Starting phenix.real_space_refine on Sun May 18 15:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uws_42680/05_2025/8uws_42680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uws_42680/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uws_42680/05_2025/8uws_42680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uws_42680/05_2025/8uws_42680.map" model { file = "/net/cci-nas-00/data/ceres_data/8uws_42680/05_2025/8uws_42680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uws_42680/05_2025/8uws_42680.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 4} 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: 10.40, per 1000 atoms: 0.61 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: 3.90 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.97 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: 6.79 Time building geometry restraints manager: 4.67 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 536 or resid 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 536 or resid 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 536 or resid 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 536 or resid 60 \ 1)) } 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: 6.030 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.500 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.510 ------------------------------------------------------------------------------- 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 : 6.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.002 TRP B 48 HIS 0.010 0.001 HIS C 227 PHE 0.034 0.002 PHE B 506 TYR 0.021 0.002 TYR B 79 ARG 0.010 0.001 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.20156 ( 586) hydrogen bonds : angle 8.43647 ( 1980) covalent geometry : bond 0.00517 (17738) covalent geometry : angle 0.72764 (24234) *********************** 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 : 1.809 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: 0.7912 (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: 1.1599 time to fit residues: 683.1203 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 : 1.841 ------------------------------------------------------------------------------- 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 179 optimal weight: 0.4980 chunk 160 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 64 optimal weight: 0.0770 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 B 160 GLN B 323 GLN B 403 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110325 restraints weight = 23792.046| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.69 r_work: 0.3456 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17738 Z= 0.132 Angle : 0.584 6.410 24234 Z= 0.304 Chirality : 0.045 0.160 2460 Planarity : 0.005 0.061 3155 Dihedral : 5.875 56.576 2415 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.01 % Favored : 95.80 % Rotamer: Outliers : 4.06 % Allowed : 21.51 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2119 helix: -3.65 (0.60), residues: 36 sheet: 0.98 (0.19), residues: 741 loop : -0.98 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 419 HIS 0.007 0.001 HIS B 403 PHE 0.012 0.001 PHE B 506 TYR 0.022 0.001 TYR D 413 ARG 0.006 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 586) hydrogen bonds : angle 5.63585 ( 1980) covalent geometry : bond 0.00311 (17738) covalent geometry : angle 0.58355 (24234) *********************** 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 552 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 478 time to evaluate : 1.914 Fit side-chains REVERT: C 64 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7995 (tttp) REVERT: C 206 THR cc_start: 0.8230 (t) cc_final: 0.7940 (m) REVERT: C 533 TYR cc_start: 0.8510 (t80) cc_final: 0.8290 (t80) REVERT: D 206 THR cc_start: 0.8135 (t) cc_final: 0.7744 (m) REVERT: A 155 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7888 (p0) REVERT: A 250 SER cc_start: 0.8320 (t) cc_final: 0.8118 (m) REVERT: A 297 GLU cc_start: 0.7550 (pt0) cc_final: 0.7316 (pt0) REVERT: A 497 SER cc_start: 0.8109 (p) cc_final: 0.7753 (p) REVERT: A 507 PHE cc_start: 0.8239 (m-10) cc_final: 0.7949 (m-80) REVERT: B 32 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: B 44 ASP cc_start: 0.7948 (p0) cc_final: 0.7732 (p0) REVERT: B 63 MET cc_start: 0.7896 (mtm) cc_final: 0.7685 (mtm) REVERT: B 152 ASN cc_start: 0.8436 (p0) cc_final: 0.8226 (p0) REVERT: B 507 PHE cc_start: 0.8126 (m-80) cc_final: 0.7814 (m-80) outliers start: 74 outliers final: 33 residues processed: 