Starting phenix.real_space_refine on Sat Jul 4 00:27:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uws_42680/07_2026/8uws_42680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uws_42680/07_2026/8uws_42680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uws_42680/07_2026/8uws_42680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uws_42680/07_2026/8uws_42680.map" model { file = "/net/cci-nas-00/data/ceres_data/8uws_42680/07_2026/8uws_42680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uws_42680/07_2026/8uws_42680.cif" } resolution = 2.65 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 72 5.16 5 C 10981 2.51 5 N 2913 2.21 5 O 3167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17137 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 4301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4301 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 494} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 4285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4285 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 5, 'PTRANS': 36, 'TRANS': 492} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4264 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 5, 'PTRANS': 36, 'TRANS': 490} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4283 Classifications: {'peptide': 531} Link IDs: {'PCIS': 5, 'PTRANS': 36, 'TRANS': 489} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 3.87, per 1000 atoms: 0.23 Number of scatterers: 17137 At special positions: 0 Unit cell: (110.55, 103.18, 113.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 72 16.00 O 3167 8.00 N 2913 7.00 C 10981 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: 1.46 Conformation dependent library (CDL) restraints added in 721.7 milliseconds 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 51 sheets defined 1.7% alpha, 53.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 497 through 502 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 16 through 20 removed outlier: 6.925A pdb=" N ILE C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 132 removed outlier: 5.517A pdb=" N ASP C 127 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 143 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 138 " --> pdb=" O PHE C 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 132 removed outlier: 5.517A pdb=" N ASP C 127 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 143 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 138 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 157 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 186 through 193 removed outlier: 4.886A pdb=" N GLY C 187 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA C 202 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 212 " --> pdb=" O MET C 232 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL C 214 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL C 230 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 12.173A pdb=" N ARG C 216 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 244 through 253 removed outlier: 5.212A pdb=" N LYS C 245 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER C 266 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 249 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C 262 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU C 251 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TRP C 259 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 331 through 333 Processing sheet with id=AB2, first strand: chain 'C' and resid 331 through 333 removed outlier: 5.678A pdb=" N PHE C 528 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLN C 398 " --> pdb=" O PHE C 528 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR C 530 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG C 396 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR C 473 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR C 475 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 380 through 385 removed outlier: 4.305A pdb=" N SER C 380 " --> pdb=" O CYS C 516 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN C 406 " --> pdb=" O TYR C 426 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR C 426 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 408 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C 418 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 380 through 385 removed outlier: 4.305A pdb=" N SER C 380 " --> pdb=" O CYS C 516 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN C 406 " --> pdb=" O TYR C 426 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR C 426 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 408 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C 418 " --> pdb=" O TYR C 414 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 453 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AB6, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.928A pdb=" N ILE D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AB8, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 125 through 132 removed outlier: 5.847A pdb=" N ASP D 127 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG D 143 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS D 138 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 168 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 125 through 132 removed outlier: 5.847A pdb=" N ASP D 127 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG D 143 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS D 138 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE D 157 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 186 through 193 removed outlier: 5.190A pdb=" N GLY D 187 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA D 202 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 212 " --> pdb=" O MET D 232 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL D 214 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL D 230 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 12.092A pdb=" N ARG D 216 