Starting phenix.real_space_refine on Tue May 5 19:10:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rmi_54060/05_2026/9rmi_54060_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rmi_54060/05_2026/9rmi_54060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rmi_54060/05_2026/9rmi_54060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rmi_54060/05_2026/9rmi_54060.map" model { file = "/net/cci-nas-00/data/ceres_data/9rmi_54060/05_2026/9rmi_54060_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rmi_54060/05_2026/9rmi_54060_trim.cif" } resolution = 3.92 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= 0.015 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 42 5.16 5 C 9900 2.51 5 N 2676 2.21 5 O 3030 1.98 5 H 15450 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31110 Number of models: 1 Model: "" Number of chains: 2 Chain: "G" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5158 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: K, C, E, I, A Time building chain proxies: 5.12, per 1000 atoms: 0.16 Number of scatterers: 31110 At special positions: 0 Unit cell: (161.15, 172.328, 76.383, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 12 15.00 O 3030 8.00 N 2676 7.00 C 9900 6.00 H 15450 1.00 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: 2.37 Conformation dependent library (CDL) restraints added in 670.0 milliseconds 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 44.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'G' and resid 76 through 82 removed outlier: 3.673A pdb=" N VAL G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 95 removed outlier: 3.816A pdb=" N MET G 94 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 114 Processing helix chain 'G' and resid 127 through 139 Processing helix chain 'G' and resid 155 through 171 removed outlier: 3.734A pdb=" N GLU G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 205 removed outlier: 3.628A pdb=" N LEU G 200 " --> pdb=" O GLY G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 212 removed outlier: 4.359A pdb=" N GLY G 211 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 219 removed outlier: 3.796A pdb=" N LYS G 218 " --> pdb=" O ASP G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 263 removed outlier: 3.803A pdb=" N LEU G 259 " --> pdb=" O LYS G 255 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU G 263 " --> pdb=" O LEU G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 280 removed outlier: 3.578A pdb=" N SER G 276 " --> pdb=" O LEU G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 319 removed outlier: 4.369A pdb=" N LEU G 305 " --> pdb=" O SER G 301 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 318 " --> pdb=" O CYS G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 348 removed outlier: 3.705A pdb=" N GLU G 336 " --> pdb=" O GLY G 332 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU G 340 " --> pdb=" O GLU G 336 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP G 341 " --> pdb=" O PHE G 337 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP G 348 " --> pdb=" O ARG G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 378 Processing helix chain 'K' and resid 61 through 65 Processing helix chain 'K' and resid 76 through 82 removed outlier: 3.673A pdb=" N VAL K 80 " --> pdb=" O SER K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 removed outlier: 3.816A pdb=" N MET K 94 " --> pdb=" O ASP K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 114 Processing helix chain 'K' and resid 127 through 139 Processing helix chain 'K' and resid 155 through 171 removed outlier: 3.734A pdb=" N GLU K 160 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 205 removed outlier: 3.627A pdb=" N LEU K 200 " --> pdb=" O GLY K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 212 removed outlier: 4.359A pdb=" N GLY K 211 " --> pdb=" O LYS K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 219 removed outlier: 3.797A pdb=" N LYS K 218 " --> pdb=" O ASP K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 263 removed outlier: 3.803A pdb=" N LEU K 259 " --> pdb=" O LYS K 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU K 263 " --> pdb=" O LEU K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 280 removed outlier: 3.578A pdb=" N SER K 276 " --> pdb=" O LEU K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 319 removed outlier: 4.369A pdb=" N LEU K 305 " --> pdb=" O SER K 301 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU K 318 " --> pdb=" O CYS K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 348 removed outlier: 3.705A pdb=" N GLU K 336 " --> pdb=" O GLY K 332 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU K 340 " --> pdb=" O GLU K 336 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP K 341 " --> pdb=" O PHE K 337 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP K 348 " --> pdb=" O ARG K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 378 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 76 through 82 removed outlier: 