Starting phenix.real_space_refine on Wed Mar 4 23:46:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sef_25067/03_2026/7sef_25067_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sef_25067/03_2026/7sef_25067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sef_25067/03_2026/7sef_25067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sef_25067/03_2026/7sef_25067.map" model { file = "/net/cci-nas-00/data/ceres_data/7sef_25067/03_2026/7sef_25067_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sef_25067/03_2026/7sef_25067_neut.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 42 5.16 5 C 10848 2.51 5 N 2922 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17154 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2859 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 21, 'TRANS': 354} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.57, per 1000 atoms: 0.15 Number of scatterers: 17154 At special positions: 0 Unit cell: (113.208, 114.48, 120.84, 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 42 16.00 O 3342 8.00 N 2922 7.00 C 10848 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: 1.43 Conformation dependent library (CDL) restraints added in 752.4 milliseconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 24 sheets defined 12.0% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 95 through 100 removed outlier: 4.028A pdb=" N ASP A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 209 through 215 removed outlier: 5.397A pdb=" N ASP A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 215 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.750A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 333' Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 383 through 386 removed outlier: 4.432A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 386' Processing helix chain 'B' and resid 95 through 100 removed outlier: 4.028A pdb=" N ASP B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 209 through 215 removed outlier: 5.398A pdb=" N ASP B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 215 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.750A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 333 " --> pdb=" O PRO B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 333' Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 383 through 386 removed outlier: 4.431A pdb=" N LEU B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 386' Processing helix chain 'C' and resid 95 through 100 removed outlier: 4.028A pdb=" N ASP C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 209 through 215 removed outlier: 5.398A pdb=" N ASP C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 215 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 328 through 333 removed outlier: 3.751A pdb=" N VAL C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 333' Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 383 through 386 removed outlier: 4.432A pdb=" N LEU C 386 " --> pdb=" O GLU C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 386' Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.028A pdb=" N ASP D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 209 through 215 removed outlier: 5.398A pdb=" N ASP D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D 215 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 328 through 333 removed outlier: 3.751A pdb=" N VAL D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR D 333 " --> pdb=" O PRO D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 333' Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 383 through 386 removed outlier: 4.431A pdb=" N LEU D 386 " --> pdb=" O GLU D 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 383 through 386' Processing helix chain 'E' and resid 95 through 100 removed outlier: 4.029A pdb=" N ASP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 209 through 215 removed outlier: 5.398A pdb=" N ASP E 213 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL E 215 " --> pdb=" O THR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 249 Processing helix chain 'E' and resid 328 through 333 removed outlier: 3.749A pdb=" N VAL E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR E 333 " --> pdb=" O PRO E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 328 through 333' Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 383 through 386 removed outlier: 4.432A pdb=" N LEU E 386 " --> pdb=" O GLU E 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 95 through 100 removed outlier: 4.027A pdb=" N ASP F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 209 through 215 removed outlier: 5.397A pdb=" N ASP F 213 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL F 215 " --> pdb=" O THR F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 249 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.749A pdb=" N VAL F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR F 333 " --> pdb=" O PRO F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 328 through 333' Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 383 through 386 removed outlier: 4.431A pdb=" N LEU F 386 " --> pdb=" O GLU F 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 383 through 386' Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE A 132 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 71 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS A 91 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 79 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 