508 average time/residue: 1.1079 time to fit residues: 636.2795 Evaluate side-chains 488 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 452 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 336 ASP 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 26 ILE 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 315 VAL Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 32 GLU 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 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 188 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 189 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN D 155 ASN D 312 GLN D 379 GLN D 515 HIS ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.118249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108911 restraints weight = 23928.548| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.70 r_work: 0.3438 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17738 Z= 0.132 Angle : 0.568 6.896 24234 Z= 0.293 Chirality : 0.045 0.172 2460 Planarity : 0.005 0.050 3155 Dihedral : 4.768 33.202 2380 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.92 % Favored : 95.89 % Rotamer: Outliers : 4.61 % Allowed : 22.01 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2119 helix: -3.72 (0.54), residues: 36 sheet: 1.11 (0.19), residues: 748 loop : -0.95 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 48 HIS 0.007 0.001 HIS B 403 PHE 0.015 0.001 PHE A 391 TYR 0.023 0.001 TYR B 413 ARG 0.006 0.000 ARG B 192 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 586) hydrogen bonds : angle 5.22339 ( 1980) covalent geometry : bond 0.00325 (17738) covalent geometry : angle 0.56826 (24234) *********************** 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 541 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 457 time to evaluate : 1.898 Fit side-chains REVERT: C 44 ASP cc_start: 0.7969 (p0) cc_final: 0.7724 (p0) REVERT: C 48 TRP cc_start: 0.8519 (m100) cc_final: 0.8211 (m100) REVERT: C 64 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7920 (tttp) REVERT: C 95 ASP cc_start: 0.7564 (t0) cc_final: 0.7350 (t0) REVERT: C 445 SER cc_start: 0.8344 (t) cc_final: 0.8046 (m) REVERT: D 69 SER cc_start: 0.8219 (t) cc_final: 0.7991 (t) REVERT: D 206 THR cc_start: 0.8082 (t) cc_final: 0.7827 (m) REVERT: D 438 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: A 95 ASP cc_start: 0.7647 (t0) cc_final: 0.7389 (t0) REVERT: A 155 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7870 (p0) REVERT: A 206 THR cc_start: 0.8210 (t) cc_final: 0.7895 (m) REVERT: A 238 LEU cc_start: 0.7940 (mt) cc_final: 0.7725 (mt) REVERT: A 297 GLU cc_start: 0.7548 (pt0) cc_final: 0.7347 (pt0) REVERT: A 319 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7775 (mm-40) REVERT: A 497 SER cc_start: 0.8039 (p) cc_final: 0.7623 (p) REVERT: A 507 PHE cc_start: 0.8275 (m-10) cc_final: 0.8037 (m-80) REVERT: B 46 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.7021 (ttpt) REVERT: B 152 ASN cc_start: 0.8409 (p0) cc_final: 0.8175 (p0) REVERT: B 206 THR cc_start: 0.8164 (t) cc_final: 0.7758 (m) REVERT: B 322 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6875 (mt-10) REVERT: B 507 PHE cc_start: 0.8168 (m-10) cc_final: 0.7840 (m-80) outliers start: 84 outliers final: 49 residues processed: 493 average time/residue: 1.0812 time to fit residues: 603.8261 Evaluate side-chains 499 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 446 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 349 ILE 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 2 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 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 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 517 GLU 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 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 446 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 55 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN D 155 ASN ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 323 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.117135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.107687 restraints weight = 23937.029| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.71 r_work: 0.3420 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17738 Z= 0.205 Angle : 0.615 9.032 24234 Z= 0.314 Chirality : 0.047 0.194 2460 Planarity : 0.005 0.050 3155 Dihedral : 4.872 33.408 2379 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.25 % Favored : 95.56 % Rotamer: Outliers : 5.10 % Allowed : 21.62 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2119 helix: -3.82 (0.44), residues: 36 sheet: 1.19 (0.19), residues: 756 loop : -1.00 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 463 HIS 0.008 0.001 HIS B 403 PHE 0.013 0.002 PHE A 423 TYR 0.020 0.002 TYR D 413 ARG 0.005 0.001 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 586) hydrogen bonds : angle 5.08402 ( 1980) covalent geometry : bond 0.00508 (17738) covalent geometry : angle 0.61506 (24234) *********************** 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 559 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 466 time to evaluate : 1.939 Fit side-chains REVERT: C 44 ASP cc_start: 0.7958 (p0) cc_final: 0.7724 (p0) REVERT: C 48 TRP cc_start: 0.8526 (m100) cc_final: 0.8245 (m100) REVERT: C 95 ASP cc_start: 0.7610 (t0) cc_final: 0.7394 (t0) REVERT: C 206 THR cc_start: 0.8176 (t) cc_final: 0.7901 (m) REVERT: C 445 SER cc_start: 0.8361 (t) cc_final: 0.8082 (m) REVERT: D 69 SER cc_start: 0.8200 (t) cc_final: 0.7873 (t) REVERT: D 438 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: D 507 PHE cc_start: 0.8257 (m-10) cc_final: 0.7810 (m-80) REVERT: A 57 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7820 (mtm180) REVERT: A 86 LEU cc_start: 0.8361 (tp) cc_final: 0.8156 (tt) REVERT: A 95 ASP cc_start: 0.7673 (t0) cc_final: 0.7408 (t0) REVERT: A 155 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7809 (p0) REVERT: A 206 THR cc_start: 0.8199 (t) cc_final: 0.7953 (m) REVERT: A 297 GLU cc_start: 0.7600 (pt0) cc_final: 0.7399 (pt0) REVERT: A 407 SER cc_start: 0.8480 (p) cc_final: 0.8260 (m) REVERT: A 497 SER cc_start: 0.8025 (p) cc_final: 0.7781 (p) REVERT: A 507 PHE cc_start: 0.8305 (m-10) cc_final: 0.8029 (m-80) REVERT: B 152 ASN cc_start: 0.8462 (p0) cc_final: 0.8214 (p0) REVERT: B 206 THR cc_start: 0.8111 (t) cc_final: 0.7854 (m) REVERT: B 322 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6873 (mt-10) REVERT: B 507 PHE cc_start: 0.8190 (m-80) cc_final: 0.7856 (m-80) outliers start: 93 outliers final: 56 residues processed: 506 average time/residue: 1.1063 time to fit residues: 633.4944 Evaluate side-chains 502 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 444 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 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 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 417 LYS 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 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 347 LEU 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 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 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 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 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 60 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN D 155 ASN D 379 GLN D 515 HIS A 100 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.117669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108218 restraints weight = 24061.358| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.72 r_work: 0.3426 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17738 Z= 0.153 Angle : 0.579 7.933 24234 Z= 0.297 Chirality : 0.045 0.184 2460 Planarity : 0.005 0.048 3155 Dihedral : 4.719 33.169 2376 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.96 % Favored : 95.85 % Rotamer: Outliers : 4.72 % Allowed : 22.28 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2119 helix: -3.39 (0.53), residues: 36 sheet: 1.25 (0.19), residues: 756 loop : -0.95 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 463 HIS 0.007 0.001 HIS B 403 PHE 0.021 0.002 PHE D 506 TYR 0.024 0.001 TYR D 413 ARG 0.009 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 586) hydrogen bonds : angle 4.92606 ( 1980) covalent geometry : bond 0.00379 (17738) covalent geometry : angle 0.57876 (24234) *********************** 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 557 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 471 time to evaluate : 2.110 Fit side-chains REVERT: C 48 TRP cc_start: 0.8509 (m100) cc_final: 0.8201 (m100) REVERT: C 95 ASP cc_start: 0.7580 (t0) cc_final: 0.7355 (t0) REVERT: C 206 THR cc_start: 0.8133 (t) cc_final: 0.7884 (m) REVERT: C 445 SER cc_start: 0.8358 (t) cc_final: 0.8091 (m) REVERT: D 69 SER cc_start: 0.8220 (t) cc_final: 0.8015 (t) REVERT: D 95 ASP cc_start: 0.7749 (t0) cc_final: 0.7512 (t0) REVERT: D 143 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8174 (ttt180) REVERT: D 438 