Starting phenix.real_space_refine on Sun Aug 24 05:05:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uws_42680/08_2025/8uws_42680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uws_42680/08_2025/8uws_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 { model { file = "/net/cci-nas-00/data/ceres_data/8uws_42680/08_2025/8uws_42680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uws_42680/08_2025/8uws_42680.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uws_42680/08_2025/8uws_42680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uws_42680/08_2025/8uws_42680.map" } 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-2.0-5787/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.80, per 1000 atoms: 0.22 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: 1.23 Conformation dependent library (CDL) restraints added in 638.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.65 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: 3.59 Time building geometry restraints manager: 1.64 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: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.540 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 aren 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 covalent geometry : bond 0.00517 (17738) covalent geometry : angle 0.72764 (24234) hydrogen bonds : bond 0.20156 ( 586) hydrogen bonds : angle 8.43647 ( 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 : 0.401 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: 0.8340 (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: 0.5273 time to fit residues: 309.9136 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 : 0.438 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3644 r_free = 0.3644 target = 0.118072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108836 restraints weight = 23932.425| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.69 r_work: 0.3432 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0959 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= 0.240 Angle : 0.649 7.486 24234 Z= 0.335 Chirality : 0.048 0.190 2460 Planarity : 0.006 0.066 3155 Dihedral : 6.143 56.281 2415 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.15 % Favored : 95.66 % Rotamer: Outliers : 5.10 % Allowed : 20.91 % Favored : 73.98 % 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 aren not related in a simple way. whole: -0.53 (0.18), residues: 2119 helix: -3.92 (0.49), residues: 42 sheet: 0.98 (0.19), residues: 751 loop : -1.09 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 474 TYR 0.018 0.002 TYR A 473 PHE 0.017 0.002 PHE B 506 TRP 0.012 0.002 TRP C 98 HIS 0.008 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00588 (17738) covalent geometry : angle 0.64923 (24234) hydrogen bonds : bond 0.04304 ( 586) hydrogen bonds : angle 5.66015 ( 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 570 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 477 time to evaluate : 0.519 Fit side-chains REVERT: C 64 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8057 (ttpp) REVERT: C 127 ASP cc_start: 0.7251 (t70) cc_final: 0.6968 (p0) REVERT: C 201 VAL cc_start: 0.8434 (m) cc_final: 0.8137 (t) REVERT: C 206 THR cc_start: 0.8272 (t) cc_final: 0.7969 (m) REVERT: C 445 SER cc_start: 0.8411 (t) cc_final: 0.8103 (m) REVERT: C 533 TYR cc_start: 0.8513 (t80) cc_final: 0.8274 (t80) REVERT: D 143 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8098 (ttt-90) REVERT: D 206 THR cc_start: 0.8169 (t) cc_final: 0.7806 (m) REVERT: D 438 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: A 95 ASP cc_start: 0.7603 (t0) cc_final: 0.7380 (t0) REVERT: A 155 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7878 (p0) REVERT: A 297 GLU cc_start: 0.7608 (pt0) cc_final: 0.7374 (pt0) REVERT: A 319 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7728 (mm-40) REVERT: A 497 SER cc_start: 0.8138 (p) cc_final: 0.7815 (p) REVERT: A 507 PHE cc_start: 0.8272 (m-10) cc_final: 0.8050 (m-80) REVERT: B 44 ASP cc_start: 0.7957 (p0) cc_final: 0.7738 (p0) REVERT: B 152 ASN cc_start: 0.8491 (p0) cc_final: 0.8274 (p0) REVERT: B 507 PHE cc_start: 0.8155 (m-80) cc_final: 0.7867 (m-80) outliers start: 93 outliers final: 47 residues processed: 518 average time/residue: 0.4695 time to fit residues: 275.4364 Evaluate side-chains 507 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 456 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 143 ARG 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 357 SER Chi-restraints excluded: chain D residue 359 THR 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 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 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 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 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 