167 removed outlier: 5.878A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE A 181 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 187 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A 178 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE A 253 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR A 180 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 221 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 302 removed outlier: 3.568A pdb=" N GLY A 308 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR A 302 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLU A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 321 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 379 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU A 286 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 341 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 340 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 367 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 342 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA A 436 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL A 421 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE B 132 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 71 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 91 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE B 79 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU B 89 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 167 removed outlier: 5.878A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE B 181 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 187 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 178 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE B 253 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR B 180 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 221 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 299 through 302 removed outlier: 3.567A pdb=" N GLY B 308 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR B 302 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 321 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 379 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 286 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 341 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 340 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 367 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 342 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 393 through 395 removed outlier: 5.968A pdb=" N ALA B 436 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL B 421 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE C 132 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 71 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 161 through 167 removed outlier: 5.879A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE C 181 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 187 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU C 178 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE C 253 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR C 180 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 221 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 299 through 302 removed outlier: 3.567A pdb=" N GLY C 308 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR C 302 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL C 321 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL C 379 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 286 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 341 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG C 340 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 367 " --> pdb=" O ARG C 340 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 342 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA C 436 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N VAL C 421 " --> pdb=" O ALA C 436 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE D 132 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 71 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS D 91 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE D 79 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 161 through 167 removed outlier: 5.878A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE D 181 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 187 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU D 178 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE D 253 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR D 180 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 221 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 299 through 302 removed outlier: 3.566A pdb=" N GLY D 308 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR D 302 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU D 306 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL D 321 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL D 379 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU D 286 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 341 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG D 340 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 367 " --> pdb=" O ARG D 340 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU D 342 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA D 436 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL D 421 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE E 132 " --> pdb=" O