 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.163098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.153880 restraints weight = 12588.152| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 0.65 r_work: 0.3321 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work: 0.3125 rms_B_bonded: 3.37 restraints_weight: 0.1250 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11913 Z= 0.183 Angle : 0.575 6.866 16251 Z= 0.304 Chirality : 0.042 0.146 1905 Planarity : 0.004 0.035 1944 Dihedral : 4.760 59.959 1576 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.54 % Allowed : 17.07 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1491 helix: 1.18 (0.16), residues: 1149 sheet: None (None), residues: 0 loop : -2.41 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 337 TYR 0.018 0.002 TYR C 425 PHE 0.019 0.002 PHE C 193 TRP 0.021 0.001 TRP A 140 HIS 0.006 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.18 (11913) covalent geometry : angle 0.57481 / 0.30 (16251) hydrogen bonds : bond 0.05702 / 3.76 ( 717) hydrogen bonds : angle 3.64645 / 2.58 ( 2151) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.356 Fit side-chains REVERT: A 324 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7072 (t80) REVERT: A 383 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: A 482 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7170 (mt) REVERT: B 11 PHE cc_start: 0.7817 (t80) cc_final: 0.7471 (t80) REVERT: B 56 MET cc_start: 0.8378 (tpt) cc_final: 0.7773 (tpt) REVERT: B 92 MET cc_start: 0.5791 (mmp) cc_final: 0.5057 (mmt) REVERT: B 383 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: C 56 MET cc_start: 0.8406 (tpt) cc_final: 0.7731 (tpt) REVERT: C 81 LYS cc_start: 0.7152 (ttmt) cc_final: 0.6771 (tttp) REVERT: C 331 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7239 (m-80) REVERT: C 383 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7966 (mp0) outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 0.0820 time to fit residues: 18.3766 Evaluate side-chains 140 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 383 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 104 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.168686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.159369 restraints weight = 12402.092| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 0.64 r_work: 0.3573 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11913 Z= 0.135 Angle : 0.521 7.214 16251 Z= 0.274 Chirality : 0.039 0.139 1905 Planarity : 0.004 0.036 1944 Dihedral : 4.662 59.826 1576 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.63 % Allowed : 17.32 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.23), residues: 1491 helix: 1.26 (0.16), residues: 1140 sheet: None (None), residues: 0 loop : -2.49 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 337 TYR 0.019 0.001 TYR C 425 PHE 0.018 0.001 PHE C 193 TRP 0.015 0.001 TRP A 140 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (11913) covalent geometry : angle 0.52139 / 0.27 (16251) hydrogen bonds : bond 0.04848 / 3.19 ( 717) hydrogen bonds : angle 3.56317 / 2.52 ( 2151) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 324 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6835 (t80) REVERT: A 383 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: A 482 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7047 (mt) REVERT: B 11 PHE cc_start: 0.7569 (t80) cc_final: 0.7199 (t80) REVERT: B 56 MET cc_start: 0.8344 (tpt) cc_final: 0.7763 (tpt) REVERT: B 92 MET cc_start: 0.5414 (mmp) cc_final: 0.4842 (mmt) REVERT: B 108 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7941 (pp) REVERT: B 383 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: C 56 MET cc_start: 0.8467 (tpt) cc_final: 0.7863 (tpt) REVERT: C 81 LYS cc_start: 0.6659 (ttmt) cc_final: 0.6450 (tttp) REVERT: C 92 MET cc_start: 0.4464 (mmp) cc_final: 0.4057 (mmt) REVERT: C 383 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7753 (mp0) outliers start: 20 outliers final: 9 residues processed: 141 average time/residue: 0.0808 time to fit residues: 18.0815 Evaluate side-chains 138 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain C residue 383 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 0.4980 chunk 78 optimal weight: 0.0980 chunk 140 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.168179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.158989 restraints weight = 12494.927| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 0.64 r_work: 0.3604 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11913 Z= 0.103 Angle : 0.485 10.651 16251 Z= 0.250 Chirality : 0.037 0.133 1905 Planarity : 0.003 0.033 1944 Dihedral : 4.449 59.120 1576 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.38 % Allowed : 17.40 % Favored : 81.22 % 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: 1.01 (0.23), residues: 1491 helix: 1.52 (0.16), residues: 