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 252 LEU 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: 0.7980 chunk 127 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 ASN ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107947 restraints weight = 24229.286| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.72 r_work: 0.3424 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17738 Z= 0.191 Angle : 0.608 8.830 24234 Z= 0.313 Chirality : 0.046 0.168 2460 Planarity : 0.005 0.053 3155 Dihedral : 5.393 52.444 2389 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.06 % Favored : 95.75 % Rotamer: Outliers : 5.43 % Allowed : 21.51 % 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 aren not related in a simple way. whole: -0.43 (0.18), residues: 2119 helix: -3.92 (0.47), residues: 36 sheet: 1.09 (0.19), residues: 758 loop : -1.08 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 474 TYR 0.020 0.002 TYR B 413 PHE 0.018 0.002 PHE D 507 TRP 0.011 0.001 TRP C 98 HIS 0.008 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00469 (17738) covalent geometry : angle 0.60806 (24234) hydrogen bonds : bond 0.03675 ( 586) hydrogen bonds : angle 5.28218 ( 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 568 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 469 time to evaluate : 0.604 Fit side-chains REVERT: C 48 TRP cc_start: 0.8539 (m100) cc_final: 0.8223 (m100) REVERT: C 95 ASP cc_start: 0.7609 (t0) cc_final: 0.7388 (t0) REVERT: C 192 ARG cc_start: 0.8339 (ttt90) cc_final: 0.8101 (ttt90) REVERT: C 201 VAL cc_start: 0.8429 (m) cc_final: 0.8131 (t) REVERT: C 206 THR cc_start: 0.8191 (t) cc_final: 0.7934 (m) REVERT: C 445 SER cc_start: 0.8400 (t) cc_final: 0.8092 (m) REVERT: D 206 THR cc_start: 0.8073 (t) cc_final: 0.7792 (m) REVERT: D 438 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: A 95 ASP cc_start: 0.7692 (t0) cc_final: 0.7446 (t0) REVERT: A 155 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7855 (p0) REVERT: A 192 ARG cc_start: 0.8373 (ttt90) cc_final: 0.8062 (ttt90) REVERT: A 206 THR cc_start: 0.8234 (t) cc_final: 0.7945 (m) REVERT: A 238 LEU cc_start: 0.7976 (mt) cc_final: 0.7738 (mp) REVERT: A 297 GLU cc_start: 0.7664 (pt0) cc_final: 0.7443 (pt0) REVERT: A 407 SER cc_start: 0.8511 (p) cc_final: 0.8285 (m) REVERT: A 497 SER cc_start: 0.8063 (p) cc_final: 0.7661 (p) REVERT: A 507 PHE cc_start: 0.8309 (m-10) cc_final: 0.8080 (m-80) REVERT: B 46 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.7030 (ttpt) REVERT: B 57 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7707 (mtm-85) REVERT: B 152 ASN cc_start: 0.8442 (p0) cc_final: 0.8218 (p0) REVERT: B 322 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6838 (mt-10) REVERT: B 507 PHE cc_start: 0.8193 (m-80) cc_final: 0.7858 (m-80) outliers start: 99 outliers final: 56 residues processed: 515 average time/residue: 0.5159 time to fit residues: 299.3048 Evaluate side-chains 516 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 457 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 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 9 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 58 VAL 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 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 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 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 256 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 457 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 46 LYS 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 233 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 206 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 186 optimal weight: 0.0270 chunk 124 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 ASN D 515 HIS A 100 ASN A 323 GLN A 515 HIS B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.118476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109017 restraints weight = 24136.180| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.73 r_work: 0.3438 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17738 Z= 0.116 Angle : 0.558 7.779 24234 Z= 0.288 Chirality : 0.044 0.171 2460 Planarity : 0.005 0.049 3155 Dihedral : 5.036 48.734 2386 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.06 % Favored : 95.75 % Rotamer: Outliers : 4.50 % Allowed : 22.39 % Favored : 73.11 % 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 aren not related in a simple way. whole: -0.29 (0.18), residues: 2119 helix: -3.69 (0.47), residues: 36 sheet: 1.18 (0.19), residues: 762 loop : -0.98 (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 0.023 0.001 PHE D 507 TRP 0.009 0.001 TRP C 463 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00282 (17738) covalent geometry : angle 0.55849 (24234) hydrogen