Starting phenix.real_space_refine on Wed Feb 4 22:06:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnz_33331/02_2026/7xnz_33331_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnz_33331/02_2026/7xnz_33331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xnz_33331/02_2026/7xnz_33331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnz_33331/02_2026/7xnz_33331.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnz_33331/02_2026/7xnz_33331_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnz_33331/02_2026/7xnz_33331_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 P 4 5.49 5 S 60 5.16 5 C 8484 2.51 5 N 2336 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13524 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "A" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "C" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "D" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.65, per 1000 atoms: 0.20 Number of scatterers: 13524 At special positions: 0 Unit cell: (86.67, 146.59, 84.53, 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) S 60 16.00 P 4 15.00 O 2640 8.00 N 2336 7.00 C 8484 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 465.0 milliseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 20 sheets defined 42.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.732A pdb=" N LEU B 10 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 removed outlier: 4.383A pdb=" N ILE B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.913A pdb=" N ARG B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.667A pdb=" N ARG B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.600A pdb=" N VAL B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.638A pdb=" N HIS B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.776A pdb=" N THR B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 196 removed outlier: 4.086A pdb=" N TYR B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 262 removed outlier: 3.624A pdb=" N SER B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 281 removed outlier: 3.742A pdb=" N GLY B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.434A pdb=" N SER B 303 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.503A pdb=" N TYR B 314 " --> pdb=" O TRP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.906A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 334' Processing helix chain 'B' and resid 335 through 338 Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.746A pdb=" N SER B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.732A pdb=" N LEU A 10 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 58 removed outlier: 4.383A pdb=" N ILE A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.913A pdb=" N ARG A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.667A pdb=" N ARG A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.600A pdb=" N VAL A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.638A pdb=" N HIS A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.776A pdb=" N THR A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 4.086A pdb=" N TYR A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 262 removed outlier: 3.623A pdb=" N SER A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.742A pdb=" N GLY A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 removed outlier: 4.434A pdb=" N SER A 303 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.503A pdb=" N TYR A 314 " --> pdb=" O TRP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.906A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 335 through 338 Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.746A pdb=" N SER A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.733A pdb=" N LEU C 10 " --> pdb=" O ILE C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 removed outlier: 4.383A pdb=" N ILE C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.913A pdb=" N ARG C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.668A pdb=" N ARG C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 139 removed outlier: 3.601A pdb=" N VAL C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.637A pdb=" N HIS C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.776A pdb=" N THR C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 removed outlier: 4.086A pdb=" N TYR C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 262 removed outlier: 3.623A pdb=" N SER C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 removed outlier: 3.742A pdb=" N GLY C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 removed outlier: 4.434A pdb=" N SER C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.503A pdb=" N TYR C 314 " --> pdb=" O TRP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.907A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 334' Processing helix chain 'C' and resid 335 