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 244 through 253 removed outlier: 6.758A pdb=" N SER D 246 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N SER D 266 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS D 248 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU D 264 " --> pdb=" O HIS D 248 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP D 259 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AC6, first strand: chain 'D' and resid 331 through 333 removed outlier: 5.743A pdb=" N PHE D 528 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLN D 398 " --> pdb=" O PHE D 528 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR D 530 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG D 396 " --> pdb=" O TYR D 530 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR D 473 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR D 475 " --> pdb=" O VAL D 487 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 380 through 385 removed outlier: 4.413A pdb=" N SER D 380 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN D 406 " --> pdb=" O TYR D 426 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR D 426 " --> pdb=" O GLN D 406 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 408 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN D 418 " --> pdb=" O TYR D 414 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 380 through 385 removed outlier: 4.413A pdb=" N SER D 380 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN D 406 " --> pdb=" O TYR D 426 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR D 426 " --> pdb=" O GLN D 406 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 408 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN D 418 " --> pdb=" O TYR D 414 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AD1, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.876A pdb=" N ILE A 39 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AD3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AD4, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'A' and resid 125 through 132 removed outlier: 5.811A pdb=" N ASP A 127 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG A 143 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 138 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 168 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 125 through 132 removed outlier: 5.811A pdb=" N ASP A 127 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG A 143 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 138 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 157 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 186 through 193 removed outlier: 4.055A pdb=" N ALA A 188 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET A 200 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 190 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A 198 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG A 192 " --> pdb=" O TRP A 196 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 212 " --> pdb=" O MET A 232 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 214 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 230 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 11.927A pdb=" N ARG A 216 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 244 through 253 removed outlier: 6.892A pdb=" N SER A 246 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N SER A 266 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS A 248 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 264 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP A 259 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 331 through 333 removed outlier: 5.656A pdb=" N PHE A 528 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLN A 398 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR A 530 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A 396 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 356 through 357 removed outlier: 5.656A pdb=" N PHE A 528 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLN A 398 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR A 530 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A 396 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 380 through 385 removed outlier: 4.265A pdb=" N SER A 380 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN A 406 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR A 426 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 408 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 380 through 385 removed outlier: 4.265A pdb=" N SER A 380 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN A 406 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR A 426 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 408 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AE5, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.912A pdb=" N ILE B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AE7, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AE8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AE9, first strand: chain 'B' and resid 125 through 132 removed outlier: 5.795A pdb=" N ASP B 127 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG B 143 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 138 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 157 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 186 through 193 removed outlier: 4.078A pdb=" N ALA B 188 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET B 200 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU B 190 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR B 198 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG B 192 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 212 " --> pdb=" O MET B 232 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 214 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 230 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ARG B 216 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 244 through 253 removed outlier: 6.667A pdb=" N SER