PRO E 65 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL E 71 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS E 91 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE E 79 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 161 through 167 removed outlier: 5.879A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE E 181 " --> pdb=" O PRO E 185 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY E 187 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU E 178 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE E 253 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR E 180 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE E 221 " --> pdb=" O GLY E 269 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 299 through 302 removed outlier: 3.567A pdb=" N GLY E 308 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR E 302 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLU E 306 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL E 321 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL E 379 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU E 286 " --> pdb=" O VAL E 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 341 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG E 340 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 367 " --> pdb=" O ARG E 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 342 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA E 436 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL E 421 " --> pdb=" O ALA E 436 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 107 through 110 removed outlier: 3.935A pdb=" N ILE F 132 " --> pdb=" O PRO F 65 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 71 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS F 91 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE F 79 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU F 89 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 161 through 167 removed outlier: 5.878A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE F 181 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY F 187 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU F 178 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE F 253 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR F 180 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE F 221 " --> pdb=" O GLY F 269 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 299 through 302 removed outlier: 3.566A pdb=" N GLY F 308 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR F 302 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLU F 306 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL F 321 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL F 379 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU F 286 " --> pdb=" O VAL F 379 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 341 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG F 340 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 367 " --> pdb=" O ARG F 340 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 342 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 393 through 395 removed outlier: 5.969A pdb=" N ALA F 436 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N VAL F 421 " --> pdb=" O ALA F 436 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1116 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: 3.15 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5760 1.34 - 1.46: 2810 1.46 - 1.57: 8770 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 17424 Sorted by residual: bond pdb=" CA TYR B 68 " pdb=" CB TYR B 68 " ideal model delta sigma weight residual 1.527 1.494 0.033 2.48e-02 1.63e+03 1.76e+00 bond pdb=" CA TYR C 68 " pdb=" CB TYR C 68 " ideal model delta sigma weight residual 1.527 1.495 0.033 2.48e-02 1.63e+03 1.73e+00 bond pdb=" CA TYR D 68 " pdb=" CB TYR D 68 " ideal model delta sigma weight residual 1.527 1.495 0.032 2.48e-02 1.63e+03 1.72e+00 bond pdb=" CA TYR E 68 " pdb=" CB TYR E 68 " ideal model delta sigma weight residual 1.527 1.495 0.032 2.48e-02 1.63e+03 1.67e+00 bond pdb=" CA TYR F 68 " pdb=" CB TYR F 68 " ideal model delta sigma weight residual 1.527 1.495 0.032 2.48e-02 1.63e+03 1.67e+00 ... (remaining 17419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 21700 1.07 - 2.14: 1580 2.14 - 3.21: 171 3.21 - 4.28: 104 4.28 - 5.35: 49 Bond angle restraints: 23604 Sorted by residual: angle pdb=" N SER A 297 " pdb=" CA SER A 297 " pdb=" C SER A 297 " ideal model delta sigma weight residual 114.56 111.01 3.55 1.27e+00 6.20e-01 7.82e+00 angle pdb=" N SER B 297 " pdb=" CA SER B 297 " pdb=" C SER B 297 " ideal model delta sigma weight residual 114.56 111.02 3.54 1.27e+00 6.20e-01 7.75e+00 angle pdb=" CA VAL F 331 " pdb=" CB VAL F 331 " pdb=" CG1 VAL F 331 " ideal model delta sigma weight residual 110.40 114.33 -3.93 1.70e+00 3.46e-01 5.34e+00 angle pdb=" CA VAL E 331 " pdb=" CB VAL E 331 " pdb=" CG1 VAL E 331 " ideal model delta sigma weight residual 110.40 114.28 -3.88 1.70e+00 3.46e-01 5.22e+00 angle pdb=" CA VAL C 331 " pdb=" CB VAL C 331 " pdb=" CG1 VAL C 331 " ideal model delta sigma weight residual 110.40 114.28 -3.88 1.70e+00 3.46e-01 5.21e+00 ... (remaining 23599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 10002 15.97 - 31.95: 486 31.95 - 47.92: 78 47.92 - 63.90: 42 63.90 - 79.87: 6 Dihedral angle restraints: 10614 sinusoidal: 4254 harmonic: 6360 Sorted by residual: dihedral pdb=" CA SER F 177 " pdb=" C SER F 177 " pdb=" N LEU F 178 " pdb=" CA