bonds : bond 0.03014 ( 586) hydrogen bonds : angle 5.03372 ( 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 550 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 468 time to evaluate : 0.681 Fit side-chains REVERT: C 48 TRP cc_start: 0.8510 (m100) cc_final: 0.8243 (m100) REVERT: C 95 ASP cc_start: 0.7623 (t0) cc_final: 0.7407 (t0) REVERT: C 192 ARG cc_start: 0.8304 (ttt90) cc_final: 0.8072 (ttt90) REVERT: C 206 THR cc_start: 0.8102 (t) cc_final: 0.7876 (m) REVERT: C 290 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7759 (pt0) REVERT: C 415 ASN cc_start: 0.8068 (p0) cc_final: 0.7867 (p0) REVERT: C 445 SER cc_start: 0.8359 (t) cc_final: 0.8070 (m) REVERT: D 102 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7678 (mmt180) REVERT: D 143 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.6656 (ttt-90) REVERT: D 206 THR cc_start: 0.8012 (t) cc_final: 0.7796 (m) REVERT: A 95 ASP cc_start: 0.7693 (t0) cc_final: 0.7463 (t0) REVERT: A 155 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7804 (p0) REVERT: A 192 ARG cc_start: 0.8351 (ttt90) cc_final: 0.8091 (ttt90) REVERT: A 206 THR cc_start: 0.8186 (t) cc_final: 0.7923 (m) REVERT: A 238 LEU cc_start: 0.7965 (mt) cc_final: 0.7721 (mp) REVERT: A 407 SER cc_start: 0.8440 (p) cc_final: 0.8234 (m) REVERT: A 497 SER cc_start: 0.7999 (p) cc_final: 0.7755 (p) REVERT: A 507 PHE cc_start: 0.8310 (m-10) cc_final: 0.8039 (m-80) REVERT: B 152 ASN cc_start: 0.8412 (p0) cc_final: 0.8151 (p0) REVERT: B 206 THR cc_start: 0.8132 (t) cc_final: 0.7803 (m) REVERT: B 322 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6898 (mt-10) REVERT: B 507 PHE cc_start: 0.8180 (m-80) cc_final: 0.7815 (m-80) outliers start: 82 outliers final: 44 residues processed: 503 average time/residue: 0.5110 time to fit residues: 290.0537 Evaluate side-chains 502 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 455 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 256 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP 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 28 THR Chi-restraints excluded: chain D residue 58 VAL 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 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 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 508 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 28 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 256 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER 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 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 498 ASP 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: 2.9990 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 202 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 ASN D 403 HIS B 403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108223 restraints weight = 23915.516| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.70 r_work: 0.3420 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1548 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= 0.201 Angle : 0.611 8.380 24234 Z= 0.312 Chirality : 0.047 0.187 2460 Planarity : 0.005 0.048 3155 Dihedral : 4.725 32.896 2374 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 5.21 % Allowed : 22.28 % Favored : 72.50 % 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 aren not related in a simple way. whole: -0.27 (0.18), residues: 2119 helix: -3.49 (0.53), residues: 36 sheet: 1.23 (0.19), residues: 757 loop : -1.00 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 474 TYR 0.022 0.002 TYR D 413 PHE 0.028 0.002 PHE D 507 TRP 0.013 0.001 TRP C 463 HIS 0.008 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00497 (17738) covalent geometry : angle 0.61105 (24234) hydrogen bonds : bond 0.03364 ( 586) hydrogen bonds : angle 4.96551 ( 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 570 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 475 time to evaluate : 0.623 Fit side-chains REVERT: C 48 TRP cc_start: 0.8524 (m100) cc_final: 0.8205 (m100) REVERT: C 95 ASP cc_start: 0.7584 (t0) cc_final: 0.7376 (t0) REVERT: C 445 SER cc_start: 0.8354 (t) cc_final: 0.8085 (m) REVERT: D 143 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.6812 (ttt-90) REVERT: D 438 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: A 57 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7804 (mtm180) REVERT: A 86 LEU cc_start: 0.8359 (tp) cc_final: 0.8153 (tt) REVERT: A 95 ASP cc_start: 0.7713 (t0) cc_final: 0.7478 (t0) REVERT: A 143 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.6395 (ttt-90) REVERT: A 155 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7824 (p0) REVERT: A 192 ARG cc_start: 0.8364 (ttt90) cc_final: 0.8012 (ttt90) REVERT: A 206 THR cc_start: 0.8189 (t) cc_final: 0.7973 (m) REVERT: A 407 SER cc_start: 0.8472 (p) cc_final: 