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: A 86 LEU cc_start: 0.8358 (tp) cc_final: 0.8152 (tt) REVERT: A 95 ASP cc_start: 0.7701 (t0) cc_final: 0.7434 (t0) REVERT: A 155 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7778 (p0) REVERT: A 206 THR cc_start: 0.8189 (t) cc_final: 0.7968 (m) REVERT: A 407 SER cc_start: 0.8455 (p) cc_final: 0.8243 (m) REVERT: A 497 SER cc_start: 0.8015 (p) cc_final: 0.7770 (p) REVERT: A 507 PHE cc_start: 0.8322 (m-10) cc_final: 0.8062 (m-80) REVERT: B 152 ASN cc_start: 0.8431 (p0) cc_final: 0.8178 (p0) REVERT: B 507 PHE cc_start: 0.8192 (m-80) cc_final: 0.7837 (m-80) outliers start: 86 outliers final: 55 residues processed: 504 average time/residue: 1.1314 time to fit residues: 644.4326 Evaluate side-chains 522 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 464 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 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 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 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 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 128 optimal weight: 0.0770 chunk 152 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN D 155 ASN D 403 HIS A 100 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.117662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108258 restraints weight = 24048.840| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.71 r_work: 0.3429 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17738 Z= 0.162 Angle : 0.584 7.854 24234 Z= 0.299 Chirality : 0.046 0.185 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.698 33.064 2376 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.15 % Favored : 95.66 % Rotamer: Outliers : 4.83 % Allowed : 22.94 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2119 helix: -3.16 (0.60), residues: 36 sheet: 1.26 (0.19), residues: 752 loop : -0.94 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 48 HIS 0.007 0.001 HIS D 403 PHE 0.023 0.002 PHE D 506 TYR 0.023 0.002 TYR D 413 ARG 0.008 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 586) hydrogen bonds : angle 4.87227 ( 1980) covalent geometry : bond 0.00402 (17738) covalent geometry : angle 0.58361 (24234) *********************** 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 553 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 465 time to evaluate : 1.816 Fit side-chains REVERT: C 48 TRP cc_start: 0.8512 (m100) cc_final: 0.8211 (m100) REVERT: C 206 THR cc_start: 0.8102 (t) cc_final: 0.7879 (m) REVERT: C 445 SER cc_start: 0.8362 (t) cc_final: 0.8095 (m) REVERT: D 69 SER cc_start: 0.8245 (t) cc_final: 0.7881 (t) REVERT: D 95 ASP cc_start: 0.7785 (t0) cc_final: 0.7530 (t0) REVERT: D 143 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8161 (ttt180) REVERT: D 438 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: A 86 LEU cc_start: 0.8367 (tp) cc_final: 0.8163 (tt) REVERT: A 95 ASP cc_start: 0.7681 (t0) cc_final: 0.7416 (t0) REVERT: A 143 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6581 (ttt-90) REVERT: A 155 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7801 (p0) REVERT: A 192 ARG cc_start: 0.8356 (ttt90) cc_final: 0.8049 (ttt90) REVERT: A 206 THR cc_start: 0.8174 (t) cc_final: 0.7966 (m) REVERT: A 407 SER cc_start: 0.8442 (p) cc_final: 0.8222 (m) REVERT: A 438 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 497 SER cc_start: 0.8085 (p) cc_final: 0.7822 (p) REVERT: A 507 PHE cc_start: 0.8315 (m-10) cc_final: 0.8062 (m-80) REVERT: B 152 ASN cc_start: 0.8439 (p0) cc_final: 0.8143 (p0) REVERT: B 209 GLU cc_start: 0.7746 (mp0) cc_final: 0.7487 (mp0) REVERT: B 507 PHE cc_start: 0.8156 (m-80) cc_final: 0.7840 (m-80) outliers start: 88 outliers final: 60 residues processed: 500 average time/residue: 1.0867 time to fit residues: 614.3565 Evaluate side-chains 522 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 457 time to evaluate : 1.921 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 9 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 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 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 256 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 517 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 110 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN D 155 ASN D 403 HIS ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108664 restraints weight = 23945.711| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.71 r_work: 0.3434 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17738 Z= 0.140 