3.673A pdb=" N VAL C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.816A pdb=" N MET C 94 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 155 through 171 removed outlier: 3.734A pdb=" N GLU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.628A pdb=" N LEU C 200 " --> pdb=" O GLY C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 removed outlier: 4.359A pdb=" N GLY C 211 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.797A pdb=" N LYS C 218 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.803A pdb=" N LEU C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 280 removed outlier: 3.578A pdb=" N SER C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 319 removed outlier: 4.369A pdb=" N LEU C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 348 removed outlier: 3.705A pdb=" N GLU C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 378 Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 76 through 82 removed outlier: 3.672A pdb=" N VAL E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.816A pdb=" N MET E 94 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 114 Processing helix chain 'E' and resid 127 through 139 Processing helix chain 'E' and resid 155 through 171 removed outlier: 3.734A pdb=" N GLU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 205 removed outlier: 3.627A pdb=" N LEU E 200 " --> pdb=" O GLY E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 4.358A pdb=" N GLY E 211 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 removed outlier: 3.796A pdb=" N LYS E 218 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.803A pdb=" N LEU E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 280 removed outlier: 3.578A pdb=" N SER E 276 " --> pdb=" O LEU E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 319 removed outlier: 4.368A pdb=" N LEU E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 348 removed outlier: 3.705A pdb=" N GLU E 336 " --> pdb=" O GLY E 332 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 341 " --> pdb=" O PHE E 337 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP E 348 " --> pdb=" O ARG E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 378 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'I' and resid 76 through 82 removed outlier: 3.672A pdb=" N VAL I 80 " --> pdb=" O SER I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 95 removed outlier: 3.815A pdb=" N MET I 94 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 114 Processing helix chain 'I' and resid 127 through 139 Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.734A pdb=" N GLU I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 205 removed outlier: 3.629A pdb=" N LEU I 200 " --> pdb=" O GLY I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 212 removed outlier: 4.358A pdb=" N GLY I 211 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 219 removed outlier: 3.796A pdb=" N LYS I 218 " --> pdb=" O ASP I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 263 removed outlier: 3.803A pdb=" N LEU I 259 " --> pdb=" O LYS I 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU I 263 " --> pdb=" O LEU I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 280 removed outlier: 3.578A pdb=" N SER I 276 " --> pdb=" O LEU I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 319 removed outlier: 4.369A pdb=" N LEU I 305 " --> pdb=" O SER I 301 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 318 " --> pdb=" O CYS I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 348 removed outlier: 3.706A pdb=" N GLU I 336 " --> pdb=" O GLY I 332 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU I 340 " --> pdb=" O GLU I 336 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP I 341 " --> pdb=" O PHE I 337 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP I 348 " --> pdb=" O ARG I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 378 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.672A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 removed outlier: 3.816A pdb=" N MET A 94 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.734A pdb=" N GLU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.627A pdb=" N LEU A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 4.358A pdb=" N GLY A 211 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.797A pdb=" N LYS A 218 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.803A pdb=" N LEU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.577A pdb=" N SER A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.368A pdb=" N LEU A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 348 removed outlier: 3.706A pdb=" N GLU A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 378 Processing sheet with id=AA1, first strand: chain 'G' and resid 66 through 69 removed outlier: 6.779A pdb=" N LEU G 45 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLY G 150 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL G 47 " --> pdb=" O GLY G 150 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N