0.8271 (m) REVERT: A 438 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: A 497 SER cc_start: 0.8013 (p) cc_final: 0.7760 (p) REVERT: A 507 PHE cc_start: 0.8330 (m-10) cc_final: 0.8072 (m-80) REVERT: B 152 ASN cc_start: 0.8449 (p0) cc_final: 0.8187 (p0) REVERT: B 206 THR cc_start: 0.8077 (t) cc_final: 0.7861 (m) REVERT: B 507 PHE cc_start: 0.8209 (m-80) cc_final: 0.7841 (m-80) outliers start: 95 outliers final: 57 residues processed: 515 average time/residue: 0.4882 time to fit residues: 283.7753 Evaluate side-chains 526 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 464 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 215 LEU 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 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 407 SER 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 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 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 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 190 LEU Chi-restraints excluded: chain B residue 200 MET 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: 0.0770 chunk 98 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 0.0270 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 ASN D 403 HIS 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 = 0.3653 r_free = 0.3653 target = 0.118660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109290 restraints weight = 23980.170| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.70 r_work: 0.3441 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17738 Z= 0.112 Angle : 0.557 6.881 24234 Z= 0.288 Chirality : 0.044 0.180 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.505 33.285 2374 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.82 % Favored : 95.99 % Rotamer: Outliers : 4.67 % Allowed : 22.83 % Favored : 72.50 % 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 aren not related in a simple way. whole: -0.19 (0.19), residues: 2119 helix: -3.24 (0.61), residues: 36 sheet: 1.25 (0.19), residues: 771 loop : -0.94 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 474 TYR 0.026 0.001 TYR D 413 PHE 0.030 0.001 PHE D 507 TRP 0.010 0.001 TRP C 463 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00275 (17738) covalent geometry : angle 0.55661 (24234) hydrogen bonds : bond 0.02854 ( 586) hydrogen bonds : angle 4.79646 ( 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 563 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 478 time to evaluate : 0.605 Fit side-chains REVERT: C 4 THR cc_start: 0.8245 (m) cc_final: 0.8038 (p) REVERT: C 48 TRP cc_start: 0.8501 (m100) cc_final: 0.8212 (m100) REVERT: C 106 VAL cc_start: 0.7978 (t) cc_final: 0.7655 (m) REVERT: C 445 SER cc_start: 0.8362 (t) cc_final: 0.8095 (m) REVERT: D 143 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8198 (ttt180) REVERT: D 438 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: A 86 LEU cc_start: 0.8349 (tp) cc_final: 0.8140 (tt) REVERT: A 95 ASP cc_start: 0.7707 (t0) cc_final: 0.7477 (t0) REVERT: A 143 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7233 (ttt-90) REVERT: A 206 THR cc_start: 0.8147 (t) cc_final: 0.7937 (m) REVERT: A 238 LEU cc_start: 0.7919 (mt) cc_final: 0.7686 (mt) REVERT: A 250 SER cc_start: 0.8258 (t) cc_final: 0.8053 (m) REVERT: A 407 SER cc_start: 0.8426 (p) cc_final: 0.8222 (m) REVERT: A 497 SER cc_start: 0.8073 (p) cc_final: 0.7807 (p) REVERT: A 507 PHE cc_start: 0.8326 (m-10) cc_final: 0.8064 (m-80) REVERT: B 152 ASN cc_start: 0.8406 (p0) cc_final: 0.8151 (p0) REVERT: B 507 PHE cc_start: 0.8178 (m-80) cc_final: 0.7848 (m-80) outliers start: 85 outliers final: 50 residues processed: 513 average time/residue: 0.5067 time to fit residues: 294.1534 Evaluate side-chains 516 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 463 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 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 443 VAL 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 58 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 285 CYS 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 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 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 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 349 ILE Chi-restraints excluded: chain A residue 372 SER 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 200 MET 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 Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 153 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 ASN D 403 HIS A 100 ASN A 155 ASN B 155 ASN B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.109009 restraints weight = 23870.380| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.70 r_work: 0.3439 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17738 Z= 