through 338 Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 388 through 397 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.746A pdb=" N SER C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.732A pdb=" N LEU D 10 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 58 removed outlier: 4.383A pdb=" N ILE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.913A pdb=" N ARG D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.667A pdb=" N ARG D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.601A pdb=" N VAL D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 161 removed outlier: 3.638A pdb=" N HIS D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.777A pdb=" N THR D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 196 removed outlier: 4.086A pdb=" N TYR D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 262 removed outlier: 3.623A pdb=" N SER D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 281 removed outlier: 3.742A pdb=" N GLY D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 removed outlier: 4.434A pdb=" N SER D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 removed outlier: 3.502A pdb=" N TYR D 314 " --> pdb=" O TRP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 338 removed outlier: 4.222A pdb=" N ARG D 336 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS D 337 " --> pdb=" O LEU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.746A pdb=" N SER D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.781A pdb=" N VAL B 30 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 29 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 292 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 31 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 69 removed outlier: 5.883A pdb=" N ILE B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 93 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU B 69 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS B 90 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL B 114 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE B 92 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS B 116 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS B 94 " --> pdb=" O CYS B 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 175 through 179 removed outlier: 5.888A pdb=" N PHE B 176 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA B 206 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA B 178 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL B 246 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASP B 207 " --> pdb=" O VAL B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 367 through 370 Processing sheet with id=AA5, first strand: chain 'B' and resid 416 through 418 removed outlier: 4.245A pdb=" N GLY B 446 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU B 440 " --> pdb=" O PRO B 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 17 through 19 removed outlier: 4.781A pdb=" N VAL A 30 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 29 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 292 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A 31 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 67 through 69 removed outlier: 5.883A pdb=" N ILE A 67 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL A 93 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU A 69 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS A 90 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 114 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE A 92 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N CYS A 116 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS A 94 " --> pdb=" O CYS A 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 175 through 179 removed outlier: 5.889A pdb=" N PHE A 176 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ALA A 206 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 178 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 246 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASP A 207 " --> pdb=" O VAL A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 367 through 370 Processing sheet with id=AB1, first strand: chain 'A' and resid 416 through 418 removed outlier: 4.244A pdb=" N GLY A 446 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU A 440 " --> pdb=" O PRO A 444 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 19 removed outlier: 4.781A pdb=" N VAL C 30 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 29 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 292 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA C 31 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 67 through 69 removed outlier: 5.884A pdb=" N ILE C 67 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL C 93 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU C 