B 246 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N SER B 266 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N HIS B 248 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 264 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TRP B 259 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AF4, first strand: chain 'B' and resid 331 through 333 removed outlier: 5.746A pdb=" N PHE B 528 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN B 398 " --> pdb=" O PHE B 528 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR B 530 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG B 396 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR B 473 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR B 475 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 380 through 385 removed outlier: 4.294A pdb=" N SER B 380 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN B 406 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR B 426 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 408 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 418 " --> pdb=" O TYR B 414 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 380 through 385 removed outlier: 4.294A pdb=" N SER B 380 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN B 406 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR B 426 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 408 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 418 " --> pdb=" O TYR B 414 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 1980 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: 3.65 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3987 1.33 - 1.45: 4445 1.45 - 1.57: 9194 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 17738 Sorted by residual: bond pdb=" CA TRP C 331 " pdb=" C TRP C 331 " ideal model delta sigma weight residual 1.524 1.444 0.079 1.31e-02 5.83e+03 3.64e+01 bond pdb=" CA GLU C 322 " pdb=" C GLU C 322 " ideal model delta sigma weight residual 1.523 1.446 0.078 1.30e-02 5.92e+03 3.57e+01 bond pdb=" CA TYR D 500 " pdb=" C TYR D 500 " ideal model delta sigma weight residual 1.521 1.473 0.048 9.90e-03 1.02e+04 2.33e+01 bond pdb=" CA HIS C 227 " pdb=" C HIS C 227 " ideal model delta sigma weight residual 1.527 1.468 0.060 1.25e-02 6.40e+03 2.29e+01 bond pdb=" CA PHE A 506 " pdb=" C PHE A 506 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.34e-02 5.57e+03 1.93e+01 ... (remaining 17733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 23889 2.65 - 5.30: 310 5.30 - 7.96: 25 7.96 - 10.61: 9 10.61 - 13.26: 1 Bond angle restraints: 24234 Sorted by residual: angle pdb=" N SER C 330 " pdb=" CA SER C 330 " pdb=" C SER C 330 " ideal model delta sigma weight residual 110.80 97.54 13.26 2.13e+00 2.20e-01 3.87e+01 angle pdb=" N ARG C 504 " pdb=" CA ARG C 504 " pdb=" C ARG C 504 " ideal model delta sigma weight residual 113.30 105.25 8.05 1.34e+00 5.57e-01 3.61e+01 angle pdb=" N THR A 4 " pdb=" CA THR A 4 " pdb=" C THR A 4 " ideal model delta sigma weight residual 107.73 117.78 -10.05 1.80e+00 3.09e-01 3.12e+01 angle pdb=" N GLN C 323 " pdb=" CA GLN C 323 " pdb=" C GLN C 323 " ideal model delta sigma weight residual 109.84 102.63 7.21 1.39e+00 5.18e-01 2.69e+01 angle pdb=" N ARG B 504 " pdb=" CA ARG B 504 " pdb=" C ARG B 504 " ideal model delta sigma weight residual 112.88 106.41 6.47 1.29e+00 6.01e-01 2.52e+01 ... (remaining 24229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8856 17.95 - 35.91: 972 35.91 - 53.86: 264 53.86 - 71.81: 53 71.81 - 89.76: 27 Dihedral angle restraints: 10172 sinusoidal: 4052 harmonic: 6120 Sorted by residual: dihedral pdb=" CA THR A 219 " pdb=" C THR A 219 " pdb=" N ILE A 220 " pdb=" CA ILE A 220 " ideal model delta harmonic sigma weight residual 180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASP C 127 " pdb=" CB ASP C 127 " pdb=" CG ASP C 127 " pdb=" OD1 ASP C 127 " ideal model delta sinusoidal sigma weight residual -30.00 -94.13 64.13 1 2.00e+01 2.50e-03 1.35e+01 dihedral pdb=" CA CYS D 412 " pdb=" C CYS D 412 " pdb=" N TYR D 413 " pdb=" CA TYR D 413 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 10169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2224 0.085 - 0.170: 222 0.170 - 0.255: 11 0.255 - 0.339: 0 0.339 - 0.424: 3 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA CYS C 183 " pdb=" N CYS C 183 " pdb=" C CYS C 183 " pdb=" CB CYS C 183 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA CYS D 183 " pdb=" N CYS D 183 " pdb=" C CYS D 183 " pdb=" CB CYS D 183 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA CYS B 183 " pdb=" N CYS B 183 " pdb=" C CYS B 183 " pdb=" CB CYS B 183 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 2457 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 501 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ILE C 501 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE C 501 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY C 502 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 499 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C ASP D 499 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP D 499 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR D 500 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 501 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C ILE B 501 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE B 501 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY B 502 " 0.016 2.00e-02 2.50e+03 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 3 2.24 - 2.91: 7012 2.91 - 3.57: 21468 3.57 - 4.24: 41783 4.24 - 4.90: 72702 Nonbonded interactions: 142968 Sorted by model distance: nonbonded pdb=" ND1 HIS D 227 " pdb=" CD PRO D 228 " model vdw 1.576 3.520 nonbonded pdb=" O ASN B 155 " pdb=" ND2 ASN B 155 " model vdw 2.236 3.120 nonbonded pdb=" O ASN A 155 " pdb=" ND2 ASN A 155 " model vdw 2.240 3.120 nonbonded pdb=" O ASN C 155 " pdb=" ND2 ASN C 155 " model vdw 2.241 3.120 nonbonded pdb=" OD2 ASP C 68 " pdb=" OG SER C 416 " model vdw 2.242 3.040 ... (remaining 