0.137 Angle : 0.582 7.222 24234 Z= 0.299 Chirality : 0.045 0.205 2460 Planarity : 0.005 0.045 3155 Dihedral : 4.375 18.956 2370 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.61 % Rotamer: Outliers : 4.50 % Allowed : 23.66 % Favored : 71.84 % 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 aren not related in a simple way. whole: -0.16 (0.18), residues: 2119 helix: -3.05 (0.65), residues: 36 sheet: 1.30 (0.19), residues: 762 loop : -0.93 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 474 TYR 0.026 0.001 TYR D 413 PHE 0.066 0.002 PHE D 507 TRP 0.012 0.001 TRP B 48 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00339 (17738) covalent geometry : angle 0.58231 (24234) hydrogen bonds : bond 0.02923 ( 586) hydrogen bonds : angle 4.76612 ( 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 558 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 476 time to evaluate : 0.688 Fit side-chains REVERT: C 48 TRP cc_start: 0.8506 (m100) cc_final: 0.8225 (m100) REVERT: C 445 SER cc_start: 0.8367 (t) cc_final: 0.8101 (m) REVERT: D 95 ASP cc_start: 0.7751 (t0) cc_final: 0.7481 (t0) REVERT: D 143 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8195 (ttt180) REVERT: D 438 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: A 57 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7760 (mtm180) REVERT: A 86 LEU cc_start: 0.8351 (tp) cc_final: 0.8143 (tt) REVERT: A 95 ASP cc_start: 0.7714 (t0) cc_final: 0.7497 (t0) REVERT: A 143 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7267 (ttt-90) REVERT: A 192 ARG cc_start: 0.8383 (ttt90) cc_final: 0.8111 (ttt90) REVERT: A 206 THR cc_start: 0.8139 (t) cc_final: 0.7938 (m) REVERT: A 238 LEU cc_start: 0.7941 (mt) cc_final: 0.7704 (mt) REVERT: A 250 SER cc_start: 0.8263 (t) cc_final: 0.8044 (m) REVERT: A 438 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: A 497 SER cc_start: 0.8060 (p) cc_final: 0.7813 (p) REVERT: A 507 PHE cc_start: 0.8326 (m-10) cc_final: 0.8098 (m-80) REVERT: B 44 ASP cc_start: 0.7938 (p0) cc_final: 0.7733 (p0) REVERT: B 152 ASN cc_start: 0.8417 (p0) cc_final: 0.8184 (p0) REVERT: B 507 PHE cc_start: 0.8173 (m-80) cc_final: 0.7816 (m-80) outliers start: 82 outliers final: 56 residues processed: 510 average time/residue: 0.4670 time to fit residues: 269.6149 Evaluate side-chains 528 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 468 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR 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 256 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 443 VAL 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 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 215 LEU Chi-restraints excluded: chain D residue 285 CYS 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 28 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 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 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 58 VAL 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 359 THR 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: 0.2980 chunk 1 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 ASN D 403 HIS A 155 ASN 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 = 0.3653 r_free = 0.3653 target = 0.118540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109096 restraints weight = 24025.605| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.72 r_work: 0.3439 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17738 Z= 0.128 Angle : 0.567 7.337 24234 Z= 0.293 Chirality : 0.045 0.199 2460 Planarity : 0.005 0.045 3155 Dihedral : 4.339 18.478 2370 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.61 % Rotamer: Outliers : 4.56 % Allowed : 23.87 % Favored : 71.57 % 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 aren not related in a simple way. whole: -0.14 (0.18), residues: 2119 helix: -2.52 (0.74), residues: 30 sheet: 1.31 (0.19), residues: 766 loop : -0.95 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 474 TYR 0.027 0.001 TYR D 413 PHE 0.055 0.001 PHE D 507 TRP 0.015 0.001 TRP B 48 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00316 (17738) covalent geometry : angle 0.56678 (24234) hydrogen bonds : bond 0.02864 ( 586) hydrogen bonds : angle 4.71863 ( 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 560 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 477 time to evaluate : 0.402 Fit side-chains REVERT: C 48 TRP cc_start: 0.8501 (m100) cc_final: 0.8236 (m100) REVERT: C 445 SER cc_start: 0.8375 (t) cc_final: 0.8114 (m) REVERT: D 95 ASP cc_start: 0.7777 (t0) cc_final: 0.7496 (t0) REVERT: D 143 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8196 (ttt180) REVERT: D 185 THR cc_start: 0.8084 (t) cc_final: 0.7857 (m) REVERT: D 438 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: A 86 LEU cc_start: 