Angle : 0.577 7.339 24234 Z= 0.298 Chirality : 0.045 0.179 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.637 33.105 2376 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 4.12 % Allowed : 23.66 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2119 helix: -3.07 (0.62), residues: 36 sheet: 1.26 (0.19), residues: 762 loop : -0.94 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 48 HIS 0.007 0.001 HIS B 403 PHE 0.051 0.002 PHE D 507 TYR 0.025 0.001 TYR D 413 ARG 0.009 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 586) hydrogen bonds : angle 4.80790 ( 1980) covalent geometry : bond 0.00347 (17738) covalent geometry : angle 0.57738 (24234) *********************** 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 545 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 470 time to evaluate : 1.766 Fit side-chains REVERT: C 4 THR cc_start: 0.8269 (m) cc_final: 0.8063 (p) REVERT: C 206 THR cc_start: 0.8083 (t) cc_final: 0.7870 (m) REVERT: C 265 THR cc_start: 0.7843 (t) cc_final: 0.7641 (t) REVERT: C 373 LEU cc_start: 0.8259 (mt) cc_final: 0.7981 (mp) REVERT: C 445 SER cc_start: 0.8359 (t) cc_final: 0.8089 (m) REVERT: D 95 ASP cc_start: 0.7790 (t0) cc_final: 0.7521 (t0) REVERT: D 143 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8200 (ttt180) REVERT: A 86 LEU cc_start: 0.8367 (tp) cc_final: 0.8157 (tt) REVERT: A 95 ASP cc_start: 0.7710 (t0) cc_final: 0.7445 (t0) REVERT: A 143 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.6820 (ttt-90) REVERT: A 155 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7790 (p0) REVERT: A 192 ARG cc_start: 0.8343 (ttt90) cc_final: 0.8037 (ttt90) REVERT: A 206 THR cc_start: 0.8170 (t) cc_final: 0.7962 (m) REVERT: A 238 LEU cc_start: 0.7953 (mt) cc_final: 0.7718 (mt) REVERT: A 407 SER cc_start: 0.8457 (p) cc_final: 0.8240 (m) REVERT: A 497 SER cc_start: 0.8084 (p) cc_final: 0.7822 (p) REVERT: A 507 PHE cc_start: 0.8332 (m-10) cc_final: 0.8080 (m-80) REVERT: B 152 ASN cc_start: 0.8438 (p0) cc_final: 0.8186 (p0) REVERT: B 209 GLU cc_start: 0.7745 (mp0) cc_final: 0.7474 (mp0) REVERT: B 507 PHE cc_start: 0.8143 (m-80) cc_final: 0.7824 (m-80) outliers start: 75 outliers final: 53 residues processed: 498 average time/residue: 1.1195 time to fit residues: 631.5041 Evaluate side-chains 517 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 461 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 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 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 9 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 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR 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 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 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 498 ASP 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 372 SER Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 146 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN D 12 ASN D 155 ASN D 403 HIS A 100 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.117760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.108415 restraints weight = 23944.799| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.70 r_work: 0.3426 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17738 Z= 0.182 Angle : 0.603 7.792 24234 Z= 0.309 Chirality : 0.046 0.190 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.723 32.911 2376 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.25 % Favored : 95.56 % Rotamer: Outliers : 4.50 % Allowed : 24.20 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2119 helix: -3.01 (0.61), residues: 36 sheet: 1.28 (0.19), residues: 757 loop : -0.96 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 48 HIS 0.008 0.001 HIS B 403 PHE 0.043 0.002 PHE D 507 TYR 0.023 0.002 TYR D 413 ARG 0.009 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 586) hydrogen bonds : angle 4.84552 ( 1980) covalent geometry : bond 0.00447 (17738) covalent geometry : angle 0.60300 (24234) *********************** 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 558 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 476 time to evaluate : 1.998 Fit side-chains REVERT: C 344 LEU cc_start: 0.8382 (mp) cc_final: 0.8160 (mp) REVERT: C 445 SER cc_start: 0.8353 (t) cc_final: 0.8094 (m) REVERT: D 95 ASP cc_start: 0.7793 (t0) cc_final: 0.7520 (t0) REVERT: D 143 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8179 (ttt180) REVERT: D 438 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: A 86 LEU cc_start: 