142963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 324 or resid 330 through 427 or (resid 428 and ( \ name N or name CA or name C or name O or name CB )) or resid 429 through 457 or \ (resid 458 through 459 and (name N or name CA or name C or name O or name CB )) \ or resid 460 through 601)) selection = (chain 'B' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 164 or (resid 165 and (name N or \ name CA or name C or name O or name CB )) or resid 166 through 427 or (resid 42 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 429 through \ 449 or (resid 450 through 451 and (name N or name CA or name C or name O or name \ CB )) or resid 452 through 457 or (resid 458 through 459 and (name N or name CA \ or name C or name O or name CB )) or resid 460 through 481 or (resid 482 and (n \ ame N or name CA or name C or name O or name CB )) or resid 483 through 533 or ( \ resid 534 and (name N or name CA or name C or name O or name CB )) or resid 535 \ through 601)) selection = (chain 'C' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 164 or (resid 165 and (name N or \ name CA or name C or name O or name CB )) or resid 166 through 324 or resid 330 \ through 427 or (resid 428 and (name N or name CA or name C or name O or name CB \ )) or resid 429 through 481 or (resid 482 and (name N or name CA or name C or n \ ame O or name CB )) or resid 483 through 533 or (resid 534 and (name N or name C \ A or name C or name O or name CB )) or resid 535 through 601)) selection = (chain 'D' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 324 or resid 330 through 449 or \ (resid 450 through 451 and (name N or name CA or name C or name O or name CB )) \ or resid 452 through 457 or (resid 458 through 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 533 or (resid 534 and (name N o \ r name CA or name C or name O or name CB )) or resid 535 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.950 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 0.079 17738 Z= 0.300 Angle : 0.728 13.259 24234 Z= 0.417 Chirality : 0.050 0.424 2460 Planarity : 0.005 0.063 3155 Dihedral : 16.680 89.763 6302 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.53 % Favored : 95.19 % Rotamer: Outliers : 2.74 % Allowed : 24.31 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2119 helix: -4.02 (0.64), residues: 24 sheet: 0.67 (0.19), residues: 776 loop : -1.19 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 474 TYR 0.021 0.002 TYR B 79 PHE 0.034 0.002 PHE B 506 TRP 0.025 0.002 TRP B 48 HIS 0.010 0.001 HIS C 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.30 (17738) covalent geometry : angle 0.72764 / 0.42 (24234) hydrogen bonds : bond 0.20156 / 13.31 ( 586) hydrogen bonds : angle 8.43647 / 5.93 ( 1980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 497 time to evaluate : 0.632 Fit side-chains REVERT: C 192 ARG cc_start: 0.7991 (ttt90) cc_final: 0.7787 (ttt90) REVERT: C 206 THR cc_start: 0.8327 (t) cc_final: 0.7997 (m) REVERT: D 178 THR cc_start: 0.8138 (p) cc_final: 0.7926 (m) REVERT: D 192 ARG cc_start: 0.8116 (ttt90) cc_final: 0.7609 (ttt90) REVERT: D 206 THR cc_start: 0.8319 (t) cc_final: 0.7960 (m) REVERT: D 330 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7644 (p) REVERT: A 391 PHE cc_start: 0.8221 (p90) cc_final: 0.7911 (p90) REVERT: A 506 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7816 (p90) REVERT: B 206 THR cc_start: 0.8339 (t) cc_final: 0.7989 (m) REVERT: B 438 GLN cc_start: 0.8325 (tt0) cc_final: 0.8045 (tt0) outliers start: 50 outliers final: 24 residues processed: 523 average time/residue: 0.4755 time to fit residues: 281.2174 Evaluate side-chains 503 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 477 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 446 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.0970 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 HIS D 155 ASN D 515 HIS A 5 ASN A 160 GLN A 398 GLN A 406 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN B 323 GLN B 403 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.109686 restraints weight = 23796.754| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.68 r_work: 0.3429 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17738 Z= 0.239 Angle : 0.648 7.411 24234 Z= 0.333 Chirality : 0.048 0.182 2460 Planarity : 0.006 0.063 3155 Dihedral : 6.129 56.504 2415 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.39 % Favored : 95.42 % Rotamer: Outliers : 5.38 % Allowed : 20.36 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2119 helix: -3.93 (0.48), residues: 42 sheet: 0.97 (0.19), residues: 741 loop : -1.06 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 504 TYR 0.019 0.002 TYR D 413 PHE 0.017 0.002 PHE D 84 TRP 0.012 0.002 TRP D 98 HIS 0.008 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.24 (17738) covalent geometry : angle 0.64778 / 0.33 (24234) hydrogen bonds : bond 0.04353 / 2.83 ( 586) hydrogen bonds : angle 5.59349 / 3.92 ( 1980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 474 time to evaluate : 0.561 Fit side-chains REVERT: C 64 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8062 (ttpp) REVERT: C 127 ASP cc_start: 0.7194 (t70) cc_final: 0.6972 (p0) REVERT: C 201 VAL cc_start: 0.8420 (m) cc_final: 0.8133 (t) REVERT: C 206 THR cc_start: 0.8254 (t) cc_final: 0.7955 (m) REVERT: C 445 SER cc_start: 0.8414 (t) cc_final: 0.8107 (m) REVERT: D 206 THR cc_start: 0.8145 (t) cc_final: 0.7820 (m) REVERT: D 438 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: A 95 ASP cc_start: 0.7649 (t0) cc_final: 0.7421 (t0) REVERT: A 155 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7857 (p0) REVERT: A 206 THR cc_start: 0.8256 (t) cc_final: 0.7926 (m) REVERT: A 297 GLU cc_start: 0.7625 (pt0) cc_final: 0.7401 (pt0) REVERT: A 319 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7690 (mm-40) REVERT: A 497 SER cc_start: 0.8182 (p) cc_final: 0.7847 (p) REVERT: A 507 PHE cc_start: 0.8286 (m-10) cc_final: 0.8050 (m-80) REVERT: B 32 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7379 (pt0) REVERT: B 44 ASP cc_start: 0.7894 (p0) cc_final: 0.7688 (p0) REVERT: B 46 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.7049 (ttpt) REVERT: B 152 ASN cc_start: 0.8464 (p0) cc_final: 0.8241 (p0) REVERT: B 322 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6724 (mt-10) REVERT: B 507 PHE cc_start: 0.8141 (m-80) cc_final: 0.7857 (m-80) outliers start: 98 outliers final: 45 residues processed: 519 average time/residue: 0.4786 time to fit residues: 281.6769 Evaluate side-chains 509 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 459 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 50 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 155 ASN ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108169 restraints weight = 24341.203| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.72 r_work: 0.3427 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17738 Z= 0.179 Angle : 0.602 8.580 24234 Z= 0.310 Chirality : 0.046 0.168 2460 Planarity : 0.005 0.051 3155 Dihedral : 5.370 51.787 2389 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.06 % Favored : 95.75 % Rotamer: Outliers : 5.16 % Allowed : 21.79 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.18), residues: 2119 helix: -3.94 (0.48), residues: 36 sheet: 1.08 (0.19), residues: 753 loop : -1.07 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 474 TYR 0.021 0.002 TYR B 413 PHE 0.020 0.002 PHE D 507 TRP 0.011 0.001 TRP C 98 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (17738) covalent geometry : angle 0.60174 / 0.31 (24234) hydrogen bonds : bond 0.03624 / 2.35 ( 586) hydrogen bonds : angle 5.26650 / 3.68 ( 1980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 470 time to evaluate : 0.688 Fit side-chains REVERT: C 48 TRP cc_start: 0.8521 (m100) cc_final: 0.8228 (m100) REVERT: C 64 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7968 (tttp) REVERT: C 95 ASP cc_start: 0.7561 (t0) cc_final: 0.7352 (t0) REVERT: C 192 ARG cc_start: 0.8331 (ttt90) cc_final: 0.8119 (ttt90) REVERT: C 201 VAL cc_start: 0.8421 (m) cc_final: 0.8118 (t) REVERT: C 206 THR cc_start: 0.8170 (t) cc_final: 0.7935 (m) REVERT: C 359 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8393 (p) REVERT: C 445 SER cc_start: 0.8403 (t) cc_final: 0.8099 (m) REVERT: D 143 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.6490 (ttt-90) REVERT: D 206 THR cc_start: 0.8059 (t) cc_final: 0.7779 (m) REVERT: D 438 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: A 95 ASP cc_start: 0.7672 (t0) cc_final: 0.7431 (t0) REVERT: A 155 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7839 (p0) REVERT: A 192 ARG cc_start: 0.8368 (ttt90) cc_final: 0.8068 (ttt90) REVERT: A 206 THR cc_start: 0.8217 (t) cc_final: 0.7939 (m) REVERT: A 238 LEU cc_start: 0.7977 (mt) cc_final: 0.7740 (mp) REVERT: A 250 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.8075 (m) REVERT: A 297 GLU cc_start: 0.7656 (pt0) cc_final: 0.7440 (pt0) REVERT: A 407 SER cc_start: 0.8510 (p) cc_final: 0.8286 (m) REVERT: A 497 SER cc_start: 0.8084 (p) cc_final: 0.7673 (p) REVERT: A 507 PHE cc_start: 0.8301 (m-10) cc_final: 0.8057 (m-80) REVERT: B 57 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7687 (mtm-85) REVERT: B 152 ASN cc_start: 0.8449 (p0) cc_final: 0.8192 (p0) REVERT: B 507 PHE cc_start: 0.8182 (m-80) cc_final: 0.7868 (m-80) outliers start: 94 outliers final: 53 residues processed: 511 average time/residue: 0.5043 time to fit residues: 292.0334 Evaluate side-chains 517 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 458 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 446 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 206 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 155 ASN ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 323 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.107819 restraints weight = 24285.580| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.73 r_work: 0.3422 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17738 Z= 0.203 Angle : 0.610 9.379 24234 Z= 0.312 Chirality : 0.047 0.185 2460 Planarity : 0.005 0.049 3155 Dihedral : 5.145 47.133 2383 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.34 % Favored : 95.47 % Rotamer: Outliers : 5.82 % Allowed : 21.35 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.18), residues: 2119 helix: -3.76 (0.46), residues: 36 sheet: 1.17 (0.19), residues: 753 loop : -1.05 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 474 TYR 0.020 0.002 TYR B 413 PHE 0.025 0.002 PHE D 506 TRP 0.012 0.001 TRP C 463 HIS 0.008 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.20 (17738) covalent geometry : angle 0.60974 / 0.31 (24234) hydrogen bonds : bond 0.03476 / 2.24 ( 586) hydrogen bonds : angle 5.10008 / 3.56 ( 1980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 471 time to evaluate : 0.502 Fit side-chains REVERT: C 95 ASP cc_start: 0.7579 (t0) cc_final: 0.7372 (t0) REVERT: C 201 VAL cc_start: 0.8420 (m) cc_final: 0.8135 (t) REVERT: C 206 THR cc_start: 0.8139 (t) cc_final: 0.7882 (m) REVERT: C 359 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8408 (p) REVERT: C 438 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: C 445 SER cc_start: 0.8386 (t) cc_final: 0.8126 (m) REVERT: D 102 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7628 (mmt180) REVERT: D 143 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.6714 (ttt-90) REVERT: D 438 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: A 86 LEU cc_start: 0.8374 (tp) cc_final: 0.8173 (tt) REVERT: A 95 ASP cc_start: 0.7716 (t0) cc_final: 0.7478 (t0) REVERT: A 155 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7789 (p0) REVERT: A 192 ARG cc_start: 0.8381 (ttt90) cc_final: 0.8055 (ttt90) REVERT: A 206 THR cc_start: 0.8193 (t) cc_final: 0.7961 (m) REVERT: A 297 GLU cc_start: 0.7632 (pt0) cc_final: 0.7427 (pt0) REVERT: A 407 SER cc_start: 0.8491 (p) cc_final: 0.8277 (m) REVERT: A 438 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: A 497 SER cc_start: 0.8049 (p) cc_final: 0.7793 (p) REVERT: A 507 PHE cc_start: 0.8320 (m-10) cc_final: 0.8069 (m-80) REVERT: B 152 ASN