0.8365 (tp) cc_final: 0.8154 (tt) REVERT: A 143 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7267 (ttt-90) REVERT: A 192 ARG cc_start: 0.8369 (ttt90) cc_final: 0.8089 (ttt90) REVERT: A 250 SER cc_start: 0.8248 (t) cc_final: 0.8040 (m) REVERT: A 438 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: A 497 SER cc_start: 0.8086 (p) cc_final: 0.7841 (p) REVERT: A 507 PHE cc_start: 0.8324 (m-10) cc_final: 0.8101 (m-80) REVERT: B 44 ASP cc_start: 0.7938 (p0) cc_final: 0.7610 (p0) REVERT: B 152 ASN cc_start: 0.8432 (p0) cc_final: 0.8204 (p0) REVERT: B 507 PHE cc_start: 0.8138 (m-80) cc_final: 0.7810 (m-80) outliers start: 83 outliers final: 58 residues processed: 514 average time/residue: 0.4496 time to fit residues: 261.0515 Evaluate side-chains 528 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 466 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR 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 256 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 512 VAL 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 143 ARG Chi-restraints excluded: chain D residue 155 ASN 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 285 CYS 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 508 THR Chi-restraints excluded: chain A residue 28 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 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 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 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 200 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 359 THR 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: 2.9990 chunk 42 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.0060 chunk 121 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN D 155 ASN D 403 HIS A 155 ASN B 155 ASN B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108061 restraints weight = 24114.234| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.72 r_work: 0.3424 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17738 Z= 0.202 Angle : 0.624 7.905 24234 Z= 0.319 Chirality : 0.047 0.209 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.519 18.494 2370 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.48 % Favored : 95.28 % Rotamer: Outliers : 4.83 % Allowed : 24.20 % Favored : 70.97 % 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 aren not related in a simple way. whole: -0.20 (0.18), residues: 2119 helix: -3.00 (0.63), residues: 36 sheet: 1.32 (0.19), residues: 760 loop : -1.00 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 474 TYR 0.023 0.002 TYR D 413 PHE 0.060 0.002 PHE D 507 TRP 0.022 0.002 TRP B 48 HIS 0.008 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00499 (17738) covalent geometry : angle 0.62373 (24234) hydrogen bonds : bond 0.03250 ( 586) hydrogen bonds : angle 4.81645 ( 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 565 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 477 time to evaluate : 0.651 Fit side-chains REVERT: C 32 GLU cc_start: 0.7818 (pm20) cc_final: 0.7593 (pm20) REVERT: C 106 VAL cc_start: 0.8093 (t) cc_final: 0.7823 (m) REVERT: C 290 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 445 SER cc_start: 0.8395 (t) cc_final: 0.8138 (m) REVERT: D 95 ASP cc_start: 0.7802 (t0) cc_final: 0.7528 (t0) REVERT: D 143 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8164 (ttt180) REVERT: D 185 THR cc_start: 0.8113 (t) cc_final: 0.7803 (m) REVERT: D 438 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: A 86 LEU cc_start: 0.8365 (tp) cc_final: 0.8144 (tt) REVERT: A 142 TYR cc_start: 0.8382 (p90) cc_final: 0.8138 (p90) REVERT: A 143 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.6609 (ttt-90) REVERT: A 192 ARG cc_start: 0.8381 (ttt90) cc_final: 0.8075 (ttt90) REVERT: A 238 LEU cc_start: 0.7937 (mt) cc_final: 0.7722 (mt) REVERT: A 497 SER cc_start: 0.8056 (p) cc_final: 0.7806 (p) REVERT: A 507 PHE cc_start: 0.8302 (m-10) cc_final: 0.8101 (m-80) REVERT: B 152 ASN cc_start: 0.8455 (p0) cc_final: 0.8194 (p0) REVERT: B 507 PHE cc_start: 0.8149 (m-80) cc_final: 0.7832 (m-80) outliers start: 88 outliers final: 64 residues processed: 515 average time/residue: 0.4682 time to fit residues: 272.4764 Evaluate side-chains 538 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 471 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 166 THR Chi-restraints excluded: chain C residue 256 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 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 155 ASN 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 285 CYS 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 407 SER 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 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 428 GLU 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 58 VAL Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 359 THR 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 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: 2.