LEU F 178 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA SER D 177 " pdb=" C SER D 177 " pdb=" N LEU D 178 " pdb=" CA LEU D 178 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA SER E 177 " pdb=" C SER E 177 " pdb=" N LEU E 178 " pdb=" CA LEU E 178 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 10611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1643 0.027 - 0.053: 608 0.053 - 0.080: 233 0.080 - 0.107: 206 0.107 - 0.133: 76 Chirality restraints: 2766 Sorted by residual: chirality pdb=" CA ILE F 203 " pdb=" N ILE F 203 " pdb=" C ILE F 203 " pdb=" CB ILE F 203 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE E 203 " pdb=" N ILE E 203 " pdb=" C ILE E 203 " pdb=" CB ILE E 203 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2763 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 331 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C VAL C 331 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL C 331 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL C 332 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 331 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C VAL F 331 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL F 331 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL F 332 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 331 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C VAL A 331 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL A 331 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 332 " -0.008 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4302 2.79 - 3.32: 16263 3.32 - 3.85: 26822 3.85 - 4.37: 31382 4.37 - 4.90: 54084 Nonbonded interactions: 132853 Sorted by model distance: nonbonded pdb=" NH1 ARG C 340 " pdb=" O ALA C 385 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG E 340 " pdb=" O ALA E 385 " model vdw 2.267 3.120 nonbonded pdb=" NH1 ARG A 340 " pdb=" O ALA A 385 " model vdw 2.267 3.120 nonbonded pdb=" NH1 ARG D 340 " pdb=" O ALA D 385 " model vdw 2.267 3.120 nonbonded pdb=" NH1 ARG B 340 " pdb=" O ALA B 385 " model vdw 2.267 3.120 ... (remaining 132848 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.200 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.005 0.033 17424 Z= 0.250 Angle : 0.672 5.352 23604 Z= 0.359 Chirality : 0.043 0.133 2766 Planarity : 0.003 0.030 3072 Dihedral : 10.539 79.872 6534 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2208 helix: -2.44 (0.29), residues: 192 sheet: -0.78 (0.17), residues: 666 loop : -1.54 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 340 TYR 0.016 0.002 TYR D 131 PHE 0.005 0.001 PHE A 253 TRP 0.005 0.001 TRP B 109 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00538 (17424) covalent geometry : angle 0.67239 (23604) hydrogen bonds : bond 0.16447 ( 450) hydrogen bonds : angle 10.75799 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8401 (tpt) cc_final: 0.8116 (tpt) REVERT: B 162 MET cc_start: 0.8147 (tpt) cc_final: 0.7726 (tpt) REVERT: C 54 MET cc_start: 0.8951 (mmp) cc_final: 0.8644 (mmp) REVERT: C 162 MET cc_start: 0.8156 (tpt) cc_final: 0.7771 (tpt) REVERT: D 301 MET cc_start: 0.8997 (mmp) cc_final: 0.8139 (mmm) REVERT: E 63 ARG cc_start: 0.9037 (ptt90) cc_final: 0.8824 (tmm160) REVERT: E 301 MET cc_start: 0.9196 (mmp) cc_final: 0.8767 (mmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1690 time to fit residues: 14.1129 Evaluate side-chains 45 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN B 440 GLN C 440 GLN D 440 GLN E 440 GLN F 440 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.036652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.027821 restraints weight = 149213.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.028722 restraints weight = 80365.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.029320 restraints weight = 53156.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.029720 restraints weight = 40053.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.029977 restraints weight = 32996.115| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17424 Z= 0.240 Angle : 0.670 8.681 23604 Z= 0.342 Chirality : 0.046 0.174 2766 Planarity : 0.004 0.042 3072 Dihedral : 5.058 18.848 2376 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.58 % Allowed : 4.85 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.16), residues: 2208 helix: -0.86 (0.32), residues: 162 sheet: -0.80 (0.18), residues: 684 loop : -1.54 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 340 TYR 0.013 0.002 TYR B 131 PHE 0.016 0.002 PHE F 221 TRP 0.017 0.002 TRP C 222 HIS 0.003 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00511 (17424) covalent geometry : angle 0.67016 (23604) hydrogen bonds : bond 0.03818 ( 450) hydrogen bonds : angle 7.78522 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.589 Fit side-chains REVERT: A 54 MET cc_start: 0.8565 (mpp) cc_final: 0.7919 (tpp) REVERT: A 301 MET cc_start: 0.9000 (mmm) cc_final: 0.8484 (mmm) REVERT: B 134 MET cc_start: 0.9148 (ppp) cc_final: 0.8681 (ppp) REVERT: B 301 MET cc_start: 0.9136 (mmm) cc_final: 0.8617 (mmm) REVERT: C 54 MET cc_start: 0.8585 (mmp) cc_final: 0.8362 (mpp) REVERT: C 301 MET cc_start: 0.8959 (mmm) cc_final: 0.8575 (mmm) REVERT: D 301 MET cc_start: 0.9167 (mmp) cc_final: 0.8670 (mmm) REVERT: E 135 MET cc_start: 0.8618 (ppp) cc_final: 0.8353 (ppp) REVERT: E 162 MET cc_start: 0.8146 (tmm) cc_final: 0.7909 (tmm) outliers start: 11 outliers final: 0 residues processed: 55 average time/residue: 0.1195 time to fit residues: 11.1168 Evaluate side-chains 42 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 85 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.036020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.027404 restraints weight = 146917.