Starting phenix.real_space_refine on Fri Jul 3 09:49:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnz_33331/07_2026/7xnz_33331_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnz_33331/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xnz_33331/07_2026/7xnz_33331_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnz_33331/07_2026/7xnz_33331_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xnz_33331/07_2026/7xnz_33331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnz_33331/07_2026/7xnz_33331.map" } 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-dev-6108/lib/python3.11/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: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 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: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 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: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 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: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.66, 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: 1.06 Conformation dependent library (CDL) restraints added in 623.1 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: 0.42 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: 2.00 Time building geometry restraints manager: 1.41 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=" C4 PLP A 501 " pdb=" C4A PLP A 501 " ideal model delta sigma weight residual 1.462 1.524 -0.062 2.00e-02 2.50e+03 9.74e+00 bond pdb=" C4 PLP D 501 " pdb=" C4A PLP D 501 " ideal model delta sigma weight residual 1.462 1.524 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C4 PLP C 501 " pdb=" C4A PLP C 501 " ideal model delta sigma weight residual 1.462 1.523 -0.061 2.00e-02 2.50e+03 9.40e+00 bond pdb=" C4 PLP B 501 " pdb=" C4A PLP B 501 " ideal model delta sigma weight residual 1.462 1.523 -0.061 2.00e-02 2.50e+03 9.29e+00 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 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 18466 2.14 - 4.28: 282 4.28 - 6.42: 11 6.42 - 8.55: 7 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 - 13.79: 7292 13.79 - 27.59: 679 27.59 - 41.38: 167 41.38 - 55.18: 43 55.18 - 68.97: 51 Dihedral angle restraints: 8232 sinusoidal: 3136 harmonic: 5096 Sorted by residual: dihedral pdb=" CA GLY A 183 " pdb=" C GLY A 183 " pdb=" N GLY A 184 " pdb=" CA GLY A 184 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLY D 183 " pdb=" C GLY D 183 " pdb=" N GLY D 184 " pdb=" CA GLY D 184 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLY C 183 " pdb=" C GLY C 183 " pdb=" N GLY C 184 " pdb=" CA GLY C 184 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 8229 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: 0.05 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: 0.940 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 0.062 13800 Z= 0.238 Angle : 0.628 10.692 18768 Z= 0.343 Chirality : 0.044 0.207 2104 Planarity : 0.004 0.034 2472 Dihedral : 13.033 68.972 5024 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/Z covalent geometry : bond 0.00442 / 0.23 (13796) covalent geometry : angle 0.62781 / 0.34 (18768) hydrogen bonds : bond 0.15257 / 10.22 ( 479) hydrogen bonds : angle 7.34663 / 5.03 ( 1332) Misc. bond : bond 0.03868 / 1.83 ( 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 : 0.502 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: 0.1134 time to fit residues: 57.1349 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 : 0.497 ------------------------------------------------------------------------------- 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... 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 = 0.127543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.103356 restraints weight = 17495.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.105818 restraints weight = 12139.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.107580 restraints weight = 9511.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.108633 restraints weight = 8059.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.109532 restraints weight = 7219.714| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13800 Z= 0.157 Angle : 0.635 8.721 18768 Z= 0.324 Chirality : 0.047 0.177 2104 Planarity : 0.005 0.059 2472 Dihedral : 7.013 57.411 2040 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.69 % Favored : 93.26 % Rotamer: Outliers : 4.63 % Allowed : 12.39 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.19), residues: 1824 helix: -0.89 (0.20), residues: 688 sheet: -2.52 (0.31), residues: 180 loop : -2.26 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 137 TYR 0.020 0.002 TYR D 129 PHE 0.006 0.001 PHE A 92 TRP 0.005 0.001 TRP D 310 HIS 0.007 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (13796) covalent geometry : angle 0.63497 / 0.32 (18768) hydrogen bonds : bond 0.04286 / 2.92 ( 479) hydrogen bonds : angle 5.02804 / 3.48 ( 1332) Misc. bond : bond 0.00022 / 0.01 ( 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 297 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 0.497 Fit side-chains REVERT: B 150 ASN cc_start: 0.8642 (t0) cc_final: 0.8403 (m-40) REVERT: B 279 LYS cc_start: 0.8551 (tptm) cc_final: 0.8012 (mttt) REVERT: A 146 ASP cc_start: 0.8022 (t0) cc_final: 0.7641 (t70) REVERT: A 311 MET cc_start: 0.8596 (mmm) cc_final: 0.8348 (tpt) outliers start: 65 outliers final: 33 residues processed: 278 average time/residue: 0.0852 time to fit residues: 37.4276 Evaluate side-chains 241 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 91 VAL 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: 0.9990 chunk 163 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 112 optimal weight: 0.0050 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** 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 = 0.3338 r_free = 0.3338 target = 0.126168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.102110 restraints weight = 17770.