Starting phenix.real_space_refine on Thu Aug 6 20:39:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10na_75298/08_2026/10na_75298_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/10na_75298/08_2026/10na_75298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10na_75298/08_2026/10na_75298_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10na_75298/08_2026/10na_75298_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10na_75298/08_2026/10na_75298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10na_75298/08_2026/10na_75298.map" } resolution = 3.49 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= 0.013 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10320 2.51 5 N 3030 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16548 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "C" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "D" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "E" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "F" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Time building chain proxies: 3.01, per 1000 atoms: 0.18 Number of scatterers: 16548 At special positions: 0 Unit cell: (134.75, 151.998, 83.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3114 8.00 N 3030 7.00 C 10320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 569.7 milliseconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 20 sheets defined 49.5% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 4.445A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS A 13 " --> pdb=" O GLY A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.824A pdb=" N ASN A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.526A pdb=" N THR A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 191 through 194 removed outlier: 4.048A pdb=" N ALA A 194 " --> pdb=" O LEU A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 194' Processing helix chain 'A' and resid 205 through 218 removed outlier: 3.509A pdb=" N MET A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.672A pdb=" N VAL A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 314 through 325 removed outlier: 3.512A pdb=" N ASP A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.504A pdb=" N ALA A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 350 removed outlier: 3.647A pdb=" N LYS A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 14 removed outlier: 3.737A pdb=" N GLN B 5 " --> pdb=" O GLY B 1 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.890A pdb=" N LEU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 118 removed outlier: 3.635A pdb=" N GLN B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 149 Processing helix chain 'B' and resid 182 through 191 Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.652A pdb=" N MET B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.507A pdb=" N VAL B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 246 through 257 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 299 through 307 removed outlier: 3.591A pdb=" N SER B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.616A pdb=" N ALA B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 350 removed outlier: 3.619A pdb=" N LYS B 350 " --> pdb=" O MET B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 13 removed outlier: 3.805A pdb=" N GLN C 5 " --> pdb=" O GLY C 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.685A pdb=" N LEU C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 118 removed outlier: 4.086A pdb=" N ASN C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 148 Processing helix chain 'C' and resid 182 through 191 Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 205 through 220 removed outlier: 4.130A pdb=" N HIS C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 removed outlier: 3.957A pdb=" N VAL C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 removed outlier: 4.131A pdb=" N GLU C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 339 through 350 removed outlier: 3.675A pdb=" N LEU C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 removed outlier: 4.445A pdb=" N LEU D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR D 12 " --> pdb=" O ASP D 8 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'D' and resid 55 through 66 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 111 through 118 removed outlier: 3.824A pdb=" N ASN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 148 removed outlier: 3.526A pdb=" N THR D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'D' and resid 191 through 194 removed outlier: 4.048A pdb=" N ALA D 194 " --> pdb=" O LEU D 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 194' Processing helix chain 'D' and resid 205 through 218 removed outlier: 3.509A pdb=" N MET D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.672A pdb=" N VAL D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 246 through 257 Processing helix chain 'D' and resid 285 through 295 Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'D' and resid 314 through 325 removed outlier: 3.512A pdb=" N ASP D 325 " --> pdb=" O GLN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 337 removed outlier: 3.504A pdb=" N ALA D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 350 removed outlier: 3.647A pdb=" N LYS D 350 " --> pdb=" O MET D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 14 removed outlier: 3.737A pdb=" N GLN E 5 " --> pdb=" O GLY E 1 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.890A pdb=" N LEU E 107 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 118 removed outlier: 3.635A pdb=" N GLN E 114 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 149 Processing helix chain 'E' and resid 182 through 191 Processing helix chain 'E' and resid 205 through 218 removed outlier: 3.652A pdb=" N MET E 209 " --> pdb=" O SER E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 242 removed outlier: 3.507A pdb=" N VAL E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 245 No H-bonds generated for 'chain 'E' and resid 243 through 245' Processing helix chain 'E' and resid 246 through 257 Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 299 through 307 removed outlier: 3.591A pdb=" N SER E 307 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 325 Processing helix chain 'E' and resid 329 through 337 removed outlier: 3.616A pdb=" N ALA E 333 " --> pdb=" O SER E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 350 removed outlier: 3.619A pdb=" N LYS E 350 " --> pdb=" O MET E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 13 removed outlier: 3.805A pdb=" N GLN F 5 " --> pdb=" O GLY F 1 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'F' and resid 55 through 66 Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.685A pdb=" N LEU F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 118 removed outlier: 4.086A pdb=" N ASN F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 148 Processing helix chain 'F' and resid 182 through 191 Processing helix chain 'F' and resid 192 through 194 No H-bonds generated for 'chain 'F' and resid 192 through 194' Processing helix chain 'F' and resid 205 through 220 removed outlier: 4.130A pdb=" N HIS F 220 " --> pdb=" O ALA F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 242 removed outlier: 3.957A pdb=" N VAL F 242 " --> pdb=" O ILE F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 257 removed outlier: 4.131A pdb=" N GLU F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN F 249 " --> pdb=" O GLU F 245 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 256 " --> pdb=" O LEU F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 298 through 306 Processing helix chain 'F' and resid 314 through 325 Processing helix chain 'F' and resid 329 through 337 Processing helix chain 'F' and resid 339 through 350 removed outlier: 3.675A pdb=" N LEU F 345 " --> pdb=" O ASN F 341 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS F 350 " --> pdb=" O MET F 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 5.307A pdb=" N THR A 21 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 17 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.120A pdb=" N ILE A 153 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS A 152 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU A 199 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 154 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 226 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY A 128 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU A 123 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 260 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 264 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 36 removed outlier: 4.043A pdb=" N ILE B 94 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG B 78 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 34 through 36 removed outlier: 4.043A pdb=" N ILE B 94 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG B 78 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 197 through 199 removed outlier: 6.197A pdb=" N ILE B 198 " --> pdb=" O MET B 223 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR B 225 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU B 123 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 264 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AA8, first strand: chain 'C' and resid 17 through 21 Processing sheet with id=AA9, first strand: chain 'C' and resid 26 through 30 Processing sheet with id=AB1, first strand: chain 'C' and resid 170 through 175 removed outlier: 6.538A pdb=" N HIS C 152 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU C 199 " --> pdb=" O HIS C 152 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 154 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR C 225 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 128 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU C 123 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 260 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 34 through 35 removed outlier: 5.307A pdb=" N THR D 21 " --> pdb=" O PRO D 25 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP D 17 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.120A pdb=" N ILE D 153 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS D 152 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 199 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU D 154 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 226 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY D 128 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU D 123 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 260 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 264 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 34 through 36 removed outlier: 4.043A pdb=" N ILE E 94 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG E 78 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 34 through 36 removed outlier: 4.043A pdb=" N ILE E 94 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG E 78 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 197 through 199 removed outlier: 6.197A pdb=" N ILE E 198 " --> pdb=" O MET E 223 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR E 225 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU E 123 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN E 264 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 152 through 153 Processing sheet with id=AB8, first strand: chain 'E' and resid 156 through 157 Processing sheet with id=AB9, first strand: chain 'F' and resid 17 through 21 Processing sheet with