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.028303 restraints weight = 77977.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.028908 restraints weight = 51156.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.029292 restraints weight = 38292.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.029543 restraints weight = 31426.746| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 17424 Z= 0.172 Angle : 0.586 8.442 23604 Z= 0.296 Chirality : 0.044 0.155 2766 Planarity : 0.003 0.029 3072 Dihedral : 4.704 17.040 2376 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.05 % Allowed : 4.54 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.17), residues: 2208 helix: 0.26 (0.39), residues: 162 sheet: -0.63 (0.18), residues: 684 loop : -1.49 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 155 TYR 0.010 0.001 TYR B 131 PHE 0.010 0.001 PHE F 221 TRP 0.011 0.002 TRP A 222 HIS 0.002 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00367 (17424) covalent geometry : angle 0.58645 (23604) hydrogen bonds : bond 0.03427 ( 450) hydrogen bonds : angle 7.42586 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.714 Fit side-chains REVERT: A 54 MET cc_start: 0.8391 (mpp) cc_final: 0.7927 (tpp) REVERT: A 120 VAL cc_start: 0.5770 (OUTLIER) cc_final: 0.5394 (t) REVERT: A 162 MET cc_start: 0.8649 (tpp) cc_final: 0.8416 (tpp) REVERT: A 301 MET cc_start: 0.9153 (mmm) cc_final: 0.8722 (mmm) REVERT: B 120 VAL cc_start: 0.4331 (OUTLIER) cc_final: 0.4022 (t) REVERT: B 162 MET cc_start: 0.8715 (tpp) cc_final: 0.8514 (tpp) REVERT: B 301 MET cc_start: 0.9190 (mmm) cc_final: 0.8815 (mmm) REVERT: C 162 MET cc_start: 0.8534 (tpp) cc_final: 0.8248 (tpp) REVERT: D 120 VAL cc_start: 0.6376 (OUTLIER) cc_final: 0.6084 (t) REVERT: D 134 MET cc_start: 0.9141 (ppp) cc_final: 0.8809 (ppp) REVERT: D 301 MET cc_start: 0.9164 (mmp) cc_final: 0.8879 (mmm) REVERT: E 120 VAL cc_start: 0.5168 (OUTLIER) cc_final: 0.4928 (t) outliers start: 20 outliers final: 4 residues processed: 61 average time/residue: 0.1010 time to fit residues: 11.1509 Evaluate side-chains 50 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 219 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.035617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.026986 restraints weight = 147832.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.027829 restraints weight = 81550.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.028391 restraints weight = 54548.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.028755 restraints weight = 41569.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.028999 restraints weight = 34554.571| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17424 Z= 0.195 Angle : 0.617 9.519 23604 Z= 0.306 Chirality : 0.044 0.154 2766 Planarity : 0.003 0.029 3072 Dihedral : 4.713 17.430 2376 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.11 % Allowed : 4.80 % Favored : 94.09 % 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: -1.55 (0.17), residues: 2208 helix: 0.40 (0.38), residues: 162 sheet: -0.59 (0.19), residues: 684 loop : -1.49 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 340 TYR 0.010 0.001 TYR C 131 PHE 0.010 0.001 PHE F 221 TRP 0.009 0.001 TRP F 222 HIS 0.004 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00418 (17424) covalent geometry : angle 0.61740 (23604) hydrogen bonds : bond 0.03317 ( 450) hydrogen bonds : angle 7.12070 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.593 Fit side-chains REVERT: A 120 VAL cc_start: 0.5864 (OUTLIER) cc_final: 0.5525 (t) REVERT: A 162 MET cc_start: 0.8390 (tpp) cc_final: 0.8141 (tpp) REVERT: A 301 MET cc_start: 0.9267 (mmm) cc_final: 0.8889 (mmm) REVERT: B 98 MET cc_start: 0.8668 (mtm) cc_final: 0.8462 (pmm) REVERT: B 120 VAL cc_start: 0.4473 (OUTLIER) cc_final: 0.4154 (t) REVERT: B 162 MET cc_start: 0.8459 (tpp) cc_final: 0.8202 (tpp) REVERT: B 301 MET cc_start: 0.9298 (mmm) cc_final: 0.8884 (mmm) REVERT: C 54 MET cc_start: 0.8392 (mmp) cc_final: 0.8175 (mpp) REVERT: C 134 MET cc_start: 0.9084 (ppp) cc_final: 0.8798 (ppp) REVERT: C 162 MET cc_start: 0.8151 (tpp) cc_final: 0.7894 (tpp) REVERT: D 81 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8388 (tp) REVERT: D 120 VAL cc_start: 0.6434 (OUTLIER) cc_final: 0.6147 (t) REVERT: D 134 MET cc_start: 0.9237 (ppp) cc_final: 0.9024 (ppp) REVERT: E 120 VAL cc_start: 0.5456 (OUTLIER) cc_final: 0.5186 (t) outliers start: 21 outliers final: 5 residues processed: 63 average time/residue: 0.1065 time to fit residues: 11.9877 Evaluate side-chains 52 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 156 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.035955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.027261 restraints weight = 146578.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.028104 restraints weight = 80726.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.028684 restraints weight = 54325.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.029057 restraints weight = 41450.