69 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS C 90 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 114 " --> pdb=" O CYS C 90 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE C 92 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS C 116 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS C 94 " --> pdb=" O CYS C 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 179 removed outlier: 5.888A pdb=" N PHE C 176 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA C 206 " --> pdb=" O PHE C 176 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA C 178 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL C 246 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP C 207 " --> pdb=" O VAL C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 370 Processing sheet with id=AB6, first strand: chain 'C' and resid 416 through 418 removed outlier: 4.244A pdb=" N GLY C 446 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU C 440 " --> pdb=" O PRO C 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 17 through 19 removed outlier: 4.782A pdb=" N VAL D 30 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR D 29 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL D 292 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA D 31 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 67 through 69 removed outlier: 5.883A pdb=" N ILE D 67 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL D 93 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU D 69 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS D 90 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL D 114 " --> pdb=" O CYS D 90 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE D 92 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N CYS D 116 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS D 94 " --> pdb=" O CYS D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 175 through 179 removed outlier: 5.888A pdb=" N PHE D 176 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ALA D 206 " --> pdb=" O PHE D 176 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA D 178 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL D 246 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASP D 207 " --> pdb=" O VAL D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 367 through 370 Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 418 removed outlier: 4.245A pdb=" N GLY D 446 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU D 440 " --> pdb=" O PRO D 444 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4493 1.34 - 1.45: 1552 1.45 - 1.57: 7643 1.57 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 13796 Sorted by residual: bond pdb=" N THR D 329 " pdb=" CA THR D 329 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.20e+00 bond pdb=" N LEU D 344 " pdb=" CA LEU D 344 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.12e+00 bond pdb=" N VAL C 345 " pdb=" CA VAL C 345 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.24e+00 bond pdb=" N HIS C 346 " pdb=" CA HIS C 346 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.26e-02 6.30e+03 6.19e+00 bond pdb=" N ALA B 343 " pdb=" CA ALA B 343 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.10e+00 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 18498 2.14 - 4.28: 264 4.28 - 6.42: 1 6.42 - 8.55: 3 8.55 - 10.69: 2 Bond angle restraints: 18768 Sorted by residual: angle pdb=" C SER B 328 " pdb=" N THR B 329 " pdb=" CA THR B 329 " ideal model delta sigma weight residual 122.92 133.61 -10.69 1.76e+00 3.23e-01 3.69e+01 angle pdb=" C SER C 328 " pdb=" N THR C 329 " pdb=" CA THR C 329 " ideal model delta sigma weight residual 122.92 133.35 -10.43 1.76e+00 3.23e-01 3.51e+01 angle pdb=" CA PRO B 342 " pdb=" C PRO B 342 " pdb=" O PRO B 342 " ideal model delta sigma weight residual 121.31 117.17 4.14 7.40e-01 1.83e+00 3.13e+01 angle pdb=" CA PRO D 342 " pdb=" C PRO D 342 " pdb=" O PRO D 342 " ideal model delta sigma weight residual 121.38 117.24 4.14 7.70e-01 1.69e+00 2.89e+01 angle pdb=" C SER A 328 " pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 122.92 130.73 -7.81 1.76e+00 3.23e-01 1.97e+01 ... (remaining 18763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 8076 33.07 - 66.15: 136 66.15 - 99.22: 6 99.22 - 132.30: 0 132.30 - 165.37: 2 Dihedral angle restraints: 8220 sinusoidal: 3124 harmonic: 5096 Sorted by residual: dihedral pdb=" C5A PLP D 501 " pdb=" O4P PLP D 501 " pdb=" P PLP D 501 " pdb=" O1P PLP D 501 " ideal model delta sinusoidal sigma weight residual 76.43 -118.20 -165.37 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5A PLP A 501 " pdb=" O4P PLP A 501 " pdb=" P PLP A 501 " pdb=" O1P PLP A 501 " ideal model delta sinusoidal sigma weight residual 76.43 -118.24 -165.33 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5A PLP C 501 " pdb=" O4P PLP C 501 " pdb=" P PLP C 501 " pdb=" O1P PLP C 501 " ideal model delta sinusoidal sigma weight residual 76.43 1.22 75.20 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 8217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1474 0.041 - 0.083: 433 0.083 - 0.124: 184 0.124 - 0.165: 9 0.165 - 0.207: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA LEU A 341 " pdb=" N LEU A 341 " pdb=" C LEU A 341 " pdb=" CB LEU A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL C 345 " pdb=" N VAL C 345 " pdb=" C VAL C 345 " pdb=" CB VAL C 345 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ALA A 343 " pdb=" N ALA A 343 " pdb=" C ALA A 343 " pdb=" CB ALA A 343 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 2101 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C GLN B 327 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN B 327 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 328 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 327 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C GLN C 327 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN C 327 " 0.012 2.00e-02 2.50e+03 pdb=" N SER C 328 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 340 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ALA C 340 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA C 340 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU C 341 " 0.009 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 447 2.70 - 3.25: 14878 3.25 - 3.80: 20654 3.80 - 4.35: 27125 4.35 - 4.90: 44982 Nonbonded interactions: 108086 Sorted by model distance: nonbonded pdb=" O PRO A 145 " pdb=" ND2 ASN A 150 " model vdw 2.146 3.120 nonbonded pdb=" O PRO C 145 " pdb=" ND2 ASN C 150 " model vdw 2.146 3.120 nonbonded pdb=" O PRO D 145 " pdb=" ND2 ASN D 150 " model vdw 2.146 3.120 nonbonded pdb=" O PRO B 145 " pdb=" ND2 ASN B 150 " model vdw 2.147 3.120 nonbonded pdb=" O LEU C 265 " pdb=" N GLY C 298 " model vdw 2.152 3.120 ... (remaining 108081 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.004 0.042 13800 Z= 0.221 Angle : 0.597 10.692 18768 Z= 0.337 Chirality : 0.044 0.207 2104 Planarity : 0.004 0.034 2472 Dihedral : 13.119 165.370 5012 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 35.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.01 % Favored : 87.72 % Rotamer: Outliers : 3.42 % Allowed : 5.56 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.17), residues: 1824 helix: -1.98 (0.18), residues: 684 sheet: -3.33 (0.28), residues: 180 loop : -3.00 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 399 TYR 0.014 0.001 TYR B 128 PHE 0.004 0.001 PHE A 316 TRP 0.007 0.001 TRP C 310 HIS 0.002 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00406 (13796) covalent geometry : angle 0.59660 (18768) hydrogen bonds : bond 0.15257 ( 479) hydrogen bonds : angle 7.34663 ( 1332) Misc. bond : bond 0.03868 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 320 time to evaluate : 0.479 Fit side-chains REVERT: B 278 LEU cc_start: 0.9272 (mt) cc_final: 0.9002 (mp) REVERT: B 311 MET cc_start: 0.9084 (tpp) cc_final: 0.8045 (tpt) REVERT: B 437 MET cc_start: 0.8404 (ptp) cc_final: 0.8140 (ptt) REVERT: A 172 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7333 (tptt) REVERT: C 311 MET cc_start: 0.9077 (tpp) cc_final: 0.8017 (tpt) REVERT: C 437 MET cc_start: 0.8393 (ptp) cc_final: 0.8145 (ptt) REVERT: D 172 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7346 (tptt) outliers start: 48 outliers final: 17 residues processed: 349 average time/residue: 0.1049 time to fit residues: 52.2902 Evaluate side-chains 216 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0070 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.127629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.103491 restraints weight = 17464.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.106013 restraints weight = 12096.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.107730 restraints weight = 9450.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.108709 restraints weight = 8008.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.109638 restraints weight = 7192.755| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13800 Z= 0.152 Angle : 0.628 8.560 18768 Z= 0.320 Chirality : 0.047 0.172 2104 Planarity : 0.005 0.061 2472 Dihedral : 8.325 157.271 2028 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.09 % Rotamer: Outliers : 4.84 % Allowed : 12.32 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.19), residues: 1824 helix: -0.85 (0.20), residues: 688 sheet: -2.48 (0.31), residues: 180 loop : -2.25 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 431 TYR 0.020 0.001 TYR D 129 PHE 0.005 0.001 PHE A 92 TRP 0.005 0.001 TRP A 310 HIS 0.007 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00364 (13796) covalent geometry : angle 0.62769 (18768) hydrogen bonds : bond 0.04204 ( 479) hydrogen bonds : angle 4.99399 ( 1332) Misc. bond : bond 0.00040 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 236 time to evaluate : 0.388 Fit side-chains REVERT: B 279 LYS cc_start: 0.8545 (tptm) cc_final: 0.7992 (mttt) REVERT: A 146 ASP cc_start: 0.8035 (t0) cc_final: 0.7670 (t0) REVERT: D 172 LYS cc_start: 0.7582 (ttpp) cc_final: 0.7382 (tptt) outliers start: 68 outliers final: 35 residues processed: 285 average time/residue: 0.0788 time to fit residues: 35.3899 Evaluate side-chains 242 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 40 optimal weight: 0.1980 chunk 163 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN D 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.128161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.104104 restraints weight = 17693.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.106577 restraints weight = 12348.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.108325 restraints weight = 9631.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.109485 restraints weight = 8187.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.110155 restraints weight = 7321.000| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13800 Z= 0.127 Angle : 0.579 8.864 18768 Z= 0.293 Chirality : 0.045 0.206 2104 Planarity : 0.005 0.046 2472 Dihedral : 7.274 131.914 2020 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 5.34 % Allowed : 15.60 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.19), residues: 1824 helix: -0.12 (0.20), residues: 692 sheet: -1.96 (0.33), residues: 180 loop : -1.92 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.017 0.001 TYR A 451 PHE 0.004 0.001 PHE A 316 TRP 0.006 0.001 TRP D 310 HIS 0.006 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00299 (13796) covalent geometry : angle 0.57881 (18768) hydrogen bonds : bond 0.03725 ( 479) hydrogen bonds : angle 4.67177 ( 1332) Misc. bond : bond 0.00036 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 204 time to evaluate : 0.474 Fit side-chains REVERT: B 279 LYS cc_start: 0.8521 (tptm) cc_final: 0.7754 (mttt) REVERT: A 146 ASP cc_start: 0.8010 (t0) cc_final: 0.7653 (t70) REVERT: A 279 LYS cc_start: 0.8742 (tptp) cc_final: 0.8257 (tppt) REVERT: C 279 LYS cc_start: 0.8433 (tptm) cc_final: 0.7775 (mttt) REVERT: D 172 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7472 (tptt) outliers start: 75 outliers final: 47 residues processed: 260 average time/residue: 0.0905 time to fit residues: 35.8843 Evaluate side-chains 234 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 60 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 0.0870 chunk 140 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.132087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.108394 restraints weight = 17535.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.110954 restraints weight = 12164.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.112708 restraints weight = 9503.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.113712 restraints weight = 8042.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.114657 restraints weight = 7215.215| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13800 Z= 0.104 Angle : 0.551 7.464 18768 Z= 0.278 Chirality : 0.045 0.198 2104 Planarity : 0.005 0.050 2472 Dihedral : 6.691 120.523 2020 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 4.20 % Allowed : 17.59 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.20), residues: 1824 helix: 0.39 (0.21), residues: 708 sheet: -1.76 (0.31), residues: 204 loop : -1.62 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 256 TYR 0.020 0.001 TYR D 129 PHE 0.006 0.001 PHE D 176 TRP 0.005 0.001 TRP D 166 HIS 0.007 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00222 (13796) covalent geometry : angle 0.55064 (18768) hydrogen bonds : bond 0.03103 ( 479) hydrogen bonds : angle 4.55384 ( 1332) Misc. bond : bond 0.00025 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 0.467 Fit side-chains REVERT: B 279 LYS cc_start: 0.8404 (tptm) cc_final: 0.7635 (mttt) REVERT: A 146 ASP cc_start: 0.7905 (t0) cc_final: 0.7494 (t70) REVERT: A 279 LYS cc_start: 0.8685 (tptp) cc_final: 0.8176 (tppt) REVERT: A 332 ASP cc_start: 0.7689 (m-30) cc_final: 0.7243 (t0) REVERT: C 34 VAL cc_start: 0.9480 (t) cc_final: 0.9207 (m) REVERT: C 279 LYS cc_start: 0.8352 (tptm) cc_final: 0.7580 (mttt) REVERT: D 172 LYS cc_start: 0.7637 (ttpp) cc_final: 0.7435 (tptt) outliers start: 59 outliers final: 37 residues processed: 275 average time/residue: 0.0852 time to fit residues: 35.8456 Evaluate side-chains 237 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 122 optimal weight: 2.9990 chunk 54 optimal weight: 0.0170 chunk 149 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 177 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104919 restraints weight = 17589.