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.104544 restraints weight = 12402.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.106266 restraints weight = 9738.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.107359 restraints weight = 8259.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.108165 restraints weight = 7380.359| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13800 Z= 0.146 Angle : 0.588 8.422 18768 Z= 0.299 Chirality : 0.046 0.210 2104 Planarity : 0.005 0.048 2472 Dihedral : 6.822 57.038 2032 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.87 % Favored : 94.08 % Rotamer: Outliers : 5.77 % Allowed : 15.46 % Favored : 78.77 % 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: -1.89 (0.19), residues: 1824 helix: -0.22 (0.20), residues: 692 sheet: -2.00 (0.33), residues: 180 loop : -1.91 (0.20), residues: 952 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 0.004 0.001 PHE C 316 TRP 0.007 0.001 TRP D 310 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (13796) covalent geometry : angle 0.58836 / 0.30 (18768) hydrogen bonds : bond 0.03916 / 2.64 ( 479) hydrogen bonds : angle 4.72270 / 3.30 ( 1332) Misc. bond : bond 0.00022 / 0.01 ( 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 292 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 211 time to evaluate : 0.479 Fit side-chains REVERT: B 150 ASN cc_start: 0.8692 (t0) cc_final: 0.8485 (m-40) REVERT: B 279 LYS cc_start: 0.8532 (tptm) cc_final: 0.7769 (mttt) REVERT: A 146 ASP cc_start: 0.8030 (t0) cc_final: 0.7681 (t70) REVERT: C 279 LYS cc_start: 0.8480 (tptm) cc_final: 0.7812 (mttt) outliers start: 81 outliers final: 44 residues processed: 269 average time/residue: 0.0942 time to fit residues: 39.2937 Evaluate side-chains 228 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 173 VAL 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 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 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 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: 3.9990 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** 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 = 0.3362 r_free = 0.3362 target = 0.127922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.103297 restraints weight = 17587.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.106021 restraints weight = 11917.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107893 restraints weight = 9143.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.109135 restraints weight = 7655.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109967 restraints weight = 6764.416| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3220 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= 0.123 Angle : 0.567 9.575 18768 Z= 0.286 Chirality : 0.045 0.201 2104 Planarity : 0.005 0.051 2472 Dihedral : 6.008 58.230 2032 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 5.13 % Allowed : 18.09 % Favored : 76.78 % 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: -1.48 (0.20), residues: 1824 helix: 0.21 (0.21), residues: 692 sheet: -2.14 (0.31), residues: 196 loop : -1.64 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.020 0.001 TYR A 129 PHE 0.005 0.001 PHE D 176 TRP 0.006 0.001 TRP A 310 HIS 0.008 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (13796) covalent geometry : angle 0.56675 / 0.29 (18768) hydrogen bonds : bond 0.03486 / 2.36 ( 479) hydrogen bonds : angle 4.60622 / 3.20 ( 1332) Misc. bond : bond 0.00014 / 0.01 ( 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 279 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 207 time to evaluate : 0.415 Fit side-chains REVERT: B 103 ARG cc_start: 0.7861 (ptt180) cc_final: 0.7655 (ptm-80) REVERT: B 264 MET cc_start: 0.9034 (mtt) cc_final: 0.8830 (mtt) REVERT: B 279 LYS cc_start: 0.8457 (tptm) cc_final: 0.7700 (mttt) REVERT: A 146 ASP cc_start: 0.8012 (t0) cc_final: 0.7595 (t70) REVERT: C 103 ARG cc_start: 0.7861 (ptt180) cc_final: 0.7651 (ptm-80) REVERT: C 279 LYS cc_start: 0.8427 (tptm) cc_final: 0.7651 (mttt) REVERT: C 296 ASP cc_start: 0.8655 (t0) cc_final: 0.8435 (t0) REVERT: D 368 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8584 (mtp) outliers start: 72 outliers final: 41 residues processed: 261 average time/residue: 0.0891 time to fit residues: 36.1622 Evaluate side-chains 228 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 173 VAL 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 305 ILE 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 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 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 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL 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 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 244 ILE Chi-restraints excluded: chain D residue 291 VAL 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 424 SER 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: 0.0020 chunk 54 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 110 optimal weight: 0.0770 chunk 177 optimal weight: 0.0670 chunk 116 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 155 optimal weight: 0.0970 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.110387 restraints weight = 17534.