ASP G 143 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS G 189 " --> pdb=" O ASP G 143 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE G 145 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N TRP G 191 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL G 147 " --> pdb=" O TRP G 191 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N MET G 193 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU G 149 " --> pdb=" O MET G 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AA3, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AA4, first strand: chain 'G' and resid 286 through 287 Processing sheet with id=AA5, first strand: chain 'K' and resid 66 through 69 removed outlier: 6.778A pdb=" N LEU K 45 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLY K 150 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL K 47 " --> pdb=" O GLY K 150 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N ASP K 143 " --> pdb=" O ILE K 187 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N LYS K 189 " --> pdb=" O ASP K 143 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE K 145 " --> pdb=" O LYS K 189 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N TRP K 191 " --> pdb=" O ILE K 145 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL K 147 " --> pdb=" O TRP K 191 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N MET K 193 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU K 149 " --> pdb=" O MET K 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 240 through 241 Processing sheet with id=AA7, first strand: chain 'K' and resid 240 through 241 Processing sheet with id=AA8, first strand: chain 'K' and resid 286 through 287 Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 69 removed outlier: 6.778A pdb=" N LEU C 45 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY C 150 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL C 47 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N ASP C 143 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS C 189 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE C 145 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N TRP C 191 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL C 147 " --> pdb=" O TRP C 191 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N MET C 193 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU C 149 " --> pdb=" O MET C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB3, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AB4, first strand: chain 'E' and resid 66 through 69 removed outlier: 6.778A pdb=" N LEU E 45 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLY E 150 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL E 47 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N ASP E 143 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS E 189 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE E 145 " --> pdb=" O LYS E 189 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N TRP E 191 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 147 " --> pdb=" O TRP E 191 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N MET E 193 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU E 149 " --> pdb=" O MET E 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 240 through 241 Processing sheet with id=AB6, first strand: chain 'E' and resid 240 through 241 Processing sheet with id=AB7, first strand: chain 'E' and resid 286 through 287 Processing sheet with id=AB8, first strand: chain 'I' and resid 66 through 69 removed outlier: 6.779A pdb=" N LEU I 45 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLY I 150 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL I 47 " --> pdb=" O GLY I 150 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N ASP I 143 " --> pdb=" O ILE I 187 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS I 189 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE I 145 " --> pdb=" O LYS I 189 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N TRP I 191 " --> pdb=" O ILE I 145 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL I 147 " --> pdb=" O TRP I 191 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N MET I 193 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU I 149 " --> pdb=" O MET I 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 240 through 241 Processing sheet with id=AC1, first strand: chain 'I' and resid 240 through 241 Processing sheet with id=AC2, first strand: chain 'I' and resid 286 through 287 Processing sheet with id=AC3, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.779A pdb=" N LEU A 45 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLY A 150 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL A 47 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N ASP A 143 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N LYS A 189 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE A 145 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N TRP A 191 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 