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 145 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN D 12 ASN D 403 HIS A 155 ASN B 155 ASN B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109005 restraints weight = 23848.529| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.69 r_work: 0.3440 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17738 Z= 0.141 Angle : 0.591 7.463 24234 Z= 0.304 Chirality : 0.045 0.197 2460 Planarity : 0.005 0.047 3155 Dihedral : 4.444 18.340 2370 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.06 % Favored : 95.71 % Rotamer: Outliers : 4.01 % Allowed : 25.80 % Favored : 70.20 % 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 aren not related in a simple way. whole: -0.18 (0.18), residues: 2119 helix: -2.70 (0.70), residues: 30 sheet: 1.28 (0.19), residues: 770 loop : -0.98 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 57 TYR 0.028 0.002 TYR D 413 PHE 0.061 0.002 PHE D 507 TRP 0.022 0.001 TRP B 48 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00345 (17738) covalent geometry : angle 0.59059 (24234) hydrogen bonds : bond 0.02965 ( 586) hydrogen bonds : angle 4.75766 ( 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 549 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 476 time to evaluate : 0.677 Fit side-chains REVERT: C 32 GLU cc_start: 0.7799 (pm20) cc_final: 0.7540 (pm20) REVERT: C 106 VAL cc_start: 0.8087 (t) cc_final: 0.7803 (m) REVERT: C 107 THR cc_start: 0.8185 (p) cc_final: 0.7969 (t) REVERT: C 290 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7629 (mt-10) REVERT: C 445 SER cc_start: 0.8380 (t) cc_final: 0.8136 (m) REVERT: C 497 SER cc_start: 0.8084 (p) cc_final: 0.7837 (p) REVERT: D 95 ASP cc_start: 0.7800 (t0) cc_final: 0.7557 (t0) REVERT: D 143 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8186 (ttt180) REVERT: D 185 THR cc_start: 0.8114 (t) cc_final: 0.7903 (m) REVERT: D 438 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: A 57 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7782 (mtm-85) REVERT: A 142 TYR cc_start: 0.8388 (p90) cc_final: 0.8142 (p90) REVERT: A 143 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7335 (ttt-90) REVERT: A 192 ARG cc_start: 0.8369 (ttt90) cc_final: 0.8100 (ttt90) REVERT: A 497 SER cc_start: 0.8076 (p) cc_final: 0.7828 (p) REVERT: B 152 ASN cc_start: 0.8429 (p0) cc_final: 0.8127 (p0) REVERT: B 507 PHE cc_start: 0.8117 (m-80) cc_final: 0.7796 (m-80) outliers start: 73 outliers final: 59 residues processed: 507 average time/residue: 0.4651 time to fit residues: 267.2215 Evaluate side-chains 530 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 468 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 166 THR Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 256 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 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL 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 285 CYS 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 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 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 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 428 GLU 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 58 VAL Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 359 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 142 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 181 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN D 155 ASN D 312 GLN D 403 HIS ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109110 restraints weight = 23999.392| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.70 r_work: 0.3442 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17738 Z= 0.136 Angle : 0.586 8.124 24234 Z= 0.302 Chirality : 0.045 0.190 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.400 18.248 2370 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.06 % Favored : 95.71 % Rotamer: Outliers : 4.06 % Allowed : 25.80 % Favored : 70.14 % 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 aren not related in a simple way. whole: -0.16 (0.18), residues: 2119 helix: -2.12 (0.82), residues: 24 sheet: 1.25 (0.19), residues: 785 loop : -0.99 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 57 TYR 0.027 0.001 TYR D 413 PHE 0.031 0.001 PHE D 506 TRP 0.025 0.001 TRP B 48 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00333 (17738) covalent geometry : angle 0.58639 (24234) hydrogen bonds : bond 0.02907 ( 586) hydrogen bonds : angle 4.72991 ( 1980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6116.71 seconds wall clock time: 104 minutes 58.15 seconds (6298.15 seconds total)