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112676 restraints weight = 12537.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.114163 restraints weight = 9991.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.115400 restraints weight = 8559.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.115992 restraints weight = 7683.155| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3736 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= 0.096 Angle : 0.545 10.255 18768 Z= 0.274 Chirality : 0.044 0.182 2104 Planarity : 0.005 0.050 2472 Dihedral : 5.187 54.484 2030 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 3.85 % Allowed : 20.09 % Favored : 76.07 % 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: -0.89 (0.20), residues: 1824 helix: 0.55 (0.21), residues: 704 sheet: -1.45 (0.32), residues: 196 loop : -1.28 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.021 0.001 TYR D 129 PHE 0.007 0.001 PHE D 176 TRP 0.003 0.000 TRP A 143 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (13796) covalent geometry : angle 0.54462 / 0.27 (18768) hydrogen bonds : bond 0.02884 / 1.94 ( 479) hydrogen bonds : angle 4.45161 / 3.10 ( 1332) Misc. bond : bond 0.00010 / 0.00 ( 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 285 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 0.506 Fit side-chains REVERT: B 279 LYS cc_start: 0.8395 (tptm) cc_final: 0.7601 (mttt) REVERT: B 289 LEU cc_start: 0.8898 (tp) cc_final: 0.8676 (tt) REVERT: A 146 ASP cc_start: 0.7883 (t0) cc_final: 0.7485 (t70) REVERT: A 332 ASP cc_start: 0.7837 (m-30) cc_final: 0.7396 (t0) REVERT: C 34 VAL cc_start: 0.9396 (t) cc_final: 0.9111 (m) REVERT: C 279 LYS cc_start: 0.8322 (tptm) cc_final: 0.7519 (mttt) REVERT: D 287 ASP cc_start: 0.7009 (m-30) cc_final: 0.6763 (t70) REVERT: D 378 MET cc_start: 0.6000 (tpp) cc_final: 0.5383 (tpp) outliers start: 54 outliers final: 34 residues processed: 268 average time/residue: 0.0938 time to fit residues: 38.3571 Evaluate side-chains 234 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL 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 414 LEU 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 173 VAL Chi-restraints excluded: chain A residue 201 VAL 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 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL 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 104 ASN 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 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 41 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3398 r_free = 0.3398 target = 0.130676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.106292 restraints weight = 17522.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.109025 restraints weight = 11802.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110889 restraints weight = 9036.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.112161 restraints weight = 7544.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.112917 restraints weight = 6669.868| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13800 Z= 0.113 Angle : 0.555 9.259 18768 Z= 0.278 Chirality : 0.044 0.157 2104 Planarity : 0.005 0.050 2472 Dihedral : 4.881 50.579 2025 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.28 % Favored : 95.67 % Rotamer: Outliers : 4.70 % Allowed : 19.02 % Favored : 76.28 % 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: 0.70 (0.20), residues: 704 sheet: -1.12 (0.34), residues: 196 loop : -1.08 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.018 0.001 TYR A 129 PHE 0.006 0.001 PHE D 176 TRP 0.006 0.001 TRP A 310 HIS 0.004 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (13796) covalent geometry : angle 0.55515 / 0.28 (18768) hydrogen bonds : bond 0.03141 / 2.09 ( 479) hydrogen bonds : angle 4.45058 / 3.11 ( 1332) Misc. bond : bond 0.00016 / 0.01 ( 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 264 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 198 time to evaluate : 0.484 Fit side-chains REVERT: B 279 LYS cc_start: 0.8392 (tptm) cc_final: 0.7556 (mttt) REVERT: B 289 LEU cc_start: 0.8967 (tp) cc_final: 0.8726 (tt) REVERT: A 146 ASP cc_start: 0.7904 (t0) cc_final: 0.7523 (t70) REVERT: A 221 TYR cc_start: 0.8552 (m-80) cc_final: 0.8179 (m-80) REVERT: A 332 ASP cc_start: 0.7880 (m-30) cc_final: 0.7405 (t0) REVERT: A 378 MET cc_start: 0.5895 (tpp) cc_final: 0.5596 (tpp) REVERT: A 441 GLU cc_start: 0.7866 (mp0) cc_final: 0.7263 (pt0) REVERT: C 164 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: C 279 LYS cc_start: 0.8393 (tptm) cc_final: 0.7534 (mttt) REVERT: C 397 