147 " --> pdb=" O TRP A 191 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N MET A 193 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 149 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AC5, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AC6, first strand: chain 'A' and resid 286 through 287 792 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 15438 1.12 - 1.30: 2700 1.30 - 1.47: 5680 1.47 - 1.64: 7532 1.64 - 1.81: 72 Bond restraints: 31422 Sorted by residual: bond pdb=" NH1 ARG C 161 " pdb="HH11 ARG C 161 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N SER K 155 " pdb=" H SER K 155 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CD2 PHE I 67 " pdb=" HD2 PHE I 67 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CD2 PHE K 67 " pdb=" HD2 PHE K 67 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N ALA I 116 " pdb=" H ALA I 116 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 ... (remaining 31417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 50082 2.84 - 5.68: 5243 5.68 - 8.53: 1435 8.53 - 11.37: 30 11.37 - 14.21: 24 Bond angle restraints: 56814 Sorted by residual: angle pdb=" CA ASP C 95 " pdb=" CB ASP C 95 " pdb=" CG ASP C 95 " ideal model delta sigma weight residual 112.60 117.84 -5.24 1.00e+00 1.00e+00 2.75e+01 angle pdb=" CA ASP E 95 " pdb=" CB ASP E 95 " pdb=" CG ASP E 95 " ideal model delta sigma weight residual 112.60 117.82 -5.22 1.00e+00 1.00e+00 2.73e+01 angle pdb=" CA ASP G 95 " pdb=" CB ASP G 95 " pdb=" CG ASP G 95 " ideal model delta sigma weight residual 112.60 117.82 -5.22 1.00e+00 1.00e+00 2.73e+01 angle pdb=" CA ASP I 95 " pdb=" CB ASP I 95 " pdb=" CG ASP I 95 " ideal model delta sigma weight residual 112.60 117.82 -5.22 1.00e+00 1.00e+00 2.72e+01 angle pdb=" CA ASP K 95 " pdb=" CB ASP K 95 " pdb=" CG ASP K 95 " ideal model delta sigma weight residual 112.60 117.79 -5.19 1.00e+00 1.00e+00 2.69e+01 ... (remaining 56809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.45: 13902 30.45 - 60.90: 690 60.90 - 91.35: 108 91.35 - 121.80: 12 121.80 - 152.24: 6 Dihedral angle restraints: 14718 sinusoidal: 8082 harmonic: 6636 Sorted by residual: dihedral pdb=" C2' ADP E 401 " pdb=" C1' ADP E 401 " pdb=" N9 ADP E 401 " pdb=" C4 ADP E 401 " ideal model delta sinusoidal sigma weight residual 91.55 -60.70 152.24 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" C2' ADP I 401 " pdb=" C1' ADP I 401 " pdb=" N9 ADP I 401 " pdb=" C4 ADP I 401 " ideal model delta sinusoidal sigma weight residual 91.55 -60.67 152.22 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" C2' ADP G 401 " pdb=" C1' ADP G 401 " pdb=" N9 ADP G 401 " pdb=" C4 ADP G 401 " ideal model delta sinusoidal sigma weight residual 91.55 -60.67 152.22 1 2.00e+01 2.50e-03 4.52e+01 ... (remaining 14715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1232 0.061 - 0.122: 766 0.122 - 0.183: 348 0.183 - 0.244: 50 0.244 - 0.305: 10 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA GLN I 350 " pdb=" N GLN I 350 " pdb=" C GLN I 350 " pdb=" CB GLN I 350 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA GLN E 350 " pdb=" N GLN E 350 " pdb=" C GLN E 350 " pdb=" CB GLN E 350 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA GLN K 350 " pdb=" N GLN K 350 " pdb=" C GLN K 350 " pdb=" CB GLN K 350 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2403 not shown) Planarity restraints: 4728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 240 " 0.642 9.50e-02 1.11e+02 2.33e-01 2.34e+02 pdb=" NE ARG A 240 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 240 " -0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG A 240 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 240 " -0.150 2.00e-02 2.50e+03 pdb="HH11 ARG A 240 " 0.073 2.00e-02 2.50e+03 pdb="HH12 ARG A 240 " -0.078 2.00e-02 2.50e+03 pdb="HH21 ARG A 240 " 0.009 2.00e-02 2.50e+03 pdb="HH22 ARG A 240 " 0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 240 " 0.643 9.50e-02 1.11e+02 2.33e-01 2.34e+02 pdb=" NE ARG I 240 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG I 240 " -0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG I 240 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG I 240 " -0.149 2.00e-02 2.50e+03 pdb="HH11 ARG I 240 " 0.073 2.00e-02 2.50e+03 pdb="HH12 ARG I 240 " -0.078 2.00e-02 2.50e+03 pdb="HH21 ARG I 240 " 0.009 2.00e-02 2.50e+03 pdb="HH22 ARG I 240 " 0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 240 " 0.643 9.50e-02 1.11e+02 2.33e-01 2.34e+02 pdb=" NE ARG E 240 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG E 240 " -0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG E 240 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG E 240 " -0.149 2.00e-02 2.50e+03 pdb="HH11 ARG E 240 " 0.074 2.00e-02 2.50e+03 pdb="HH12 ARG E 240 " -0.078 2.00e-02 2.50e+03 pdb="HH21 ARG E 240 " 0.009 2.00e-02 2.50e+03 pdb="HH22 ARG E 240 " 0.190 2.00e-02 2.50e+03 ... (remaining 4725 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 865 2.05 - 2.69: 40857 2.69 - 3.33: 92406 3.33 - 3.96: 118943 3.96 - 4.60: 176640 Nonbonded interactions: 429711 Sorted by model distance: nonbonded pdb="HG22 VAL E 84 " pdb="HH12 ARG I 243 " model vdw 1.417 2.270 nonbonded pdb="HH12 ARG E 243 " pdb="HG22 VAL A 84 " model vdw 1.424 2.270 nonbonded pdb=" HG SER G 271 " pdb=" OE1 GLU C 323 " model vdw 1.448 2.450 nonbonded pdb="HG22 VAL G 84 " pdb="HH12 ARG C 243 " model vdw 1.454 2.270 nonbonded pdb="HH12 ARG G 243 " pdb="HG22 VAL K 84 " model vdw 1.482 2.270 ... (remaining 429706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'C' selection = chain 'E' selection = chain 'I' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.310 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: 0.110 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.890 Find NCS groups from input model: 0.140 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.012 0.142 15972 Z= 0.705 Angle : 1.757 14.208 21654 Z= 1.131 Chirality : 0.087 0.305 2406 Planarity : 0.017 0.213 2802 Dihedral : 14.614 152.244 5862 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.16), residues: 2004 helix: -1.54 (0.16), residues: 756 sheet: -0.11 (0.32), residues: 198 loop : -0.69 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG I 240 TYR 0.087 0.017 TYR A 370 PHE 0.085 0.014 PHE I 239 TRP 0.055 0.015 TRP A 202 HIS 0.009 0.004 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.01191 (15972) covalent geometry : angle 1.75695 (21654) hydrogen bonds : bond 0.17528 ( 780) hydrogen bonds : angle 8.54633 ( 2106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.806 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 46 SER cc_start: 0.7674 (t) cc_final: 0.6879 (p) REVERT: C 46 SER cc_start: 0.7941 (t) cc_final: 0.7253 (p) REVERT: C 259 LEU cc_start: 0.8067 (mt) cc_final: 0.7551 (mp) REVERT: E 46 SER cc_start: 0.7592 (t) cc_final: 0.6677 (p) REVERT: I 46 SER cc_start: 0.7905 (t) cc_final: 0.7219 (p) REVERT: I 259 LEU cc_start: 0.8071 (mt) cc_final: 0.7552 (mp) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2968 time to fit residues: 173.9101 Evaluate side-chains 224 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 367 GLN K 367 GLN C 367 GLN E 367 GLN I 367 GLN A 367 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.081021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070563 restraints weight = 165833.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.073598 restraints weight = 68785.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.075595 restraints weight = 36181.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076866 restraints weight = 21885.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.077786 restraints weight = 14782.162| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15972 Z= 0.140 Angle : 0.655 6.533 21654 Z= 0.334 Chirality : 0.044 0.146 2406 Planarity : 0.005 0.058 2802 Dihedral : 11.006 137.292 2214 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.42 % Allowed : 8.88 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.62 (0.17), residues: 2004 helix: 0.28 (0.18), residues: 774 sheet: -0.18 (0.23), residues: 420 loop : -1.11 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 161 TYR 0.013 0.002 TYR A 197 PHE 0.014 0.002 PHE I 251 TRP 0.006 0.001 TRP K 339 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00288 (15972) covalent geometry : angle 0.65497 (21654) hydrogen bonds : bond 0.04398 ( 780) hydrogen bonds : angle 6.18708 ( 2106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.807 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 193 MET cc_start: 0.8372 (ptp) cc_final: 0.8169 (ptp) REVERT: C 287 TYR cc_start: 0.8457 (t80) cc_final: 0.8225 (t80) REVERT: E 81 ARG cc_start: 0.8542 (mtt180) cc_final: 0.8244 (ttm170) REVERT: E 197 TYR cc_start: 0.8294 (t80) cc_final: 0.7945 (t80) REVERT: I 287 TYR cc_start: 0.8457 (t80) cc_final: 0.8222 (t80) outliers start: 40 outliers final: 19 residues processed: 246 average time/residue: 0.3125 time to fit residues: 110.4158 Evaluate side-chains 183 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 85 PHE Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 HIS K 206 GLN K 279 ASN C 109 GLN C 206 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN I 206 GLN A 174 HIS A 206 GLN A 279 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.075737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065988 restraints weight = 172774.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068826 restraints weight = 71434.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070706 restraints weight = 37692.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071919 restraints weight = 22925.