id=AC1, first strand: chain 'F' and resid 26 through 30 Processing sheet with id=AC2, first strand: chain 'F' and resid 170 through 175 removed outlier: 6.538A pdb=" N HIS F 152 " --> pdb=" O MET F 197 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU F 199 " --> pdb=" O HIS F 152 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU F 154 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR F 225 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY F 128 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU F 123 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY F 260 " --> pdb=" O LEU F 123 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2574 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: 2.12 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5790 1.34 - 1.46: 2834 1.46 - 1.58: 7990 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 16770 Sorted by residual: bond pdb=" N GLY B 201 " pdb=" CA GLY B 201 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.01e+00 bond pdb=" N GLY E 201 " pdb=" CA GLY E 201 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.01e+00 bond pdb=" CA VAL C 310 " pdb=" CB VAL C 310 " ideal model delta sigma weight residual 1.531 1.540 -0.009 1.11e-02 8.12e+03 7.10e-01 bond pdb=" CA VAL F 310 " pdb=" CB VAL F 310 " ideal model delta sigma weight residual 1.531 1.540 -0.009 1.11e-02 8.12e+03 7.10e-01 bond pdb=" CA VAL B 242 " pdb=" CB VAL B 242 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.55e-02 4.16e+03 5.27e-01 ... (remaining 16765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 21682 0.99 - 1.98: 720 1.98 - 2.98: 140 2.98 - 3.97: 44 3.97 - 4.96: 16 Bond angle restraints: 22602 Sorted by residual: angle pdb=" N VAL C 310 " pdb=" CA VAL C 310 " pdb=" C VAL C 310 " ideal model delta sigma weight residual 106.53 110.16 -3.63 1.41e+00 5.03e-01 6.64e+00 angle pdb=" N VAL F 310 " pdb=" CA VAL F 310 " pdb=" C VAL F 310 " ideal model delta sigma weight residual 106.53 110.16 -3.63 1.41e+00 5.03e-01 6.64e+00 angle pdb=" C ASN F 230 " pdb=" N ALA F 231 " pdb=" CA ALA F 231 " ideal model delta sigma weight residual 121.54 126.00 -4.46 1.91e+00 2.74e-01 5.45e+00 angle pdb=" C ASN C 230 " pdb=" N ALA C 231 " pdb=" CA ALA C 231 " ideal model delta sigma weight residual 121.54 126.00 -4.46 1.91e+00 2.74e-01 5.45e+00 angle pdb=" C ARG E 87 " pdb=" N GLU E 88 " pdb=" CA GLU E 88 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.72e+00 ... (remaining 22597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9160 17.98 - 35.95: 950 35.95 - 53.93: 170 53.93 - 71.91: 20 71.91 - 89.88: 20 Dihedral angle restraints: 10320 sinusoidal: 4242 harmonic: 6078 Sorted by residual: dihedral pdb=" CA ASP A 326 " pdb=" CB ASP A 326 " pdb=" CG ASP A 326 " pdb=" OD1 ASP A 326 " ideal model delta sinusoidal sigma weight residual -30.00 -89.76 59.76 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP D 326 " pdb=" CB ASP D 326 " pdb=" CG ASP D 326 " pdb=" OD1 ASP D 326 " ideal model delta sinusoidal sigma weight residual -30.00 -89.76 59.76 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP E 326 " pdb=" CB ASP E 326 " pdb=" CG ASP E 326 " pdb=" OD1 ASP E 326 " ideal model delta sinusoidal sigma weight residual -30.00 -87.45 57.45 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 10317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1579 0.026 - 0.053: 647 0.053 - 0.079: 198 0.079 - 0.105: 102 0.105 - 0.132: 78 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CB ILE F 203 " pdb=" CA ILE F 203 " pdb=" CG1 ILE F 203 " pdb=" CG2 ILE F 203 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CB ILE C 203 " pdb=" CA ILE C 203 " pdb=" CG1 ILE C 203 " pdb=" CG2 ILE C 203 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 20 " pdb=" N ILE A 20 " pdb=" C ILE A 20 " pdb=" CB ILE A 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2601 not shown) Planarity restraints: 2964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 158 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO F 159 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO F 159 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 159 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 158 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO C 159 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 159 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 159 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 153 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C ILE B 153 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE B 153 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU B 154 " -0.007 2.00e-02 2.50e+03 ... (remaining 2961 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1770 2.75 - 3.29: 16348 3.29 - 3.83: 27738 3.83 - 4.36: 31587 4.36 - 4.90: 54788 Nonbonded interactions: 132231 Sorted by model distance: nonbonded pdb=" O GLY B 201 " pdb=" OG1 THR B 225 " model vdw 2.213 3.040 nonbonded pdb=" O GLY E 201 " pdb=" OG1 THR E 225 " model vdw 2.213 3.040 nonbonded pdb=" ND2 ASN B 189 " pdb=" OE1 GLU C 67 " model vdw 2.227 3.120 nonbonded pdb=" ND2 ASN E 189 " pdb=" OE1 GLU F 67 " model vdw 2.227 3.120 nonbonded pdb=" O GLY F 201 " pdb=" OG1 THR F 225 " model vdw 2.230 3.040 ... (remaining 132226 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.980 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.490 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.002 0.022 16770 Z= 0.096 Angle : 0.465 4.962 22602 Z= 0.262 Chirality : 0.038 0.132 2604 Planarity : 0.003 0.044 2964 Dihedral : 14.872 89.883 6384 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.52 (0.18), residues: 2094 helix: 0.28 (0.17), residues: 962 sheet: 0.08 (0.24), residues: 462 loop : -1.42 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 287 TYR 0.004 0.001 TYR E 19 PHE 0.006 