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107670 restraints weight = 11830.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.109520 restraints weight = 9067.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.110740 restraints weight = 7591.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.111668 restraints weight = 6711.476| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13800 Z= 0.117 Angle : 0.555 6.602 18768 Z= 0.279 Chirality : 0.045 0.195 2104 Planarity : 0.005 0.050 2472 Dihedral : 6.296 114.773 2016 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 4.84 % Allowed : 18.02 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.20), residues: 1824 helix: 0.58 (0.20), residues: 704 sheet: -1.29 (0.32), residues: 204 loop : -1.34 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.018 0.001 TYR A 451 PHE 0.005 0.001 PHE C 316 TRP 0.006 0.001 TRP A 310 HIS 0.007 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00275 (13796) covalent geometry : angle 0.55461 (18768) hydrogen bonds : bond 0.03324 ( 479) hydrogen bonds : angle 4.42758 ( 1332) Misc. bond : bond 0.00025 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 198 time to evaluate : 0.430 Fit side-chains REVERT: B 279 LYS cc_start: 0.8424 (tptm) cc_final: 0.7459 (mttt) REVERT: B 289 LEU cc_start: 0.9017 (tp) cc_final: 0.8814 (tt) REVERT: A 146 ASP cc_start: 0.7943 (t0) cc_final: 0.7473 (t70) REVERT: A 221 TYR cc_start: 0.8500 (m-80) cc_final: 0.8183 (m-80) REVERT: A 279 LYS cc_start: 0.8789 (tptp) cc_final: 0.8188 (tppt) REVERT: A 332 ASP cc_start: 0.7996 (m-30) cc_final: 0.7424 (t0) REVERT: C 279 LYS cc_start: 0.8437 (tptm) cc_final: 0.7470 (mttt) REVERT: D 172 LYS cc_start: 0.7577 (ttpp) cc_final: 0.7241 (tptt) REVERT: D 287 ASP cc_start: 0.6955 (m-30) cc_final: 0.6720 (t70) REVERT: D 368 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8650 (mtp) outliers start: 68 outliers final: 48 residues processed: 244 average time/residue: 0.0859 time to fit residues: 32.1970 Evaluate side-chains 236 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 41 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 0.0370 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 8 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 137 optimal weight: 0.0470 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109456 restraints weight = 17391.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.112014 restraints weight = 12003.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.113760 restraints weight = 9327.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.114936 restraints weight = 7866.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115785 restraints weight = 6978.904| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13800 Z= 0.098 Angle : 0.548 11.386 18768 Z= 0.270 Chirality : 0.044 0.150 2104 Planarity : 0.004 0.050 2472 Dihedral : 5.710 91.605 2016 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 4.06 % Allowed : 19.02 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.20), residues: 1824 helix: 0.82 (0.21), residues: 704 sheet: -1.07 (0.34), residues: 196 loop : -1.07 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 256 TYR 0.020 0.001 TYR D 129 PHE 0.016 0.001 PHE D 230 TRP 0.003 0.000 TRP D 310 HIS 0.006 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00221 (13796) covalent geometry : angle 0.54776 (18768) hydrogen bonds : bond 0.02897 ( 479) hydrogen bonds : angle 4.41581 ( 1332) Misc. bond : bond 0.00022 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 206 time to evaluate : 0.478 Fit side-chains REVERT: B 279 LYS cc_start: 0.8273 (tptm) cc_final: 0.7395 (mttt) REVERT: B 289 LEU cc_start: 0.8955 (tp) cc_final: 0.8706 (tt) REVERT: B 397 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6514 (mt-10) REVERT: A 146 ASP cc_start: 0.7863 (t0) cc_final: 0.7446 (t70) REVERT: A 221 TYR cc_start: 0.8526 (m-80) cc_final: 0.8135 (m-80) REVERT: A 332 ASP cc_start: 0.7913 (m-30) cc_final: 0.7421 (t0) REVERT: C 164 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: C 279 LYS cc_start: 0.8364 (tptm) cc_final: 0.7508 (mttt) REVERT: C 397 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6532 (mt-10) REVERT: D 84 GLN cc_start: 0.8766 (tt0) cc_final: 0.8498 (tp40) REVERT: D 168 ASP cc_start: 0.8559 (m-30) cc_final: 0.8024 (m-30) REVERT: D 172 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7413 (tptt) outliers start: 57 outliers final: 46 residues processed: 247 average time/residue: 0.0820 time to fit residues: 31.5187 Evaluate side-chains 244 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.098146 restraints weight = 17902.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.100398 restraints weight = 12873.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101853 restraints weight = 10326.