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.029310 restraints weight = 34546.207| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17424 Z= 0.133 Angle : 0.577 12.580 23604 Z= 0.281 Chirality : 0.043 0.155 2766 Planarity : 0.003 0.030 3072 Dihedral : 4.455 15.304 2376 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.63 % Allowed : 5.96 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.17), residues: 2208 helix: 0.71 (0.40), residues: 162 sheet: -0.45 (0.19), residues: 684 loop : -1.42 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.008 0.001 TYR B 131 PHE 0.008 0.001 PHE F 221 TRP 0.009 0.001 TRP A 222 HIS 0.003 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00287 (17424) covalent geometry : angle 0.57745 (23604) hydrogen bonds : bond 0.02999 ( 450) hydrogen bonds : angle 6.95606 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.417 Fit side-chains REVERT: A 120 VAL cc_start: 0.5789 (OUTLIER) cc_final: 0.5447 (t) REVERT: A 162 MET cc_start: 0.8538 (tpp) cc_final: 0.8272 (tpp) REVERT: A 301 MET cc_start: 0.9186 (mmm) cc_final: 0.8783 (mmm) REVERT: B 98 MET cc_start: 0.8743 (mtm) cc_final: 0.8473 (pmm) REVERT: B 120 VAL cc_start: 0.4485 (OUTLIER) cc_final: 0.4167 (t) REVERT: B 162 MET cc_start: 0.8520 (tpp) cc_final: 0.8250 (tpp) REVERT: B 301 MET cc_start: 0.9256 (mmm) cc_final: 0.8855 (mmm) REVERT: C 81 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8298 (tp) REVERT: C 162 MET cc_start: 0.8212 (tpp) cc_final: 0.7927 (tpp) REVERT: D 120 VAL cc_start: 0.6379 (OUTLIER) cc_final: 0.6095 (t) REVERT: D 134 MET cc_start: 0.9282 (ppp) cc_final: 0.9044 (ppp) REVERT: D 301 MET cc_start: 0.9097 (mmp) cc_final: 0.8751 (mmm) REVERT: E 81 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8933 (tp) REVERT: E 120 VAL cc_start: 0.5454 (OUTLIER) cc_final: 0.5169 (t) REVERT: E 135 MET cc_start: 0.8805 (ppp) cc_final: 0.8440 (ppp) outliers start: 12 outliers final: 1 residues processed: 54 average time/residue: 0.1003 time to fit residues: 9.6447 Evaluate side-chains 49 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 98 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.034989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.026162 restraints weight = 147704.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.026980 restraints weight = 82299.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.027521 restraints weight = 55727.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.027880 restraints weight = 42869.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028105 restraints weight = 35888.324| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 17424 Z= 0.328 Angle : 0.743 11.266 23604 Z= 0.361 Chirality : 0.045 0.152 2766 Planarity : 0.004 0.040 3072 Dihedral : 5.039 19.957 2376 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.90 % Allowed : 6.49 % Favored : 92.62 % 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: -1.67 (0.16), residues: 2208 helix: -0.06 (0.37), residues: 162 sheet: -0.68 (0.18), residues: 714 loop : -1.52 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 279 TYR 0.010 0.001 TYR B 131 PHE 0.011 0.002 PHE F 221 TRP 0.009 0.002 TRP B 222 HIS 0.006 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00708 (17424) covalent geometry : angle 0.74266 (23604) hydrogen bonds : bond 0.03694 ( 450) hydrogen bonds : angle 7.21095 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.674 Fit side-chains REVERT: A 81 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8277 (tp) REVERT: A 120 VAL cc_start: 0.6490 (OUTLIER) cc_final: 0.6246 (t) REVERT: A 162 MET cc_start: 0.8461 (tpp) cc_final: 0.8089 (tpp) REVERT: A 301 MET cc_start: 0.9294 (mmm) cc_final: 0.8893 (mmm) REVERT: B 120 VAL cc_start: 0.5305 (OUTLIER) cc_final: 0.4996 (t) REVERT: B 162 MET cc_start: 0.8474 (tpp) cc_final: 0.8232 (tpp) REVERT: B 301 MET cc_start: 0.9344 (mmm) cc_final: 0.8939 (mmm) REVERT: C 81 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8315 (tp) REVERT: C 162 MET cc_start: 0.8218 (tpp) cc_final: 0.8000 (tpp) REVERT: D 81 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8466 (tp) REVERT: D 120 VAL cc_start: 0.6375 (OUTLIER) cc_final: 0.6107 (t) REVERT: D 134 MET cc_start: 0.9336 (ppp) cc_final: 0.9110 (ppp) REVERT: E 120 VAL cc_start: 0.5716 (OUTLIER) cc_final: 0.5460 (t) REVERT: E 135 MET cc_start: 0.8803 (ppp) cc_final: 0.8455 (ppp) REVERT: F 81 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8603 (tp) REVERT: F 98 MET cc_start: 0.8751 (mtm) cc_final: 0.8537 (pmm) outliers start: 17 outliers final: 5 residues processed: 56 average time/residue: 0.0949 time to fit residues: 9.4652 Evaluate side-chains 55 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 202 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.035313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.026701 restraints weight = 147069.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.027549 restraints weight = 80625.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.028102 restraints weight = 53868.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028437 restraints weight = 41086.