1140 sheet: None (None), residues: 0 loop : -2.24 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 296 TYR 0.019 0.001 TYR C 425 PHE 0.018 0.001 PHE A 193 TRP 0.010 0.001 TRP C 449 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11913) covalent geometry : angle 0.48535 / 0.25 (16251) hydrogen bonds : bond 0.03786 / 2.50 ( 717) hydrogen bonds : angle 3.41921 / 2.41 ( 2151) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 324 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6532 (t80) REVERT: A 328 MET cc_start: 0.7160 (mmm) cc_final: 0.6838 (mmp) REVERT: A 383 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: A 482 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6996 (mt) REVERT: B 56 MET cc_start: 0.8404 (tpt) cc_final: 0.7904 (tpt) REVERT: B 92 MET cc_start: 0.5225 (mmp) cc_final: 0.4680 (mmt) REVERT: B 108 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7959 (pp) REVERT: B 318 TRP cc_start: 0.7464 (m-10) cc_final: 0.7224 (m-10) REVERT: B 383 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: C 56 MET cc_start: 0.8528 (tpt) cc_final: 0.7924 (tpt) REVERT: C 81 LYS cc_start: 0.6612 (ttmt) cc_final: 0.6393 (tttp) REVERT: C 92 MET cc_start: 0.4620 (mmp) cc_final: 0.4272 (mmt) REVERT: C 383 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7711 (mp0) outliers start: 17 outliers final: 10 residues processed: 133 average time/residue: 0.0838 time to fit residues: 17.6434 Evaluate side-chains 132 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 383 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 8 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 112 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.169622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.160807 restraints weight = 12489.409| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 0.63 r_work: 0.3620 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11913 Z= 0.104 Angle : 0.490 10.516 16251 Z= 0.251 Chirality : 0.038 0.135 1905 Planarity : 0.003 0.033 1944 Dihedral : 4.395 59.569 1576 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.38 % Allowed : 17.48 % Favored : 81.14 % 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: 1.14 (0.23), residues: 1491 helix: 1.62 (0.16), residues: 1146 sheet: None (None), residues: 0 loop : -2.27 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 296 TYR 0.015 0.001 TYR C 425 PHE 0.018 0.001 PHE C 193 TRP 0.012 0.001 TRP C 449 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (11913) covalent geometry : angle 0.49009 / 0.25 (16251) hydrogen bonds : bond 0.03819 / 2.52 ( 717) hydrogen bonds : angle 3.38249 / 2.38 ( 2151) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 324 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6697 (t80) REVERT: A 328 MET cc_start: 0.7301 (mmm) cc_final: 0.7054 (mmp) REVERT: A 383 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 482 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7023 (mt) REVERT: B 56 MET cc_start: 0.8409 (tpt) cc_final: 0.7971 (tpt) REVERT: B 92 MET cc_start: 0.5247 (mmp) cc_final: 0.4694 (mmt) REVERT: B 108 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7961 (pp) REVERT: B 135 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: B 383 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: C 56 MET cc_start: 0.8523 (tpt) cc_final: 0.7935 (tpt) REVERT: C 81 LYS cc_start: 0.6676 (ttmt) cc_final: 0.6443 (tttp) REVERT: C 92 MET cc_start: 0.4620 (mmp) cc_final: 0.4313 (mmt) REVERT: C 383 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7723 (mp0) outliers start: 17 outliers final: 8 residues processed: 137 average time/residue: 0.0827 time to fit residues: 17.9585 Evaluate side-chains 131 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain C residue 383 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.168092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.158663 restraints weight = 12519.569| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 0.63 r_work: 0.3621 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11913 Z= 0.109 Angle : 0.498 10.543 16251 Z= 0.255 Chirality : 0.038 0.135 1905 Planarity : 0.003 0.034 1944 Dihedral : 4.398 59.908 1576 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.30 % Allowed : 17.97 % Favored : 80.73 % 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: 1.15 (0.23), residues: 1491 helix: 1.63 (0.16), residues: 1146 sheet: None (None), residues: 0 loop : -2.29 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 296 TYR 0.016 0.001 TYR C 425 PHE 0.018 0.001 PHE C 193 TRP 0.012 0.001 TRP A 140 HIS 0.004 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11913) covalent geometry : angle 0.49807 / 0.25 (16251) hydrogen bonds : bond 0.03930 / 2.59 ( 717) hydrogen bonds : angle 3.38371 / 2.38 ( 2151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2441.31 seconds wall clock time: 42 minutes 34.04 seconds (2554.04 seconds total)