0.001 PHE A 70 HIS 0.004 0.000 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.10 (16770) covalent geometry : angle 0.46516 / 0.26 (22602) hydrogen bonds : bond 0.18549 / 12.36 ( 854) hydrogen bonds : angle 6.12448 / 4.22 ( 2574) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9064 (tm-30) REVERT: A 178 LEU cc_start: 0.9038 (mp) cc_final: 0.8753 (mp) REVERT: A 304 MET cc_start: 0.9535 (ppp) cc_final: 0.9259 (ppp) REVERT: B 197 MET cc_start: 0.8551 (tmm) cc_final: 0.7999 (tmm) REVERT: B 346 MET cc_start: 0.9082 (ttp) cc_final: 0.8722 (ptm) REVERT: C 178 LEU cc_start: 0.8793 (tp) cc_final: 0.8554 (tp) REVERT: D 64 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9064 (tm-30) REVERT: D 178 LEU cc_start: 0.9037 (mp) cc_final: 0.8753 (mp) REVERT: D 304 MET cc_start: 0.9529 (ppp) cc_final: 0.9251 (ppp) REVERT: E 197 MET cc_start: 0.8563 (tmm) cc_final: 0.8014 (tmm) REVERT: E 346 MET cc_start: 0.9082 (ttp) cc_final: 0.8724 (ptm) REVERT: F 178 LEU cc_start: 0.8791 (tp) cc_final: 0.8551 (tp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1215 time to fit residues: 28.2838 Evaluate side-chains 118 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS B 152 HIS B 264 GLN C 189 ASN C 230 ASN D 298 HIS E 264 GLN F 189 ASN F 230 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.063957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.044422 restraints weight = 75254.237| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 5.33 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16770 Z= 0.157 Angle : 0.549 8.818 22602 Z= 0.288 Chirality : 0.041 0.184 2604 Planarity : 0.003 0.041 2964 Dihedral : 3.814 17.609 2310 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.13 % Allowed : 12.02 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2094 helix: 0.62 (0.17), residues: 974 sheet: -0.03 (0.24), residues: 472 loop : -1.35 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 293 TYR 0.009 0.001 TYR A 19 PHE 0.008 0.001 PHE E 250 HIS 0.006 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (16770) covalent geometry : angle 0.54903 / 0.29 (22602) hydrogen bonds : bond 0.04086 / 2.72 ( 854) hydrogen bonds : angle 4.73827 / 3.24 ( 2574) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9144 (mp) cc_final: 0.8857 (mp) REVERT: A 209 MET cc_start: 0.9026 (tmm) cc_final: 0.8800 (tmm) REVERT: A 223 MET cc_start: 0.8643 (mtp) cc_final: 0.8391 (mtp) REVERT: A 312 MET cc_start: 0.6450 (mtm) cc_final: 0.6136 (mtm) REVERT: B 138 MET cc_start: 0.8559 (mmm) cc_final: 0.7888 (mmp) REVERT: B 160 ILE cc_start: 0.9242 (mt) cc_final: 0.8183 (mt) REVERT: B 175 GLU cc_start: 0.8792 (tt0) cc_final: 0.8116 (tp30) REVERT: B 197 MET cc_start: 0.8723 (tmm) cc_final: 0.8246 (tmm) REVERT: B 223 MET cc_start: 0.9089 (mtp) cc_final: 0.8485 (ttm) REVERT: B 304 MET cc_start: 0.8547 (tmm) cc_final: 0.8314 (tmm) REVERT: B 346 MET cc_start: 0.9083 (ttp) cc_final: 0.8721 (ptm) REVERT: C 178 LEU cc_start: 0.8828 (tp) cc_final: 0.8626 (tp) REVERT: C 209 MET cc_start: 0.9158 (tmm) cc_final: 0.8881 (tmm) REVERT: C 213 MET cc_start: 0.9147 (tpp) cc_final: 0.8807 (tpp) REVERT: C 253 ASP cc_start: 0.9152 (m-30) cc_final: 0.8648 (p0) REVERT: C 297 LEU cc_start: 0.9302 (tp) cc_final: 0.8891 (pt) REVERT: C 298 HIS cc_start: 0.9247 (p90) cc_final: 0.8786 (p90) REVERT: C 346 MET cc_start: 0.8901 (ttp) cc_final: 0.8691 (ttp) REVERT: D 178 LEU cc_start: 0.9141 (mp) cc_final: 0.8854 (mp) REVERT: D 209 MET cc_start: 0.9026 (tmm) cc_final: 0.8801 (tmm) REVERT: D 223 MET cc_start: 0.8638 (mtp) cc_final: 0.8388 (mtp) REVERT: D 312 MET cc_start: 0.6473 (mtm) cc_final: 0.6161 (mtm) REVERT: E 138 MET cc_start: 0.8564 (mmm) cc_final: 0.7891 (mmp) REVERT: E 160 ILE cc_start: 0.9238 (mt) cc_final: 0.8175 (mt) REVERT: E 175 GLU cc_start: 0.8795 (tt0) cc_final: 0.8125 (tp30) REVERT: E 197 MET cc_start: 0.8716 (tmm) cc_final: 0.8244 (tmm) REVERT: E 223 MET cc_start: 0.9083 (mtp) cc_final: 0.8484 (ttm) REVERT: E 304 MET cc_start: 0.8534 (tmm) cc_final: 0.8302 (tmm) REVERT: E 346 MET cc_start: 0.9086 (ttp) cc_final: 0.8724 (ptm) REVERT: F 178 LEU cc_start: 0.8826 (tp) cc_final: 0.8625 (tp) REVERT: F 209 MET cc_start: 0.9160 (tmm) cc_final: 0.8881 (tmm) REVERT: F 213 MET cc_start: 0.9150 (tpp) cc_final: 0.8812 (tpp) REVERT: F 253 ASP cc_start: 0.9157 (m-30) cc_final: 0.8655 (p0) REVERT: F 297 LEU cc_start: 0.9298 (tp) cc_final: 0.8887 (pt) REVERT: F 298 HIS cc_start: 0.9241 (p90) cc_final: 0.8778 (p90) REVERT: F 346 MET cc_start: 0.8895 (ttp) cc_final: 0.8688 (ttp) outliers start: 20 outliers final: 6 residues processed: 138 average time/residue: 0.1080 time to fit residues: 23.0945 Evaluate side-chains 120 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 222 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 81 optimal weight: 0.0470 chunk 63 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN A 257 ASN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 ASN ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.062007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042422 restraints weight = 77120.462| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 5.33 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16770 Z= 0.206 Angle : 0.552 7.440 22602 Z= 0.293 Chirality : 0.040 0.131 2604 Planarity : 0.003 0.037 2964 Dihedral : 3.921 16.739 2310 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.13 % Allowed : 13.78 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.09 (0.18), residues: 2094 helix: 0.81 (0.17), residues: 974 sheet: -0.06 (0.23), residues: 480 loop : -1.28 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 293 TYR 0.013 0.002 TYR B 19 PHE 0.012 0.001 PHE E 250 HIS 0.010 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (16770) covalent geometry : angle 0.55180 / 0.29 (22602) hydrogen bonds : bond 0.03810 / 2.55 ( 854) hydrogen