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.028683 restraints weight = 34432.660| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17424 Z= 0.174 Angle : 0.617 10.977 23604 Z= 0.300 Chirality : 0.044 0.154 2766 Planarity : 0.003 0.029 3072 Dihedral : 4.728 18.231 2376 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.69 % Allowed : 7.33 % Favored : 91.98 % 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: -1.56 (0.17), residues: 2208 helix: 0.23 (0.38), residues: 162 sheet: -0.73 (0.18), residues: 738 loop : -1.40 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.009 0.001 TYR C 131 PHE 0.008 0.001 PHE F 221 TRP 0.010 0.002 TRP B 222 HIS 0.005 0.001 HIS F 441 Details of bonding type rmsd covalent geometry : bond 0.00376 (17424) covalent geometry : angle 0.61725 (23604) hydrogen bonds : bond 0.03135 ( 450) hydrogen bonds : angle 7.10779 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.400 Fit side-chains REVERT: A 54 MET cc_start: 0.7931 (mmp) cc_final: 0.7723 (mpp) REVERT: A 81 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 120 VAL cc_start: 0.6393 (OUTLIER) cc_final: 0.6141 (t) REVERT: A 162 MET cc_start: 0.8550 (tpp) cc_final: 0.8235 (tpp) REVERT: A 301 MET cc_start: 0.9233 (mmm) cc_final: 0.8827 (mmm) REVERT: B 81 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8262 (tp) REVERT: B 120 VAL cc_start: 0.5388 (OUTLIER) cc_final: 0.5086 (t) REVERT: B 162 MET cc_start: 0.8369 (tpp) cc_final: 0.8131 (tpp) REVERT: B 301 MET cc_start: 0.9300 (mmm) cc_final: 0.8912 (mmm) REVERT: C 54 MET cc_start: 0.8141 (mmp) cc_final: 0.7933 (mpp) REVERT: C 81 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8420 (tp) REVERT: D 81 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8522 (tp) REVERT: D 120 VAL cc_start: 0.6314 (OUTLIER) cc_final: 0.6038 (t) REVERT: D 134 MET cc_start: 0.9342 (ppp) cc_final: 0.9092 (ppp) REVERT: E 98 MET cc_start: 0.8967 (mtm) cc_final: 0.8637 (pmm) REVERT: E 120 VAL cc_start: 0.5641 (OUTLIER) cc_final: 0.5356 (t) REVERT: E 135 MET cc_start: 0.8758 (ppp) cc_final: 0.8408 (ppp) REVERT: F 81 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8670 (tp) outliers start: 13 outliers final: 3 residues processed: 55 average time/residue: 0.1042 time to fit residues: 10.1524 Evaluate side-chains 54 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN C 440 GLN E 440 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.035763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.027081 restraints weight = 144579.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.027942 restraints weight = 78210.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.028523 restraints weight = 52296.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.028906 restraints weight = 39482.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.029155 restraints weight = 32602.935| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17424 Z= 0.140 Angle : 0.615 11.487 23604 Z= 0.294 Chirality : 0.044 0.155 2766 Planarity : 0.003 0.030 3072 Dihedral : 4.495 15.573 2376 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.74 % Allowed : 7.28 % Favored : 91.98 % 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: -1.38 (0.17), residues: 2208 helix: 0.88 (0.45), residues: 126 sheet: -0.68 (0.18), residues: 738 loop : -1.24 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 86 TYR 0.008 0.001 TYR B 131 PHE 0.008 0.001 PHE F 221 TRP 0.009 0.001 TRP B 222 HIS 0.004 0.001 HIS F 441 Details of bonding type rmsd covalent geometry : bond 0.00307 (17424) covalent geometry : angle 0.61518 (23604) hydrogen bonds : bond 0.02996 ( 450) hydrogen bonds : angle 7.00092 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.703 Fit side-chains REVERT: A 54 MET cc_start: 0.7995 (mmp) cc_final: 0.7767 (mpp) REVERT: A 81 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8530 (tp) REVERT: A 162 MET cc_start: 0.8495 (tpp) cc_final: 0.8205 (tpp) REVERT: A 301 MET cc_start: 0.9182 (mmm) cc_final: 0.8814 (mmm) REVERT: B 81 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8371 (tp) REVERT: B 120 VAL cc_start: 0.5148 (OUTLIER) cc_final: 0.4862 (t) REVERT: B 162 MET cc_start: 0.8271 (tpp) cc_final: 0.8046 (tpp) REVERT: B 301 MET cc_start: 0.9299 (mmm) cc_final: 0.8918 (mmm) REVERT: C 81 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8533 (tp) REVERT: D 54 MET cc_start: 0.7759 (mmp) cc_final: 0.7453 (mpp) REVERT: D 81 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8614 (tp) REVERT: D 120 VAL cc_start: 0.6316 (OUTLIER) cc_final: 0.6041 (t) REVERT: D 134 MET cc_start: 0.9372 (ppp) cc_final: 0.9145 (ppp) REVERT: E 73 VAL cc_start: 0.9622 (OUTLIER) cc_final: 0.9223 (m) REVERT: E 120 VAL cc_start: 0.5373 (OUTLIER) cc_final: 0.5050 (t) REVERT: E 135 MET cc_start: 0.8712 (ppp) cc_final: 0.8364 (ppp) REVERT: F 81 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8767 (tp) outliers start: 14 outliers final: 2 residues processed: 56 average time/residue: 0.1132 time to fit residues: 11.0376 Evaluate side-chains 53 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.035947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.027210 restraints weight = 144966.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.028089 restraints weight = 78667.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.028666 restraints weight = 52363.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.029019 restraints weight = 39793.