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6513 (mt-10) REVERT: D 221 TYR cc_start: 0.8559 (m-80) cc_final: 0.8163 (m-80) REVERT: D 287 ASP cc_start: 0.7048 (m-30) cc_final: 0.6797 (t70) REVERT: D 378 MET cc_start: 0.5946 (tpp) cc_final: 0.5566 (tpp) outliers start: 66 outliers final: 45 residues processed: 250 average time/residue: 0.0864 time to fit residues: 33.6374 Evaluate side-chains 232 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 177 VAL 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 290 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 305 ILE 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 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 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 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 177 VAL 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 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: 4.9990 chunk 163 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 131 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3362 r_free = 0.3362 target = 0.127608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.102731 restraints weight = 17606.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.105321 restraints weight = 12118.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107137 restraints weight = 9428.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.108358 restraints weight = 7939.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109133 restraints weight = 7053.335| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3800 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= 0.157 Angle : 0.581 8.552 18768 Z= 0.293 Chirality : 0.046 0.150 2104 Planarity : 0.005 0.050 2472 Dihedral : 4.870 50.454 2025 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer: Outliers : 5.13 % Allowed : 18.95 % Favored : 75.93 % 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: -0.49 (0.20), residues: 1824 helix: 0.71 (0.20), residues: 700 sheet: -0.78 (0.34), residues: 204 loop : -1.01 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.018 0.001 TYR D 129 PHE 0.017 0.001 PHE A 230 TRP 0.009 0.001 TRP D 310 HIS 0.007 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (13796) covalent geometry : angle 0.58109 / 0.29 (18768) hydrogen bonds : bond 0.03618 / 2.42 ( 479) hydrogen bonds : angle 4.51651 / 3.16 ( 1332) Misc. bond : bond 0.00036 / 0.02 ( 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 260 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 188 time to evaluate : 0.491 Fit side-chains REVERT: B 164 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: B 279 LYS cc_start: 0.8377 (tptm) cc_final: 0.7535 (mttt) REVERT: B 289 LEU cc_start: 0.9035 (tp) cc_final: 0.8770 (tt) REVERT: A 106 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (mt) REVERT: A 146 ASP cc_start: 0.8049 (t0) cc_final: 0.7614 (t70) REVERT: A 332 ASP cc_start: 0.7934 (m-30) cc_final: 0.7428 (t0) REVERT: A 378 MET cc_start: 0.6051 (tpp) cc_final: 0.5602 (tpp) REVERT: C 164 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: C 279 LYS cc_start: 0.8414 (tptm) cc_final: 0.7517 (mttt) REVERT: D 106 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8593 (mt) REVERT: D 287 ASP cc_start: 0.7111 (m-30) cc_final: 0.6797 (t70) outliers start: 72 outliers final: 57 residues processed: 245 average time/residue: 0.0868 time to fit residues: 33.3012 Evaluate side-chains 243 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 305 ILE 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 104 ASN Chi-restraints excluded: chain A residue 106 LEU 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 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 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 GLU 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 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 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 289 LEU 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 406 VAL Chi-restraints excluded: chain D residue 414 LEU 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: 0.0170 chunk 23 optimal weight: 0.2980 chunk 126 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104281 restraints weight = 17432.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.106961 restraints weight = 11928.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108670 restraints weight = 9236.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.110018 restraints weight = 7781.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.110742 restraints weight = 6907.926| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13800 Z= 0.132 Angle : 0.571 8.224 18768 Z= 0.287 Chirality : 0.045 0.142 2104 Planarity : 0.005 0.049 2472 Dihedral : 4.796 52.280 2025 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 4.70 % Allowed : 20.09 % Favored : 75.21 % 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: -0.37 (0.20), residues: 1824 helix: 0.81 (0.20), residues: 700 sheet: -0.65 (0.34), residues: 204 loop : -0.95 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 256 TYR 0.017 0.001 TYR A 129 PHE 0.006 0.001 PHE C 316 TRP 0.005 0.001 TRP A 310 HIS 0.007 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (13796) covalent geometry : angle 0.57097 / 0.29 (18768) hydrogen bonds : bond 0.03376 / 2.25 ( 479) hydrogen bonds : angle 4.48076 / 3.13 ( 1332) Misc. bond : bond 0.00024 / 0.01 ( 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 253 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 187 time to evaluate : 0.500 Fit side-chains REVERT: B 60 GLN cc_start: 0.7289 (mt0) cc_final: 0.7047 (mt0) REVERT: B 164 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: B 279 LYS cc_start: 0.8328 (tptm) cc_final: 0.7506 (mttt) REVERT: B 289 LEU cc_start: 0.8974 (tp) cc_final: 0.8737 (tt) REVERT: B 397 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6445 (mt-10) REVERT: A 106 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8574 (mt) REVERT: A 146 ASP cc_start: 0.8056 (t0) cc_final: 0.7660 (t70) REVERT: A 221 TYR cc_start: 0.8591 (m-80) cc_final: 0.8127 (m-80) REVERT: A 332 ASP cc_start: 0.7916 (m-30) cc_final: 0.7425 (t0) REVERT: C 60 GLN cc_start: 0.7320 (mt0) cc_final: 0.7061 (mt0) REVERT: C 164 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: C 279 LYS cc_start: 0.8388 (tptm) cc_final: 0.7490 (mttt) REVERT: D 106 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8589 (mt) REVERT: D 221 TYR cc_start: 0.8563 (m-80) cc_final: 0.8158 (m-80) REVERT: D 287 ASP cc_start: 0.7116 (m-30) cc_final: 0.6827 (t70) outliers start: 66 outliers final: 59 residues processed: 240 average time/residue: 0.0907 time to fit residues: 33.9251 Evaluate side-chains 244 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 181 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 224 GLU 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 17 VAL 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 104 ASN Chi-restraints excluded: chain A residue 106 LEU 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 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 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 23 VAL 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 224 GLU 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 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 17 VAL 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 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 289 LEU 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 406 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: 0.0570 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.0970 chunk 142 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 0.0270 chunk 144 optimal weight: 0.8980 chunk 179 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 133 optimal weight: 5.9990 overall best weight: 0.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3440 r_free = 0.3440 target = 0.133998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.110389 restraints weight = 17455.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112954 restraints weight = 12084.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.114699 restraints weight = 9419.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.115693 restraints weight = 7958.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.116697 restraints weight = 7118.738| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13800 Z= 0.097 Angle : 0.546 7.850 18768 Z= 0.275 Chirality : 0.044 0.146 2104 Planarity : 0.005 0.051 2472 Dihedral : 4.663 54.966 2025 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 3.56 % Allowed : 21.58 % Favored : 74.86 % 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: -0.06 (0.20), residues: 1824 helix: 1.07 (0.20), residues: 704 sheet: -0.54 (0.35), residues: 196 loop : -0.77 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 260 TYR 0.016 0.001 TYR D 129 PHE 0.016 0.001 PHE D 230 TRP 0.003 0.000 TRP A 166 HIS 0.004 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (13796) covalent geometry : angle 0.54634 / 0.28 (18768) hydrogen bonds : bond 0.02861 / 1.89 ( 479) hydrogen bonds : angle 4.46427 / 3.08 ( 1332) Misc. bond : bond 0.00024 / 0.01 ( 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 261 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: B 60 GLN cc_start: 0.7368 (mt0) cc_final: 0.7126 (mt0) REVERT: B 164 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: B 279 LYS cc_start: 0.8302 (tptm) cc_final: 0.7508 (mttt) REVERT: B 289 LEU cc_start: 0.8827 (tp) cc_final: 0.8588 (tt) REVERT: B 301 TYR cc_start: 0.8470 (m-80) cc_final: 0.8220 (m-80) REVERT: B 397 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6450 (mt-10) REVERT: A 146 ASP cc_start: 0.7818 (t0) cc_final: 0.7382 (t70) REVERT: A 221 TYR cc_start: 0.8594 (m-80) cc_final: 0.8251 (m-80) REVERT: A 332 ASP cc_start: 0.7891 (m-30) cc_final: 0.7426 (t0) REVERT: C 164 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: C 279 LYS cc_start: 0.8333 (tptm) cc_final: 0.7456 (mttt) REVERT: C 301 TYR cc_start: 0.8434 (m-80) cc_final: 0.8218 (m-80) REVERT: C 378 MET cc_start: 0.7408 (tpp) cc_final: 0.6886 (ttm) REVERT: C 437 MET cc_start: 0.8123 (ptm) cc_final: 0.7842 (ttp) REVERT: D 138 ASP cc_start: 0.8185 (m-30) cc_final: 0.7958 (m-30) REVERT: D 221 TYR cc_start: 0.8574 (m-80) cc_final: 0.8287 (m-80) REVERT: D 287 ASP cc_start: 0.7174 (m-30) cc_final: 0.6910 (t70) outliers start: 50 outliers final: 40 residues processed: 254 average time/residue: 0.1049 time to fit residues: 40.7491 Evaluate side-chains 