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.103022 restraints weight = 8898.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.103623 restraints weight = 8029.715| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 13800 Z= 0.278 Angle : 0.692 9.915 18768 Z= 0.350 Chirality : 0.049 0.202 2104 Planarity : 0.005 0.050 2472 Dihedral : 6.135 90.631 2015 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 5.98 % Allowed : 17.88 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 1824 helix: 0.35 (0.20), residues: 700 sheet: -1.14 (0.33), residues: 204 loop : -1.14 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 336 TYR 0.021 0.002 TYR A 451 PHE 0.011 0.001 PHE A 230 TRP 0.016 0.002 TRP A 310 HIS 0.010 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00684 (13796) covalent geometry : angle 0.69211 (18768) hydrogen bonds : bond 0.04600 ( 479) hydrogen bonds : angle 4.73097 ( 1332) Misc. bond : bond 0.00104 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 179 time to evaluate : 0.414 Fit side-chains REVERT: B 164 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: B 279 LYS cc_start: 0.8530 (tptm) cc_final: 0.7657 (mttt) REVERT: A 146 ASP cc_start: 0.8158 (t0) cc_final: 0.7700 (t70) REVERT: A 279 LYS cc_start: 0.8846 (tptp) cc_final: 0.8364 (tppt) REVERT: A 332 ASP cc_start: 0.7972 (m-30) cc_final: 0.7440 (t0) REVERT: C 60 GLN cc_start: 0.7546 (mt0) cc_final: 0.7322 (mt0) REVERT: C 164 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: C 279 LYS cc_start: 0.8540 (tptm) cc_final: 0.7662 (mttt) REVERT: D 106 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8641 (mt) outliers start: 84 outliers final: 60 residues processed: 242 average time/residue: 0.0844 time to fit residues: 31.4828 Evaluate side-chains 232 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 163 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 126 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.128172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.102485 restraints weight = 17435.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.105389 restraints weight = 11556.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107392 restraints weight = 8766.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.108655 restraints weight = 7277.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109630 restraints weight = 6430.031| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13800 Z= 0.119 Angle : 0.584 10.118 18768 Z= 0.291 Chirality : 0.045 0.148 2104 Planarity : 0.005 0.050 2472 Dihedral : 5.736 79.566 2015 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 4.56 % Allowed : 19.94 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1824 helix: 0.71 (0.20), residues: 700 sheet: -1.15 (0.34), residues: 196 loop : -0.98 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.019 0.001 TYR D 129 PHE 0.009 0.001 PHE A 230 TRP 0.003 0.001 TRP D 310 HIS 0.007 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00273 (13796) covalent geometry : angle 0.58370 (18768) hydrogen bonds : bond 0.03340 ( 479) hydrogen bonds : angle 4.59882 ( 1332) Misc. bond : bond 0.00021 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 0.421 Fit side-chains REVERT: B 164 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: B 279 LYS cc_start: 0.8347 (tptm) cc_final: 0.7475 (mttt) REVERT: B 397 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6540 (mt-10) REVERT: A 146 ASP cc_start: 0.7944 (t0) cc_final: 0.7493 (t70) REVERT: A 279 LYS cc_start: 0.8837 (tptp) cc_final: 0.8297 (tppt) REVERT: A 332 ASP cc_start: 0.7943 (m-30) cc_final: 0.7446 (t0) REVERT: C 164 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: C 279 LYS cc_start: 0.8421 (tptm) cc_final: 0.7505 (mttt) outliers start: 64 outliers final: 48 residues processed: 240 average time/residue: 0.0931 time to fit residues: 34.5398 Evaluate side-chains 234 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 142 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.124820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.099031 restraints weight = 17802.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.101819 restraints weight = 11960.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103763 restraints weight = 9165.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.105126 restraints weight = 7644.