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.029267 restraints weight = 33201.879| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17424 Z= 0.138 Angle : 0.616 12.941 23604 Z= 0.294 Chirality : 0.044 0.154 2766 Planarity : 0.003 0.030 3072 Dihedral : 4.405 15.765 2376 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.63 % Allowed : 7.33 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2208 helix: 1.00 (0.46), residues: 126 sheet: -0.38 (0.19), residues: 684 loop : -1.31 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 86 TYR 0.007 0.001 TYR C 131 PHE 0.008 0.001 PHE F 221 TRP 0.009 0.001 TRP B 222 HIS 0.004 0.001 HIS F 441 Details of bonding type rmsd covalent geometry : bond 0.00303 (17424) covalent geometry : angle 0.61642 (23604) hydrogen bonds : bond 0.02970 ( 450) hydrogen bonds : angle 6.88464 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.688 Fit side-chains REVERT: A 81 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8538 (tp) REVERT: A 134 MET cc_start: 0.9134 (ppp) cc_final: 0.8783 (ppp) REVERT: A 162 MET cc_start: 0.8475 (tpp) cc_final: 0.8233 (tpp) REVERT: A 301 MET cc_start: 0.9148 (mmm) cc_final: 0.8809 (mmm) REVERT: B 81 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8448 (tp) REVERT: B 162 MET cc_start: 0.8175 (tpp) cc_final: 0.7959 (tpp) REVERT: B 301 MET cc_start: 0.9258 (mmm) cc_final: 0.8906 (mmm) REVERT: C 81 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8668 (tp) REVERT: C 98 MET cc_start: 0.8629 (pmm) cc_final: 0.8129 (pmm) REVERT: D 54 MET cc_start: 0.7757 (mmp) cc_final: 0.7447 (mpp) REVERT: D 81 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8611 (tp) REVERT: D 134 MET cc_start: 0.9402 (ppp) cc_final: 0.9150 (ppp) REVERT: E 120 VAL cc_start: 0.5269 (OUTLIER) cc_final: 0.4922 (t) REVERT: E 135 MET cc_start: 0.8699 (ppp) cc_final: 0.8362 (ppp) REVERT: F 81 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8789 (tp) REVERT: F 135 MET cc_start: 0.8802 (ppp) cc_final: 0.8465 (ppp) outliers start: 12 outliers final: 3 residues processed: 53 average time/residue: 0.1070 time to fit residues: 10.2130 Evaluate side-chains 51 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 147 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.035575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.026873 restraints weight = 143440.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.027731 restraints weight = 78069.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028309 restraints weight = 52239.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.028692 restraints weight = 39556.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.028931 restraints weight = 32703.757| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17424 Z= 0.161 Angle : 0.640 13.271 23604 Z= 0.306 Chirality : 0.044 0.153 2766 Planarity : 0.003 0.035 3072 Dihedral : 4.435 14.879 2376 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.58 % Allowed : 7.38 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2208 helix: 0.97 (0.46), residues: 126 sheet: -0.37 (0.19), residues: 684 loop : -1.30 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 86 TYR 0.008 0.001 TYR A 68 PHE 0.008 0.001 PHE F 221 TRP 0.008 0.001 TRP B 222 HIS 0.004 0.001 HIS F 441 Details of bonding type rmsd covalent geometry : bond 0.00353 (17424) covalent geometry : angle 0.64042 (23604) hydrogen bonds : bond 0.03033 ( 450) hydrogen bonds : angle 6.88325 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.681 Fit side-chains REVERT: A 81 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8575 (tp) REVERT: A 134 MET cc_start: 0.9133 (ppp) cc_final: 0.8689 (ppp) REVERT: A 162 MET cc_start: 0.8444 (tpp) cc_final: 0.8197 (tpp) REVERT: A 301 MET cc_start: 0.9152 (mmm) cc_final: 0.8813 (mmm) REVERT: B 81 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8458 (tp) REVERT: B 162 MET cc_start: 0.8188 (tpp) cc_final: 0.7970 (tpp) REVERT: B 301 MET cc_start: 0.9264 (mmm) cc_final: 0.8911 (mmm) REVERT: C 54 MET cc_start: 0.8225 (mmp) cc_final: 0.7984 (mpp) REVERT: C 81 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8678 (tp) REVERT: C 98 MET cc_start: 0.8561 (pmm) cc_final: 0.8150 (pmm) REVERT: D 54 MET cc_start: 0.7688 (mmp) cc_final: 0.7394 (mpp) REVERT: D 81 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8645 (tp) REVERT: D 134 MET cc_start: 0.9383 (ppp) cc_final: 0.9139 (ppp) REVERT: E 120 VAL cc_start: 0.5330 (OUTLIER) cc_final: 0.4984 (t) REVERT: E 135 MET cc_start: 0.8697 (ppp) cc_final: 0.8370 (ppp) REVERT: F 81 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8759 (tp) outliers start: 11 outliers final: 3 residues processed: 52 average time/residue: 0.1064 time to fit residues: 9.8818 Evaluate side-chains 51 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 154 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 94 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.035792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.027128 restraints weight = 145747.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.028017 restraints weight = 78851.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.028605 restraints weight = 52015.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.028980 restraints weight = 39098.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.029226 restraints weight = 32209.360| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17424 Z= 0.131 Angle : 0.619 13.186 23604 Z= 0.294 Chirality : 0.044 0.153 2766 Planarity : 0.003 0.038 3072 Dihedral : 4.303 14.381 2376 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.47 % Allowed : 7.38 % Favored : 92.14 % 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: -1.20 (0.17), residues: 2208 helix: 1.13 (0.47), residues: 126 sheet: -0.33 (0.19), residues: 684 loop : -1.26 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 86 TYR 0.007 0.001 TYR A 68 PHE 0.007 0.001 PHE F 221 TRP 0.009 0.001 TRP B 222 HIS 0.003 0.001 HIS F 441 Details of bonding type rmsd covalent geometry : bond 0.00290 (17424) covalent geometry : angle 0.61924 (23604) hydrogen bonds : bond 0.02902 ( 450) hydrogen bonds : angle 6.78259 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.30 seconds wall clock time: 38 minutes 53.15 seconds (2333.15 seconds total)