bonds : angle 4.56633 / 3.12 ( 2574) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9212 (mp) cc_final: 0.8965 (mp) REVERT: A 312 MET cc_start: 0.6293 (mtm) cc_final: 0.5967 (mtm) REVERT: B 54 MET cc_start: 0.9190 (mtm) cc_final: 0.8980 (mtm) REVERT: B 138 MET cc_start: 0.8591 (mmm) cc_final: 0.7849 (mmp) REVERT: B 175 GLU cc_start: 0.8795 (tt0) cc_final: 0.8406 (tp30) REVERT: B 184 GLU cc_start: 0.9059 (mp0) cc_final: 0.8773 (mp0) REVERT: B 304 MET cc_start: 0.8440 (tmm) cc_final: 0.7957 (tmm) REVERT: B 312 MET cc_start: 0.4508 (mmt) cc_final: 0.4246 (mmt) REVERT: B 346 MET cc_start: 0.9070 (ttp) cc_final: 0.8690 (ptm) REVERT: C 213 MET cc_start: 0.9229 (tpp) cc_final: 0.8985 (tpp) REVERT: C 253 ASP cc_start: 0.9141 (m-30) cc_final: 0.8755 (p0) REVERT: C 297 LEU cc_start: 0.9494 (tp) cc_final: 0.8973 (pt) REVERT: C 298 HIS cc_start: 0.9366 (p90) cc_final: 0.8872 (p90) REVERT: D 178 LEU cc_start: 0.9208 (mp) cc_final: 0.8960 (mp) REVERT: D 312 MET cc_start: 0.6289 (mtm) cc_final: 0.5968 (mtm) REVERT: E 54 MET cc_start: 0.9183 (mtm) cc_final: 0.8972 (mtm) REVERT: E 138 MET cc_start: 0.8592 (mmm) cc_final: 0.7852 (mmp) REVERT: E 175 GLU cc_start: 0.8795 (tt0) cc_final: 0.8403 (tp30) REVERT: E 184 GLU cc_start: 0.9058 (mp0) cc_final: 0.8770 (mp0) REVERT: E 304 MET cc_start: 0.8421 (tmm) cc_final: 0.7938 (tmm) REVERT: E 312 MET cc_start: 0.4480 (mmt) cc_final: 0.4219 (mmt) REVERT: E 346 MET cc_start: 0.9069 (ttp) cc_final: 0.8687 (ptm) REVERT: F 213 MET cc_start: 0.9231 (tpp) cc_final: 0.8989 (tpp) REVERT: F 253 ASP cc_start: 0.9144 (m-30) cc_final: 0.8760 (p0) REVERT: F 297 LEU cc_start: 0.9487 (tp) cc_final: 0.8965 (pt) REVERT: F 298 HIS cc_start: 0.9361 (p90) cc_final: 0.8863 (p90) outliers start: 20 outliers final: 16 residues processed: 122 average time/residue: 0.1009 time to fit residues: 19.4193 Evaluate side-chains 122 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 230 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.042430 restraints weight = 75862.126| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 5.31 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16770 Z= 0.147 Angle : 0.517 8.333 22602 Z= 0.271 Chirality : 0.040 0.213 2604 Planarity : 0.003 0.036 2964 Dihedral : 3.892 17.086 2310 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.70 % Allowed : 14.68 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.03 (0.18), residues: 2094 helix: 0.90 (0.17), residues: 970 sheet: -0.07 (0.24), residues: 480 loop : -1.28 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 293 TYR 0.010 0.001 TYR B 19 PHE 0.010 0.001 PHE B 250 HIS 0.004 0.001 HIS F 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (16770) covalent geometry : angle 0.51672 / 0.27 (22602) hydrogen bonds : bond 0.03330 / 2.24 ( 854) hydrogen bonds : angle 4.36591 / 2.99 ( 2574) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9212 (mp) cc_final: 0.8977 (mp) REVERT: B 54 MET cc_start: 0.9171 (mtm) cc_final: 0.8846 (mtm) REVERT: B 138 MET cc_start: 0.8491 (mmm) cc_final: 0.8065 (mmp) REVERT: B 175 GLU cc_start: 0.8807 (tt0) cc_final: 0.8396 (tp30) REVERT: B 197 MET cc_start: 0.9235 (tmm) cc_final: 0.8257 (tmm) REVERT: B 304 MET cc_start: 0.8457 (tmm) cc_final: 0.8190 (tmm) REVERT: B 312 MET cc_start: 0.4473 (mmt) cc_final: 0.4170 (mmt) REVERT: B 346 MET cc_start: 0.9068 (ttp) cc_final: 0.8663 (ptm) REVERT: C 213 MET cc_start: 0.9254 (tpp) cc_final: 0.8985 (tpp) REVERT: C 253 ASP cc_start: 0.9117 (m-30) cc_final: 0.8720 (p0) REVERT: C 297 LEU cc_start: 0.9500 (tp) cc_final: 0.8989 (pt) REVERT: C 298 HIS cc_start: 0.9372 (p90) cc_final: 0.8881 (p90) REVERT: D 178 LEU cc_start: 0.9206 (mp) cc_final: 0.8969 (mp) REVERT: E 54 MET cc_start: 0.9172 (mtm) cc_final: 0.8847 (mtm) REVERT: E 138 MET cc_start: 0.8488 (mmm) cc_final: 0.8065 (mmp) REVERT: E 175 GLU cc_start: 0.8799 (tt0) cc_final: 0.8384 (tp30) REVERT: E 197 MET cc_start: 0.9228 (tmm) cc_final: 0.8247 (tmm) REVERT: E 304 MET cc_start: 0.8445 (tmm) cc_final: 0.8184 (tmm) REVERT: E 312 MET cc_start: 0.4459 (mmt) cc_final: 0.4154 (mmt) REVERT: E 346 MET cc_start: 0.9070 (ttp) cc_final: 0.8663 (ptm) REVERT: F 213 MET cc_start: 0.9246 (tpp) cc_final: 0.8977 (tpp) REVERT: F 253 ASP cc_start: 0.9121 (m-30) cc_final: 0.8725 (p0) REVERT: F 297 LEU cc_start: 0.9493 (tp) cc_final: 0.8981 (pt) REVERT: F 298 HIS cc_start: 0.9368 (p90) cc_final: 0.8874 (p90) outliers start: 30 outliers final: 18 residues processed: 134 average time/residue: 0.1026 time to fit residues: 21.7398 Evaluate side-chains 130 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 303 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 10 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN E 264 GLN ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.062199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.042575 restraints weight = 76478.873| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 5.37 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16770 Z= 0.127 Angle : 0.512 8.435 22602 Z= 0.267 Chirality : 0.040 0.155 2604 Planarity : 0.003 0.034 2964 Dihedral : 3.896 16.652 2310 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.81 % Allowed : 15.48 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.05 (0.18), residues: 2094 helix: 0.90 (0.17), residues: 970 sheet: -0.15 (0.24), residues: 464 loop : -1.22 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 293 TYR 0.008 0.001 TYR B 320 PHE 0.009 0.001 PHE B 250 HIS 0.006 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (16770) covalent geometry : angle 0.51212 / 0.27 (22602) hydrogen bonds : bond 0.03164 / 2.14 ( 854) hydrogen bonds : angle 4.27799 / 2.92 ( 2574) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLU cc_start: 0.8185 (pm20) cc_final: 0.7940 (pm20) REVERT: A 178 LEU cc_start: 0.9213 (mp) cc_final: 0.8983 (mp) REVERT: B 54 MET cc_start: 0.9093 (mtm) cc_final: 0.8721 (mtm) REVERT: B 138 MET cc_start: 0.8599 (mmm) cc_final: 0.8131 (mmp) REVERT: B 175 GLU cc_start: 0.8805 (tt0) cc_final: 0.8099 (tp30) REVERT: B 197 MET cc_start: 0.9256 (tmm) cc_final: 0.8745 (tmm) REVERT: B 304 MET cc_start: 0.8542 (tmm) cc_final: 0.8080 (tmm) REVERT: B 346 MET cc_start: 0.9069 (ttp) cc_final: 0.8675 (ptm) REVERT: C 138 MET cc_start: 0.9396 (mmt) cc_final: 0.9010 (mmp) REVERT: C 297 LEU cc_start: 0.9457 (tp) cc_final: 0.8949 (pt) REVERT: C 298 HIS cc_start: 0.9364 (p90) cc_final: 0.8898 (p90) REVERT: C 320 TYR cc_start: 0.9404 (t80) cc_final: 0.8996 (t80) REVERT: D 157 GLU cc_start: 0.8178 (pm20) cc_final: 0.7932 (pm20) REVERT: D 178 LEU cc_start: 0.9210 (mp) cc_final: 0.8978 (mp) REVERT: E 54 MET cc_start: 0.9088 (mtm) cc_final: 0.8716 (mtm) REVERT: E 138 MET cc_start: 0.8598 (mmm) cc_final: 0.8132 (mmp) REVERT: E 175 GLU cc_start: 0.8803 (tt0) cc_final: 0.8096 (tp30) REVERT: E 197 MET cc_start: 0.9249 (tmm) cc_final: 0.8738 (tmm) REVERT: E 304 MET cc_start: 0.8532 (tmm) cc_final: 0.8070 (tmm) REVERT: E 346 MET cc_start: 0.9072 (ttp) cc_final: 0.8677 (ptm) REVERT: F 138 MET cc_start: 0.9393 (mmt) cc_final: 0.9004 (mmp) REVERT: F 297 LEU cc_start: 0.9456 (tp) cc_final: 0.8948 (pt) REVERT: F 298 HIS cc_start: 0.9366 (p90) cc_final: 0.8902 (p90) REVERT: F 320 TYR cc_start: 0.9405 (t80) cc_final: 0.8997 (t80) outliers start: 32 outliers final: 20 residues processed: 149 average time/residue: 0.1025 time to fit residues: 24.7888 Evaluate side-chains 133 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 303 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 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 = 0.3420 r_free = 0.3420 target = 0.061597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.042407 restraints weight = 75175.759| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 5.22 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16770 Z= 0.125 Angle : 0.556 11.027 22602 Z= 0.279 Chirality : 0.041 0.338 2604 Planarity : 0.003 0.034 2964 Dihedral : 3.929 16.102 2310 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.42 % Allowed : 17.57 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.10 (0.18), residues: 2094 helix: 0.86 (0.17), residues: 974 sheet: -0.20 (0.24), residues: 472 loop : -1.26 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 293 TYR 0.009 0.001 TYR B 320 PHE 0.007 0.001 PHE B 250 HIS 0.006 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (16770) covalent geometry : angle 0.55619 / 0.28 (22602) hydrogen bonds : bond 0.03096 / 2.09 ( 854) hydrogen bonds : angle 4.23720 / 2.89 ( 2574) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLU cc_start: 0.8217 (pm20) cc_final: 0.7996 (pm20) REVERT: A 178 LEU cc_start: 0.9270 (mp) cc_final: 0.9049 (mp) REVERT: B 54 MET cc_start: 0.9114 (mtm) cc_final: 0.8690 (mtm) REVERT: B 138 MET cc_start: 0.8710 (mmm) cc_final: 0.8220 (mmp) REVERT: B 197 MET cc_start: 0.9292 (tmm) cc_final: 0.8813 (tmm) REVERT: B 304 MET cc_start: 0.8389 (tmm) cc_final: 0.7953 (tmm) REVERT: B 346 MET cc_start: 0.9086 (ttp) cc_final: 0.8662 (ptm) REVERT: C 213 MET cc_start: 0.9161 (tpp) cc_final: 0.8201 (tpp) REVERT: C 253 ASP cc_start: 0.9127 (m-30) cc_final: 0.8813 (p0) REVERT: C 297 LEU cc_start: 0.9363 (tp) cc_final: 0.8827 (pt) REVERT: C 298 HIS cc_start: 0.9308 (p90) cc_final: 0.8822 (p90) REVERT: C 314 THR cc_start: 0.6030 (OUTLIER) cc_final: 0.5770 (m) REVERT: C 320 TYR cc_start: 0.9463 (t80) cc_final: 0.9221 (t80) REVERT: D 157 GLU cc_start: 0.8221 (pm20) cc_final: 0.7996 (pm20) REVERT: D 178 LEU cc_start: 0.9264 (mp) cc_final: 0.9042 (mp) REVERT: E 54 MET cc_start: 0.9107 (mtm) cc_final: 0.8681 (mtm) REVERT: E 138 MET cc_start: 0.8715 (mmm) cc_final: 0.8228 (mmp) REVERT: E 197 MET cc_start: 0.9289 (tmm) cc_final: 0.8807 (tmm) REVERT: E 304 MET cc_start: 0.8386 (tmm) cc_final: 0.7952 (tmm) REVERT: E 346 MET cc_start: 0.9085 (ttp) cc_final: 0.8665 (ptm) REVERT: F 213 MET cc_start: 0.9154 (tpp) cc_final: 0.8192 (tpp) REVERT: F 253 ASP cc_start: 0.9127 (m-30) cc_final: 0.8815 (p0) REVERT: F 297 LEU cc_start: 0.9352 (tp) cc_final: 0.8817 (pt) REVERT: F 298 HIS cc_start: 0.9294 (p90) cc_final: 0.8804 (p90) REVERT: F 314 THR cc_start: 0.6030 (OUTLIER) cc_final: 0.5770 (m) REVERT: F 320 TYR cc_start: 0.9460 (t80) cc_final: 0.9218 (t80) outliers start: 25 outliers final: 16 residues processed: 134 average time/residue: 0.0916 time to fit residues: 19.9099 Evaluate side-chains 134 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 111 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 54 optimal weight: 0.0010 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 264 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 HIS ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.062363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.043103 restraints weight = 75237.617| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 5.24 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16770 Z= 0.100 Angle : 0.548 10.577 22602 Z= 0.274 Chirality : 0.041 0.249 2604 Planarity : 0.003 0.032 2964 Dihedral : 3.900 17.050 2310 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.30 % Allowed : 18.08 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.03 (0.18), residues: 2094 helix: 0.90 (0.17), residues: 972 sheet: -0.08 (0.24), residues: 464 loop : -1.26 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 293 TYR 0.008 0.001 TYR B 320 PHE 0.007 0.001 PHE D 70 HIS 0.007 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (16770) covalent geometry : angle 0.54778 / 0.27 (22602) hydrogen bonds : bond 0.02891 / 1.96 ( 854) hydrogen bonds : angle 4.15406 / 2.84 ( 2574) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLU cc_start: 0.8288 (pm20) cc_final: 0.8002 (pm20) REVERT: A 178 LEU cc_start: 0.9260 (mp) cc_final: 0.9039 (mp) REVERT: A 312 MET cc_start: 0.5906 (mtm) cc_final: 0.5378 (ttp) REVERT: B 54 MET cc_start: 0.9076 (mtm) cc_final: 0.8682 (mtm) REVERT: B 138 MET cc_start: 0.8758 (mmm) cc_final: 0.8230 (mmp) REVERT: B 197 MET cc_start: 0.9282 (tmm) cc_final: 0.8809 (tmm) REVERT: B 304 MET cc_start: 0.8351 (tmm) cc_final: 0.7919 (tmm) REVERT: B 346 MET cc_start: 0.9081 (ttp) cc_final: 0.8646 (ptm) REVERT: C 213 MET cc_start: 0.9228 (tpp) cc_final: 0.8293 (tpp) REVERT: C 253 ASP cc_start: 0.9093 (m-30) cc_final: 0.8777 (p0) REVERT: C 297 LEU cc_start: 0.9334 (tp) cc_final: 0.8803 (pt) REVERT: C 298 HIS cc_start: 0.9321 (p90) cc_final: 0.8835 (p90) REVERT: C 320 TYR cc_start: 0.9471 (t80) cc_final: 0.9227 (t80) REVERT: D 157 GLU cc_start: 0.8290 (pm20) cc_final: 0.8004 (pm20) REVERT: D 178 LEU cc_start: 0.9261 (mp) cc_final: 0.9040 (mp) REVERT: D 312 MET cc_start: 0.5895 (mtm) cc_final: 0.5369 (ttp) REVERT: E 54 MET cc_start: 0.9065 (mtm) cc_final: 0.8664 (mtm) REVERT: E 138 MET cc_start: 0.8761 (mmm) cc_final: 0.8232 (mmp) REVERT: E 197 MET cc_start: 0.9278 (tmm) cc_final: 0.8808 (tmm) REVERT: E 304 MET cc_start: 0.8345 (tmm) cc_final: 0.7914 (tmm) REVERT: E 346 MET cc_start: 0.9080 (ttp) cc_final: 0.8648 (ptm) REVERT: F 213 MET cc_start: 0.9222 (tpp) cc_final: 0.8291 (tpp) REVERT: F 253 ASP cc_start: 0.9095 (m-30) cc_final: 0.8779 (p0) REVERT: F 297 LEU cc_start: 0.9329 (tp) cc_final: 0.8798 (pt) REVERT: F 298 HIS cc_start: 0.9315 (p90) cc_final: 0.8826 (p90) REVERT: F 320 TYR cc_start: 0.9472 (t80) cc_final: 0.9230 (t80) outliers start: 23 outliers final: 14 residues processed: 136 average time/residue: 0.1159 time to fit residues: 25.3814 Evaluate side-chains 130 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 303 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 123 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 124 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 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 = 0.3430 r_free = 0.3430 target = 0.061912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.042745 restraints weight = 75246.688| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 5.25 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16770 Z= 0.109 Angle : 0.541 10.907 22602 Z= 0.273 Chirality : 0.040 0.171 2604 Planarity : 0.003 0.032 2964 Dihedral : 3.872 18.750 2310 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.76 % Allowed : 18.08 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.01 (0.18), residues: 2094 helix: 0.91 (0.17), residues: 972 sheet: -0.05 (0.24), residues: 464 loop : -1.23 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 293 TYR 0.009 0.001 TYR B 19 PHE 0.007 0.001 PHE D 70 HIS 0.007 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (16770) covalent geometry : angle 0.54052 / 0.27 (22602) hydrogen bonds : bond 0.02859 / 1.95 ( 854) hydrogen bonds : angle 4.12032 / 2.82 ( 2574) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLU cc_start: 0.8279 (pm20) cc_final: 0.8006 (pm20) REVERT: A 178 LEU cc_start: 0.9260 (mp) cc_final: 0.9036 (mp) REVERT: A 312 MET cc_start: 0.5924 (mtm) cc_final: 0.5429 (ttp) REVERT: B 54 MET cc_start: 0.9070 (mtm) cc_final: 0.8711 (mtm) REVERT: B 138 MET cc_start: 0.8754 (mmm) cc_final: 0.8207 (mmp) REVERT: B 157 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: B 197 MET cc_start: 0.9308 (tmm) cc_final: 0.9046 (tmm) REVERT: B 304 MET cc_start: 0.8372 (tmm) cc_final: 0.7936 (tmm) REVERT: B 346 MET cc_start: 0.9076 (ttp) cc_final: 0.8633 (ptm) REVERT: C 213 MET cc_start: 0.9258 (tpp) cc_final: 0.8383 (tpp) REVERT: C 253 ASP cc_start: 0.9156 (m-30) cc_final: 0.8810 (p0) REVERT: C 297 LEU cc_start: 0.9303 (tp) cc_final: 0.8806 (pt) REVERT: C 298 HIS cc_start: 0.9280 (p90) cc_final: 0.8806 (p90) REVERT: C 320 TYR cc_start: 0.9479 (t80) cc_final: 0.9209 (t80) REVERT: D 157 GLU cc_start: 0.8284 (pm20) cc_final: 0.8008 (pm20) REVERT: D 178 LEU cc_start: 0.9262 (mp) cc_final: 0.9038 (mp) REVERT: D 312 MET cc_start: 0.5917 (mtm) cc_final: 0.5423 (ttp) REVERT: E 54 MET cc_start: 0.9066 (mtm) cc_final: 0.8706 (mtm) REVERT: E 138 MET cc_start: 0.8761 (mmm) cc_final: 0.8215 (mmp) REVERT: E 157 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: E 197 MET cc_start: 0.9305 (tmm) cc_final: 0.9043 (tmm) REVERT: E 304 MET cc_start: 0.8372 (tmm) cc_final: 0.7935 (tmm) REVERT: E 346 MET cc_start: 0.9075 (ttp) cc_final: 0.8638 (ptm) REVERT: F 213 MET cc_start: 0.9252 (tpp) cc_final: 0.8380 (tpp) REVERT: F 253 ASP cc_start: 0.9159 (m-30) cc_final: 0.8815 (p0) REVERT: F 297 LEU cc_start: 0.9299 (tp) cc_final: 0.8803 (pt) REVERT: F 298 HIS cc_start: 0.9274 (p90) cc_final: 0.8800 (p90) REVERT: F 320 TYR cc_start: 0.9478 (t80) cc_final: 0.9208 (t80) outliers start: 31 outliers final: 18 residues processed: 142 average time/residue: 0.1089 time to fit residues: 24.5738 Evaluate side-chains 136 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 303 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 HIS ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.041966 restraints weight = 77311.572| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 5.18 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16770 Z= 0.191 Angle : 0.602 11.093 22602 Z= 0.305 Chirality : 0.040 0.132 2604 Planarity : 0.003 0.034 2964 Dihedral : 3.976 19.249 2310 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.59 % Allowed : 18.48 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.08 (0.18), residues: 2094 helix: 0.85 (0.17), residues: 978 sheet: -0.13 (0.24), residues: 472 loop : -1.27 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 293 TYR 0.013 0.001 TYR E 19 PHE 0.010 0.001 PHE E 279 HIS 0.006 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (16770) covalent geometry : angle 