235 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 17 VAL 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 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR 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 201 VAL Chi-restraints excluded: chain C residue 224 GLU 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 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 177 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 289 LEU 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 23 optimal weight: 0.0470 chunk 100 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 57 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN 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 = 0.3418 r_free = 0.3418 target = 0.132137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.107745 restraints weight = 17450.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.110293 restraints weight = 12243.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.112043 restraints weight = 9607.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.113162 restraints weight = 8151.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.114073 restraints weight = 7283.408| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13800 Z= 0.110 Angle : 0.586 12.750 18768 Z= 0.287 Chirality : 0.044 0.149 2104 Planarity : 0.005 0.049 2472 Dihedral : 4.665 54.711 2024 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 3.56 % Allowed : 20.94 % 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: 0.06 (0.20), residues: 1824 helix: 1.15 (0.20), residues: 704 sheet: -0.46 (0.35), residues: 196 loop : -0.68 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 256 TYR 0.022 0.001 TYR B 88 PHE 0.008 0.001 PHE D 230 TRP 0.004 0.000 TRP A 310 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (13796) covalent geometry : angle 0.58645 / 0.29 (18768) hydrogen bonds : bond 0.03037 / 2.02 ( 479) hydrogen bonds : angle 4.38624 / 3.04 ( 1332) Misc. bond : bond 0.00013 / 0.01 ( 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: 50 poor density : 191 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: B 164 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: B 279 LYS cc_start: 0.8264 (tptm) cc_final: 0.7405 (mttt) REVERT: B 301 TYR cc_start: 0.8529 (m-80) cc_final: 0.8295 (m-80) REVERT: B 397 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6498 (mt-10) REVERT: A 146 ASP cc_start: 0.7939 (t0) cc_final: 0.7484 (t70) REVERT: A 221 TYR cc_start: 0.8596 (m-80) cc_final: 0.8270 (m-80) REVERT: A 332 ASP cc_start: 0.7937 (m-30) cc_final: 0.7434 (t0) REVERT: C 164 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: C 279 LYS cc_start: 0.8316 (tptm) cc_final: 0.7398 (mttt) REVERT: C 378 MET cc_start: 0.7388 (tpp) cc_final: 0.6939 (ttm) REVERT: D 138 ASP cc_start: 0.8086 (m-30) cc_final: 0.7870 (m-30) REVERT: D 221 TYR cc_start: 0.8582 (m-80) cc_final: 0.8301 (m-80) REVERT: D 287 ASP cc_start: 0.7227 (m-30) cc_final: 0.6839 (t70) outliers start: 50 outliers final: 43 residues processed: 232 average time/residue: 0.1039 time to fit residues: 36.7493 Evaluate side-chains 229 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL 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 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 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 352 THR 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 201 VAL 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 414 LEU Chi-restraints excluded: chain D residue 17 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 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 289 LEU 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: 4.9990 chunk 50 optimal weight: 0.0970 chunk 153 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 178 optimal weight: 0.1980 chunk 23 optimal weight: 0.0670 chunk 155 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 151 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.112343 restraints weight = 17424.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.114652 restraints weight = 12499.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.116261 restraints weight = 9977.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117333 restraints weight = 8551.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.118174 restraints weight = 7664.164| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13800 Z= 0.100 Angle : 0.583 12.631 18768 Z= 0.284 Chirality : 0.044 0.147 2104 Planarity : 0.005 0.048 2472 Dihedral : 4.596 54.024 2024 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 3.28 % Allowed : 21.30 % Favored : 75.43 % 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: 0.18 (0.20), residues: 1824 helix: 1.26 (0.20), residues: 704 sheet: -0.31 (0.35), residues: 196 loop : -0.65 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 256 TYR 0.019 0.001 TYR B 88 PHE 0.015 0.001 PHE D 230 TRP 0.003 0.000 TRP A 166 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (13796) covalent geometry : angle 0.58276 / 0.28 (18768) hydrogen bonds : bond 0.02799 / 1.85 ( 479) hydrogen bonds : angle 4.37299 / 3.03 ( 1332) Misc. bond : bond 0.00018 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1996.74 seconds wall clock time: 35 minutes 21.63 seconds (2121.63 seconds total)