cc_start: 0.8456 (p0) cc_final: 0.8230 (p0) REVERT: B 206 THR cc_start: 0.8119 (t) cc_final: 0.7839 (m) REVERT: B 507 PHE cc_start: 0.8203 (m-80) cc_final: 0.7825 (m-80) outliers start: 106 outliers final: 67 residues processed: 514 average time/residue: 0.4898 time to fit residues: 285.8925 Evaluate side-chains 527 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 453 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 147 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 202 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 155 ASN ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.117665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108232 restraints weight = 24007.021| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.73 r_work: 0.3427 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17738 Z= 0.174 Angle : 0.597 8.545 24234 Z= 0.307 Chirality : 0.046 0.183 2460 Planarity : 0.005 0.048 3155 Dihedral : 5.059 47.290 2382 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.06 % Favored : 95.75 % Rotamer: Outliers : 5.71 % Allowed : 21.90 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 2119 helix: -3.48 (0.54), residues: 36 sheet: 1.22 (0.19), residues: 753 loop : -1.01 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 474 TYR 0.021 0.002 TYR D 413 PHE 0.028 0.002 PHE D 507 TRP 0.012 0.001 TRP C 463 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 (17738) covalent geometry : angle 0.59746 / 0.31 (24234) hydrogen bonds : bond 0.03276 / 2.11 ( 586) hydrogen bonds : angle 4.97799 / 3.48 ( 1980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 463 time to evaluate : 0.676 Fit side-chains REVERT: C 201 VAL cc_start: 0.8409 (m) cc_final: 0.8113 (t) REVERT: C 206 THR cc_start: 0.8091 (t) cc_final: 0.7882 (m) REVERT: C 359 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8403 (p) REVERT: C 445 SER cc_start: 0.8385 (t) cc_final: 0.8117 (m) REVERT: D 143 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8180 (ttt180) REVERT: D 438 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: A 57 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7768 (mtm180) REVERT: A 95 ASP cc_start: 0.7703 (t0) cc_final: 0.7484 (t0) REVERT: A 143 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6506 (ttt-90) REVERT: A 155 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7804 (p0) REVERT: A 192 ARG cc_start: 0.8375 (ttt90) cc_final: 0.8079 (ttt90) REVERT: A 206 THR cc_start: 0.8168 (t) cc_final: 0.7953 (m) REVERT: A 297 GLU cc_start: 0.7631 (pt0) cc_final: 0.7430 (pt0) REVERT: A 407 SER cc_start: 0.8477 (p) cc_final: 0.8260 (m) REVERT: A 438 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: A 497 SER cc_start: 0.8040 (p) cc_final: 0.7786 (p) REVERT: A 507 PHE cc_start: 0.8330 (m-10) cc_final: 0.8090 (m-80) REVERT: B 152 ASN cc_start: 0.8444 (p0) cc_final: 0.8123 (p0) REVERT: B 206 THR cc_start: 0.8064 (t) cc_final: 0.7844 (m) REVERT: B 507 PHE cc_start: 0.8221 (m-80) cc_final: 0.7861 (m-80) outliers start: 104 outliers final: 63 residues processed: 505 average time/residue: 0.4993 time to fit residues: 285.7438 Evaluate side-chains 526 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 457 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 146 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 145 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 155 ASN ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108533 restraints weight = 24043.091| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.71 r_work: 0.3429 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17738 Z= 0.163 Angle : 0.587 7.913 24234 Z= 0.302 Chirality : 0.045 0.179 2460 Planarity : 0.005 0.047 3155 Dihedral : 4.872 47.195 2379 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.15 % Favored : 95.66 % Rotamer: Outliers : 5.38 % Allowed : 22.45 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2119 helix: -3.21 (0.63), residues: 36 sheet: 1.23 (0.19), residues: 763 loop : -0.98 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 474 TYR 0.023 0.002 TYR D 413 PHE 0.029 0.002 PHE D 507 TRP 0.016 0.001 TRP C 48 HIS 0.008 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.16 (17738) covalent geometry : angle 0.58722 / 0.30 (24234) hydrogen bonds : bond 0.03157 / 2.03 ( 586) hydrogen bonds : angle 4.88457 / 3.42 ( 1980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 472 time to evaluate : 0.701 Fit side-chains REVERT: C 4 THR cc_start: 0.8252 (m) cc_final: 0.8046 (p) REVERT: C 32 GLU cc_start: 0.7963 (pm20) cc_final: 0.7760 (pm20) REVERT: C 106 VAL cc_start: 0.7996 (t) cc_final: 0.7709 (m) REVERT: C 152 ASN cc_start: 0.8489 (p0) cc_final: 0.8280 (p0) REVERT: C 201 VAL cc_start: 0.8393 (m) cc_final: 0.8095 (t) REVERT: C 206 THR cc_start: 0.8081 (t) cc_final: 0.7878 (m) REVERT: C 290 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7789 (mt-10) REVERT: C 359 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8411 (p) REVERT: C 445 SER cc_start: 0.8368 (t) cc_final: 0.8109 (m) REVERT: D 95 ASP cc_start: 0.7755 (t0) cc_final: 0.7488 (t0) REVERT: D 143 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8171 (ttt180) REVERT: D 185 THR cc_start: 0.8287 (t) cc_final: 0.8056 (m) REVERT: D 438 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: A 4 THR cc_start: 0.8272 (m) cc_final: 0.8067 (p) REVERT: A 95 ASP cc_start: 0.7708 (t0) cc_final: 0.7489 (t0) REVERT: A 143 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6517 (ttt-90) REVERT: A 155 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7806 (p0) REVERT: A 192 ARG cc_start: 0.8337 (ttt90) cc_final: 0.8027 (ttt90) REVERT: A 250 SER cc_start: 0.8279 (t) cc_final: 0.8067 (m) REVERT: A 407 SER cc_start: 0.8486 (p) cc_final: 0.8267 (m) REVERT: A 438 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: A 497 SER cc_start: 0.8077 (p) cc_final: 0.7806 (p) REVERT: A 507 PHE cc_start: 0.8346 (m-10) cc_final: 0.8106 (m-80) REVERT: B 152 ASN cc_start: 0.8437 (p0) cc_final: 0.8191 (p0) REVERT: B 245 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8404 (mttt) REVERT: B 507 PHE cc_start: 0.8209 (m-80) cc_final: 0.7817 (m-80) outliers start: 98 outliers final: 67 residues processed: 514 average time/residue: 0.5124 time to fit residues: 299.5022 Evaluate side-chains 541 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 467 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 0.0170 chunk 153 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 155 ASN D 515 HIS ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.118186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108883 restraints weight = 23909.144| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.70 r_work: 0.3435 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17738 Z= 0.146 Angle : 0.580 7.357 24234 Z= 0.299 Chirality : 0.045 0.185 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.788 46.642 2378 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.61 % Rotamer: Outliers : 5.10 % Allowed : 23.71 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2119 helix: -3.11 (0.65), residues: 36 sheet: 1.26 (0.19), residues: 762 loop : -0.96 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 474 TYR 0.024 0.001 TYR D 413 PHE 0.032 0.002 PHE D 507 TRP 0.020 0.001 TRP C 48 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (17738) covalent geometry : angle 0.57986 / 0.30 (24234) hydrogen bonds : bond 0.03048 / 1.96 ( 586) hydrogen bonds : angle 4.81932 / 3.38 ( 1980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 472 time to evaluate : 0.662 Fit side-chains REVERT: C 4 THR cc_start: 0.8250 (m) cc_final: 0.8046 (p) REVERT: C 32 GLU cc_start: 0.7973 (pm20) cc_final: 0.7768 (pm20) REVERT: C 152 ASN cc_start: 0.8478 (p0) cc_final: 0.8272 (p0) REVERT: C 201 VAL cc_start: 0.8388 (m) cc_final: 0.8074 (t) REVERT: C 206 THR cc_start: 0.8074 (t) cc_final: 0.7870 (m) REVERT: C 445 SER cc_start: 0.8397 (t) cc_final: 0.8133 (m) REVERT: D 95 ASP cc_start: 0.7757 (t0) cc_final: 0.7498 (t0) REVERT: D 143 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8203 (ttt180) REVERT: D 438 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: A 143 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.6831 (ttt-90) REVERT: A 155 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7788 (p0) REVERT: A 192 ARG cc_start: 0.8346 (ttt90) cc_final: 0.8055 (ttt90) REVERT: A 238 LEU cc_start: 0.7949 (mt) cc_final: 0.7713 (mt) REVERT: A 250 SER cc_start: 0.8279 (t) cc_final: 0.8058 (m) REVERT: A 438 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: A 497 SER cc_start: 0.8094 (p) cc_final: 0.7826 (p) REVERT: A 507 PHE cc_start: 0.8313 (m-10) cc_final: 0.8073 (m-80) REVERT: B 44 ASP cc_start: 0.7967 (p0) cc_final: 0.7647 (p0) REVERT: B 152 ASN cc_start: 0.8437 (p0) cc_final: 0.8127 (p0) REVERT: B 507 PHE cc_start: 0.8184 (m-80) cc_final: 0.7840 (m-80) outliers start: 93 outliers final: 64 residues processed: 515 average time/residue: 0.5144 time to fit residues: 300.2837 Evaluate side-chains 537 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 468 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 12 ASN D 403 HIS A 100 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107914 restraints weight = 24067.703| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.72 r_work: 0.3422 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17738 Z= 0.227 Angle : 0.633 8.261 24234 Z= 0.324 Chirality : 0.047 0.230 2460 Planarity : 0.006 0.048 3155 Dihedral : 4.963 47.954 2378 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.34 % Favored : 95.42 % Rotamer: Outliers : 5.32 % Allowed : 23.77 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 2119 helix: -3.08 (0.62), residues: 36 sheet: 1.25 (0.19), residues: 753 loop : -1.04 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 57 TYR 0.021 0.002 TYR D 413 PHE 0.064 0.002 PHE D 507 TRP 0.024 0.002 TRP C 48 HIS 0.008 0.001 HIS D 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (17738) covalent geometry : angle 0.63271 / 0.32 (24234) hydrogen bonds : bond 0.03417 / 2.21 ( 586) hydrogen bonds : angle 4.89793 / 3.44 ( 1980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 474 time to evaluate : 0.517 Fit side-chains REVERT: C 152 ASN cc_start: 0.8486 (p0) cc_final: 0.8267 (p0) REVERT: C 201 VAL cc_start: 0.8408 (m) cc_final: 0.8132 (t) REVERT: C 445 SER cc_start: 0.8378 (t) cc_final: 0.8129 (m) REVERT: D 95 ASP cc_start: 0.7798 (t0) cc_final: 0.7521 (t0) REVERT: D 143 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8184 (ttt180) REVERT: D 185 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.8004 (t) REVERT: D 438 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: A 57 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7695 (mtm180) REVERT: A 143 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6491 (ttt-90) REVERT: A 155 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7785 (p0) REVERT: A 192 ARG cc_start: 0.8378 (ttt90) cc_final: 0.8045 (ttt90) REVERT: A 238 LEU cc_start: 0.7964 (mt) cc_final: 0.7749 (mt) REVERT: A 438 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: A 497 SER cc_start: 0.8055 (p) cc_final: 0.7796 (p) REVERT: A 507 PHE cc_start: 0.8313 (m-10) cc_final: 0.8083 (m-80) REVERT: B 44 ASP cc_start: 0.7931 (p0) cc_final: 0.7626 (p0) REVERT: B 152 ASN cc_start: 0.8450 (p0) cc_final: 0.8108 (p0) REVERT: B 507 PHE cc_start: 0.8174 (m-80) cc_final: 0.7830 (m-80) outliers start: 97 outliers final: 67 residues processed: 519 average time/residue: 0.4879 time to fit residues: 287.3420 Evaluate side-chains 543 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 470 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 192 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 155 ASN D 312 GLN D 403 HIS ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108801 restraints weight = 24016.448| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.71 r_work: 0.3437 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17738 Z= 0.160 Angle : 0.605 7.819 24234 Z= 0.311 Chirality : 0.046 0.195 2460 Planarity : 0.005 0.047 3155 Dihedral : 4.879 47.055 2378 