0.60193 / 0.30 (22602) hydrogen bonds : bond 0.03192 / 2.17 ( 854) hydrogen bonds : angle 4.31094 / 2.96 ( 2574) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLU cc_start: 0.8419 (pm20) cc_final: 0.8138 (pm20) REVERT: A 178 LEU cc_start: 0.9306 (mp) cc_final: 0.9087 (mp) REVERT: A 312 MET cc_start: 0.6006 (mtm) cc_final: 0.5503 (ttp) REVERT: B 138 MET cc_start: 0.8724 (mmm) cc_final: 0.7978 (mmp) REVERT: B 157 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: B 304 MET cc_start: 0.8390 (tmm) cc_final: 0.7972 (tmm) REVERT: C 213 MET cc_start: 0.9368 (tpp) cc_final: 0.8483 (tpp) REVERT: C 253 ASP cc_start: 0.9171 (m-30) cc_final: 0.8863 (p0) REVERT: C 297 LEU cc_start: 0.9332 (tp) cc_final: 0.8830 (pt) REVERT: C 298 HIS cc_start: 0.9300 (p90) cc_final: 0.8828 (p90) REVERT: C 320 TYR cc_start: 0.9488 (t80) cc_final: 0.9240 (t80) REVERT: D 157 GLU cc_start: 0.8409 (pm20) cc_final: 0.8126 (pm20) REVERT: D 178 LEU cc_start: 0.9307 (mp) cc_final: 0.9089 (mp) REVERT: D 312 MET cc_start: 0.5992 (mtm) cc_final: 0.5491 (ttp) REVERT: E 138 MET cc_start: 0.8723 (mmm) cc_final: 0.7977 (mmp) REVERT: E 157 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: E 304 MET cc_start: 0.8383 (tmm) cc_final: 0.7966 (tmm) REVERT: F 213 MET cc_start: 0.9372 (tpp) cc_final: 0.8481 (tpp) REVERT: F 253 ASP cc_start: 0.9170 (m-30) cc_final: 0.8861 (p0) REVERT: F 297 LEU cc_start: 0.9329 (tp) cc_final: 0.8827 (pt) REVERT: F 298 HIS cc_start: 0.9293 (p90) cc_final: 0.8819 (p90) REVERT: F 320 TYR cc_start: 0.9493 (t80) cc_final: 0.9247 (t80) outliers start: 28 outliers final: 20 residues processed: 134 average time/residue: 0.1226 time to fit residues: 26.5225 Evaluate side-chains 132 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 159 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 194 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 186 optimal weight: 0.0670 chunk 166 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 173 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.062021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.042883 restraints weight = 75772.308| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 5.23 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16770 Z= 0.107 Angle : 0.593 12.743 22602 Z= 0.293 Chirality : 0.042 0.381 2604 Planarity : 0.003 0.031 2964 Dihedral : 3.964 19.776 2310 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.30 % Allowed : 19.10 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.03 (0.18), residues: 2094 helix: 0.86 (0.17), residues: 976 sheet: -0.01 (0.24), residues: 464 loop : -1.25 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 293 TYR 0.008 0.001 TYR B 19 PHE 0.007 0.001 PHE A 70 HIS 0.007 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (16770) covalent geometry : angle 0.59342 / 0.29 (22602) hydrogen bonds : bond 0.02904 / 1.98 ( 854) hydrogen bonds : angle 4.19764 / 2.89 ( 2574) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLU cc_start: 0.8376 (pm20) cc_final: 0.8059 (pm20) REVERT: A 178 LEU cc_start: 0.9274 (mp) cc_final: 0.9060 (mp) REVERT: A 312 MET cc_start: 0.6064 (mtm) cc_final: 0.5679 (ttp) REVERT: B 138 MET cc_start: 0.8657 (mmm) cc_final: 0.8005 (mmp) REVERT: B 157 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: B 197 MET cc_start: 0.9098 (tmm) cc_final: 0.8488 (tmm) REVERT: B 304 MET cc_start: 0.8385 (tmm) cc_final: 0.7986 (tmm) REVERT: C 213 MET cc_start: 0.9359 (tpp) cc_final: 0.8451 (tpp) REVERT: C 253 ASP cc_start: 0.9112 (m-30) cc_final: 0.8824 (p0) REVERT: C 297 LEU cc_start: 0.9302 (tp) cc_final: 0.8818 (pt) REVERT: C 298 HIS cc_start: 0.9276 (p90) cc_final: 0.8797 (p90) REVERT: C 320 TYR cc_start: 0.9467 (t80) cc_final: 0.9248 (t80) REVERT: D 157 GLU cc_start: 0.8366 (pm20) cc_final: 0.8045 (pm20) REVERT: D 178 LEU cc_start: 0.9275 (mp) cc_final: 0.9061 (mp) REVERT: D 312 MET cc_start: 0.6040 (mtm) cc_final: 0.5657 (ttp) REVERT: E 138 MET cc_start: 0.8657 (mmm) cc_final: 0.8007 (mmp) REVERT: E 157 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: E 197 MET cc_start: 0.9089 (tmm) cc_final: 0.8476 (tmm) REVERT: E 304 MET cc_start: 0.8374 (tmm) cc_final: 0.7976 (tmm) REVERT: F 213 MET cc_start: 0.9359 (tpp) cc_final: 0.8457 (tpp) REVERT: F 253 ASP cc_start: 0.9112 (m-30) cc_final: 0.8824 (p0) REVERT: F 297 LEU cc_start: 0.9302 (tp) cc_final: 0.8816 (pt) REVERT: F 298 HIS cc_start: 0.9278 (p90) cc_final: 0.8802 (p90) REVERT: F 320 TYR cc_start: 0.9467 (t80) cc_final: 0.9249 (t80) outliers start: 23 outliers final: 19 residues processed: 134 average time/residue: 0.1084 time to fit residues: 23.4367 Evaluate side-chains 135 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 335 HIS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 198 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.0050 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.042015 restraints weight = 76522.384| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 5.17 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16770 Z= 0.158 Angle : 0.605 11.540 22602 Z= 0.303 Chirality : 0.041 0.366 2604 Planarity : 0.003 0.030 2964 Dihedral : 3.985 19.653 2310 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.47 % Allowed : 18.82 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.18), residues: 2094 helix: 0.84 (0.17), residues: 978 sheet: -0.09 (0.24), residues: 472 loop : -1.23 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 293 TYR 0.012 0.001 TYR E 19 PHE 0.008 0.001 PHE E 279 HIS 0.006 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (16770) covalent geometry : angle 0.60507 / 0.30 (22602) hydrogen bonds : bond 0.03112 / 2.12 ( 854) hydrogen bonds : angle 4.28278 / 2.95 ( 2574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2477.38 seconds wall clock time: 43 minutes 43.34 seconds (2623.34 seconds total)