0.8364 (tp) cc_final: 0.8145 (tt) REVERT: A 95 ASP cc_start: 0.7680 (t0) cc_final: 0.7426 (t0) REVERT: A 143 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.6529 (ttt-90) REVERT: A 155 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7800 (p0) REVERT: A 192 ARG cc_start: 0.8349 (ttt90) cc_final: 0.8034 (ttt90) REVERT: A 238 LEU cc_start: 0.7949 (mt) cc_final: 0.7719 (mt) REVERT: A 438 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: A 497 SER cc_start: 0.8060 (p) cc_final: 0.7798 (p) REVERT: A 507 PHE cc_start: 0.8334 (m-10) cc_final: 0.8080 (m-80) REVERT: B 152 ASN cc_start: 0.8442 (p0) cc_final: 0.8168 (p0) REVERT: B 507 PHE cc_start: 0.8134 (m-80) cc_final: 0.7813 (m-80) outliers start: 82 outliers final: 59 residues processed: 509 average time/residue: 1.0864 time to fit residues: 625.3486 Evaluate side-chains 529 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 465 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 117 GLU 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 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 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 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 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 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 60 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 128 optimal weight: 0.0870 chunk 150 optimal weight: 0.0670 chunk 101 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN D 403 HIS ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.117584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108146 restraints weight = 24135.445| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.72 r_work: 0.3424 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17738 Z= 0.179 Angle : 0.606 7.691 24234 Z= 0.310 Chirality : 0.046 0.180 2460 Planarity : 0.005 0.046 3155 Dihedral : 4.739 32.978 2376 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.61 % Rotamer: Outliers : 4.50 % Allowed : 24.75 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2119 helix: -2.97 (0.61), residues: 36 sheet: 1.30 (0.19), residues: 746 loop : -0.97 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 48 HIS 0.008 0.001 HIS B 403 PHE 0.042 0.002 PHE D 507 TYR 0.024 0.002 TYR D 413 ARG 0.009 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 586) hydrogen bonds : angle 4.82688 ( 1980) covalent geometry : bond 0.00443 (17738) covalent geometry : angle 0.60582 (24234) *********************** 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 554 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 472 time to evaluate : 1.839 Fit side-chains REVERT: C 106 VAL cc_start: 0.8041 (t) cc_final: 0.7762 (m) REVERT: C 290 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7812 (mt-10) REVERT: C 445 SER cc_start: 0.8343 (t) cc_final: 0.8090 (m) REVERT: D 95 ASP cc_start: 0.7780 (t0) cc_final: 0.7518 (t0) REVERT: D 143 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8179 (ttt180) REVERT: D 438 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: A 4 THR cc_start: 0.8295 (t) cc_final: 0.8092 (p) REVERT: A 86 LEU cc_start: 0.8371 (tp) cc_final: 0.8154 (tt) REVERT: A 95 ASP cc_start: 0.7674 (t0) cc_final: 0.7432 (t0) REVERT: A 143 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.6537 (ttt-90) REVERT: A 155 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7776 (p0) REVERT: A 238 LEU cc_start: 0.7950 (mt) cc_final: 0.7717 (mt) REVERT: A 438 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: A 497 SER cc_start: 0.8066 (p) cc_final: 0.7797 (p) REVERT: A 507 PHE cc_start: 0.8315 (m-10) cc_final: 0.8102 (m-80) REVERT: B 152 ASN cc_start: 0.8451 (p0) cc_final: 0.8145 (p0) REVERT: B 507 PHE cc_start: 0.8132 (m-80) cc_final: 0.7845 (m-80) outliers start: 82 outliers final: 65 residues processed: 506 average time/residue: 1.1290 time to fit residues: 643.8718 Evaluate side-chains 534 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 464 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 GLN Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain A residue 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 180 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP 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 190 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 379 GLN 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 207 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 161 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 379 GLN D 155 ASN D 403 HIS ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.118132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108773 restraints weight = 23930.171| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.70 r_work: 0.3436 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17738 Z= 0.146 Angle : 0.589 8.150 24234 Z= 0.303 Chirality : 0.045 0.180 2460 Planarity : 0.005 0.047 3155 Dihedral : 4.674 33.204 2376 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.61 % Rotamer: Outliers : 4.34 % Allowed : 25.08 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2119 helix: -2.92 (0.60), residues: 36 sheet: 1.29 (0.19), residues: 756 loop : -0.93 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 48 HIS 0.007 0.001 HIS B 403 PHE 0.040 0.002 PHE D 507 TYR 0.026 0.002 TYR D 413 ARG 0.005 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 586) hydrogen bonds : angle 4.77588 ( 1980) covalent geometry : bond 0.00360 (17738) covalent geometry : angle 0.58937 (24234) ********************** 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 551 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 472 time to evaluate : 1.840 Fit side-chains REVERT: C 106 VAL cc_start: 0.8031 (t) cc_final: 0.7755 (m) REVERT: C 290 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7748 (mt-10) REVERT: C 344 LEU cc_start: 0.8396 (mp) cc_final: 0.8195 (mp) REVERT: C 445 SER cc_start: 0.8350 (t) cc_final: 0.8090 (m) REVERT: C 534 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 95 ASP cc_start: 0.7777 (t0) cc_final: 0.7528 (t0) REVERT: D 143 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8181 (ttt180) REVERT: D 185 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7896 (m) REVERT: D 438 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: A 4 THR cc_start: 0.8293 (t) cc_final: 0.8074 (p) REVERT: A 86 LEU cc_start: 0.8365 (tp) cc_final: 0.8149 (tt) REVERT: A 95 ASP cc_start: 0.7680 (t0) cc_final: 0.7428 (t0) REVERT: A 143 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7279 (ttt-90) REVERT: A 155 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7771 (p0) REVERT: A 192 ARG cc_start: 0.8316 (ttt90) cc_final: 0.8048 (ttt90) REVERT: A 438 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: A 497 SER cc_start: 0.8063 (p) cc_final: 0.7801 (p) REVERT: A 507 PHE cc_start: 0.8287 (m-10) cc_final: 0.8069 (m-80) REVERT: B 32 GLU cc_start: 0.7605 (pm20) cc_final: 0.7354 (pt0) REVERT: B 152 ASN cc_start: 0.8438 (p0) cc_final: 0.8188 (p0) REVERT: B 290 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7803 (mp0) REVERT: B 507 PHE cc_start: 0.8109 (m-80) cc_final: 0.7828 (m-80) outliers start: 79 outliers final: 59 residues processed: 504 average time/residue: 1.1447 time to fit residues: 650.3347 Evaluate side-chains 526 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 461 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 117 GLU 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 185 THR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 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 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 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 438 GLN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 119 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.0000 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 203 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 379 GLN D 312 GLN D 403 HIS ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108751 restraints weight = 23991.769| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.71 r_work: 0.3435 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 17738 Z= 0.196 Angle : 0.770 59.197 24234 Z= 0.438 Chirality : 0.048 0.845 2460 Planarity : 0.005 0.052 3155 Dihedral : 4.716 37.298 2376 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.61 % Rotamer: Outliers : 4.06 % Allowed : 25.41 % Favored : 70.53 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 11.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2119 helix: -2.92 (0.59), residues: 36 sheet: 1.29 (0.19), residues: 756 loop : -0.93 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 48 HIS 0.012 0.001 HIS C 515 PHE 0.039 0.002 PHE D 507 TYR 0.024 0.001 TYR D 413 ARG 0.006 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 586) hydrogen bonds : angle 4.77715 ( 1980) covalent geometry : bond 0.00433 (17738) covalent geometry : angle 0.76950 (24234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13534.03 seconds wall clock time: 233 minutes 22.54 seconds (14002.54 seconds total)