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.61 % Rotamer: Outliers : 5.05 % Allowed : 24.20 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.18), residues: 2119 helix: -2.99 (0.60), residues: 36 sheet: 1.24 (0.19), residues: 751 loop : -1.01 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 474 TYR 0.025 0.002 TYR D 413 PHE 0.030 0.002 PHE D 506 TRP 0.027 0.001 TRP C 48 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (17738) covalent geometry : angle 0.60470 / 0.31 (24234) hydrogen bonds : bond 0.03109 / 2.00 ( 586) hydrogen bonds : angle 4.82193 / 3.38 ( 1980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 476 time to evaluate : 0.831 Fit side-chains REVERT: C 4 THR cc_start: 0.8249 (m) cc_final: 0.8047 (p) REVERT: C 106 VAL cc_start: 0.8040 (t) cc_final: 0.7746 (m) REVERT: C 152 ASN cc_start: 0.8471 (p0) cc_final: 0.8260 (p0) REVERT: C 201 VAL cc_start: 0.8406 (m) cc_final: 0.8095 (t) REVERT: C 445 SER cc_start: 0.8380 (t) cc_final: 0.8136 (m) REVERT: D 95 ASP cc_start: 0.7799 (t0) cc_final: 0.7552 (t0) REVERT: D 143 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8183 (ttt180) REVERT: D 438 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: A 143 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6829 (ttt-90) REVERT: A 155 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7761 (p0) REVERT: A 192 ARG cc_start: 0.8341 (ttt90) cc_final: 0.8049 (ttt90) REVERT: A 238 LEU cc_start: 0.7955 (mt) cc_final: 0.7738 (mt) REVERT: A 438 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: A 497 SER cc_start: 0.8071 (p) cc_final: 0.7806 (p) REVERT: A 507 PHE cc_start: 0.8271 (m-10) cc_final: 0.8060 (m-80) REVERT: B 44 ASP cc_start: 0.7938 (p0) cc_final: 0.7644 (p0) REVERT: B 152 ASN cc_start: 0.8439 (p0) cc_final: 0.8117 (p0) REVERT: B 507 PHE cc_start: 0.8137 (m-80) cc_final: 0.7836 (m-80) outliers start: 92 outliers final: 66 residues processed: 518 average time/residue: 0.4880 time to fit residues: 286.6372 Evaluate side-chains 541 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 470 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 211 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 155 ASN D 403 HIS ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.118675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109243 restraints weight = 23769.481| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.71 r_work: 0.3442 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17738 Z= 0.145 Angle : 0.596 8.298 24234 Z= 0.306 Chirality : 0.046 0.192 2460 Planarity : 0.005 0.047 3155 Dihedral : 4.806 46.352 2378 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.61 % Rotamer: Outliers : 4.45 % Allowed : 25.47 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2119 helix: -2.93 (0.61), residues: 36 sheet: 1.23 (0.19), residues: 761 loop : -1.00 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 289 TYR 0.026 0.001 TYR D 413 PHE 0.034 0.002 PHE D 506 TRP 0.035 0.001 TRP C 48 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.14 (17738) covalent geometry : angle 0.59620 / 0.31 (24234) hydrogen bonds : bond 0.02996 / 1.93 ( 586) hydrogen bonds : angle 4.77894 / 3.35 ( 1980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 481 time to evaluate : 0.684 Fit side-chains REVERT: C 4 THR cc_start: 0.8234 (m) cc_final: 0.8027 (p) REVERT: C 106 VAL cc_start: 0.8040 (t) cc_final: 0.7740 (m) REVERT: C 152 ASN cc_start: 0.8466 (p0) cc_final: 0.8244 (p0) REVERT: C 290 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7842 (mt-10) REVERT: C 445 SER cc_start: 0.8371 (t) cc_final: 0.8127 (m) REVERT: C 497 SER cc_start: 0.8093 (p) cc_final: 0.7844 (p) REVERT: D 95 ASP cc_start: 0.7765 (t0) cc_final: 0.7553 (t0) REVERT: D 438 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: A 143 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.6958 (ttt-90) REVERT: A 155 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7778 (p0) REVERT: A 192 ARG cc_start: 0.8325 (ttt90) cc_final: 0.8042 (ttt90) REVERT: A 407 SER cc_start: 0.8502 (p) cc_final: 0.8283 (m) REVERT: A 438 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: A 497 SER cc_start: 0.8043 (p) cc_final: 0.7776 (p) REVERT: B 32 GLU cc_start: 0.7546 (pm20) cc_final: 0.7310 (pt0) REVERT: B 44 ASP cc_start: 0.7940 (p0) cc_final: 0.7645 (p0) REVERT: B 152 ASN cc_start: 0.8432 (p0) cc_final: 0.8122 (p0) REVERT: B 290 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 507 PHE cc_start: 0.8118 (m-80) cc_final: 0.7821 (m-80) outliers start: 81 outliers final: 62 residues processed: 514 average time/residue: 0.5321 time to fit residues: 309.7993 Evaluate side-chains 543 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 477 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 142 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 181 optimal weight: 0.4980 chunk 191 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 155 ASN D 403 HIS ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.117875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108408 restraints weight = 23886.507| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.71 r_work: 0.3430 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17738 Z= 0.213 Angle : 0.638 8.628 24234 Z= 0.326 Chirality : 0.047 0.199 2460 Planarity : 0.005 0.047 3155 Dihedral : 4.745 32.874 2374 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.20 % Favored : 95.52 % Rotamer: Outliers : 4.39 % Allowed : 25.85 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2119 helix: -2.73 (0.69), residues: 30 sheet: 1.24 (0.19), residues: 758 loop : -1.05 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 474 TYR 0.022 0.002 TYR D 413 PHE 0.059 0.002 PHE D 507 TRP 0.037 0.002 TRP C 48 HIS 0.008 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.21 (17738) covalent geometry : angle 0.63814 / 0.33 (24234) hydrogen bonds : bond 0.03293 / 2.13 ( 586) hydrogen bonds : angle 4.85189 / 3.40 ( 1980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6501.30 seconds wall clock time: 111 minutes 24.98 seconds (6684.98 seconds total)