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.106028 restraints weight = 6719.171| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13800 Z= 0.198 Angle : 0.640 9.611 18768 Z= 0.320 Chirality : 0.047 0.181 2104 Planarity : 0.005 0.050 2472 Dihedral : 5.689 72.385 2015 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 4.63 % Allowed : 19.52 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1824 helix: 0.59 (0.20), residues: 700 sheet: -0.94 (0.34), residues: 204 loop : -1.02 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.019 0.002 TYR D 451 PHE 0.010 0.001 PHE A 230 TRP 0.011 0.001 TRP A 310 HIS 0.009 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00488 (13796) covalent geometry : angle 0.64044 (18768) hydrogen bonds : bond 0.03929 ( 479) hydrogen bonds : angle 4.62884 ( 1332) Misc. bond : bond 0.00078 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 174 time to evaluate : 0.427 Fit side-chains REVERT: B 60 GLN cc_start: 0.7565 (mt0) cc_final: 0.7302 (mt0) REVERT: B 164 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: B 279 LYS cc_start: 0.8499 (tptm) cc_final: 0.7502 (mttt) REVERT: A 146 ASP cc_start: 0.8118 (t0) cc_final: 0.7558 (t70) REVERT: A 279 LYS cc_start: 0.8873 (tptp) cc_final: 0.8282 (tppt) REVERT: A 332 ASP cc_start: 0.8043 (m-30) cc_final: 0.7424 (t0) REVERT: C 164 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: C 279 LYS cc_start: 0.8522 (tptm) cc_final: 0.7572 (mttt) outliers start: 65 outliers final: 52 residues processed: 221 average time/residue: 0.0904 time to fit residues: 30.8358 Evaluate side-chains 220 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 23 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 0.0470 chunk 93 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 131 optimal weight: 0.0000 chunk 52 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.106454 restraints weight = 17587.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108792 restraints weight = 12418.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.110658 restraints weight = 9799.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.111654 restraints weight = 8306.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.112584 restraints weight = 7451.026| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13800 Z= 0.108 Angle : 0.583 9.714 18768 Z= 0.292 Chirality : 0.045 0.145 2104 Planarity : 0.005 0.049 2472 Dihedral : 5.219 58.126 2015 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 3.49 % Allowed : 20.87 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1824 helix: 0.84 (0.20), residues: 708 sheet: -0.88 (0.34), residues: 196 loop : -0.95 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.018 0.001 TYR D 129 PHE 0.009 0.001 PHE A 230 TRP 0.003 0.000 TRP A 433 HIS 0.007 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00248 (13796) covalent geometry : angle 0.58281 (18768) hydrogen bonds : bond 0.03120 ( 479) hydrogen bonds : angle 4.54850 ( 1332) Misc. bond : bond 0.00056 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.487 Fit side-chains REVERT: B 60 GLN cc_start: 0.7411 (mt0) cc_final: 0.7195 (mt0) REVERT: B 164 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: B 279 LYS cc_start: 0.8272 (tptm) cc_final: 0.7422 (mttt) REVERT: A 139 ILE cc_start: 0.8549 (mm) cc_final: 0.8346 (mt) REVERT: A 146 ASP cc_start: 0.8030 (t0) cc_final: 0.7610 (t70) REVERT: A 279 LYS cc_start: 0.8791 (tptp) cc_final: 0.8283 (tppt) REVERT: C 164 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: C 279 LYS cc_start: 0.8344 (tptm) cc_final: 0.7446 (mttt) REVERT: D 35 GLU cc_start: 0.8019 (tt0) cc_final: 0.7705 (tt0) REVERT: D 221 TYR cc_start: 0.8647 (m-80) cc_final: 0.8266 (m-80) outliers start: 49 outliers final: 41 residues processed: 227 average time/residue: 0.1005 time to fit residues: 34.2366 Evaluate side-chains 227 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 0.0970 chunk 50 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 155 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.129724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.105634 restraints weight = 17693.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.108143 restraints weight = 12423.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109945 restraints weight = 9768.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110964 restraints weight = 8261.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111939 restraints weight = 7413.413| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13800 Z= 0.120 Angle : 0.583 9.564 18768 Z= 0.292 Chirality : 0.045 0.148 2104 Planarity : 0.005 0.050 2472 Dihedral : 5.289 62.977 2015 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 3.49 % Allowed : 21.44 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1824 helix: 0.93 (0.20), residues: 704 sheet: -0.54 (0.34), residues: 204 loop : -0.95 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 361 TYR 0.017 0.001 TYR A 451 PHE 0.017 0.001 PHE A 230 TRP 0.004 0.001 TRP A 310 HIS 0.008 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00285 (13796) covalent geometry : angle 0.58323 (18768) hydrogen bonds : bond 0.03242 ( 479) hydrogen bonds : angle 4.51495 ( 1332) Misc. bond : bond 0.00057 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1776.96 seconds wall clock time: 31 minutes 30.72 seconds (1890.72 seconds total)