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072783 restraints weight = 15364.395| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15972 Z= 0.277 Angle : 0.721 6.781 21654 Z= 0.375 Chirality : 0.044 0.157 2406 Planarity : 0.006 0.074 2802 Dihedral : 10.413 145.410 2214 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.02 % Allowed : 10.27 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.90 (0.17), residues: 2004 helix: 0.35 (0.18), residues: 768 sheet: -0.48 (0.23), residues: 432 loop : -1.53 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 60 TYR 0.023 0.003 TYR K 197 PHE 0.020 0.003 PHE C 251 TRP 0.010 0.002 TRP A 97 HIS 0.011 0.004 HIS K 354 Details of bonding type rmsd covalent geometry : bond 0.00576 (15972) covalent geometry : angle 0.72091 (21654) hydrogen bonds : bond 0.04352 ( 780) hydrogen bonds : angle 6.54312 ( 2106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.745 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 197 TYR cc_start: 0.8610 (t80) cc_final: 0.8400 (t80) REVERT: G 246 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8447 (p) REVERT: K 304 ASN cc_start: 0.8004 (p0) cc_final: 0.7729 (p0) REVERT: C 287 TYR cc_start: 0.8620 (t80) cc_final: 0.8416 (t80) REVERT: E 246 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8445 (p) REVERT: I 287 TYR cc_start: 0.8611 (t80) cc_final: 0.8408 (t80) REVERT: A 127 ASP cc_start: 0.7967 (m-30) cc_final: 0.7651 (m-30) REVERT: A 304 ASN cc_start: 0.8028 (p0) cc_final: 0.7720 (p0) outliers start: 50 outliers final: 32 residues processed: 201 average time/residue: 0.2597 time to fit residues: 79.4524 Evaluate side-chains 171 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 339 TRP Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 170 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 206 GLN K 343 GLN C 158 GLN C 374 GLN E 101 GLN E 206 GLN I 374 GLN A 343 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.077457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067492 restraints weight = 167643.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.070426 restraints weight = 69458.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.072383 restraints weight = 36635.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073590 restraints weight = 22066.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074479 restraints weight = 14842.284| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15972 Z= 0.134 Angle : 0.572 6.584 21654 Z= 0.284 Chirality : 0.042 0.141 2406 Planarity : 0.005 0.059 2802 Dihedral : 9.314 143.458 2214 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.39 % Allowed : 12.08 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.55 (0.18), residues: 2004 helix: 0.82 (0.18), residues: 768 sheet: -0.43 (0.23), residues: 432 loop : -1.44 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 60 TYR 0.017 0.002 TYR G 100 PHE 0.011 0.001 PHE K 159 TRP 0.007 0.001 TRP A 339 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00274 (15972) covalent geometry : angle 0.57190 (21654) hydrogen bonds : bond 0.03204 ( 780) hydrogen bonds : angle 5.72840 ( 2106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.823 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: 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: 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: symmetry clash revert: symmetry clash REVERT: K 304 ASN cc_start: 0.7906 (p0) cc_final: 0.7642 (p0) REVERT: C 55 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8031 (mppt) REVERT: C 287 TYR cc_start: 0.8516 (t80) cc_final: 0.8291 (t80) REVERT: I 55 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8080 (mppt) REVERT: I 287 TYR cc_start: 0.8528 (t80) cc_final: 0.8304 (t80) REVERT: A 127 ASP cc_start: 0.8049 (m-30) cc_final: 0.7751 (m-30) REVERT: A 304 ASN cc_start: 0.7864 (p0) cc_final: 0.7549 (p0) outliers start: 23 outliers final: 13 residues processed: 178 average time/residue: 0.2473 time to fit residues: 68.5327 Evaluate side-chains 151 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 339 TRP Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 343 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 109 GLN K 206 GLN C 158 GLN A 109 GLN A 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.066452 restraints weight = 169505.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069374 restraints weight = 69085.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071309 restraints weight = 35988.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072510 restraints weight = 21498.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073374 restraints weight = 14262.683| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15972 Z= 0.176 Angle : 0.589 6.757 21654 Z= 0.294 Chirality : 0.041 0.135 2406 Planarity : 0.005 0.053 2802 Dihedral : 9.037 144.305 2214 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.51 % Allowed : 12.44 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.57 (0.18), residues: 2004 helix: 0.80 (0.18), residues: 768 sheet: -0.55 (0.24), residues: 432 loop : -1.38 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 60 TYR 0.018 0.002 TYR K 197 PHE 0.008 0.001 PHE E 338 TRP 0.011 0.001 TRP K 320 HIS 0.007 0.001 HIS K 354 Details of bonding type rmsd covalent geometry : bond 0.00362 (15972) covalent geometry : angle 0.58920 (21654) hydrogen bonds : bond 0.03230 ( 780) hydrogen bonds : angle 5.77297 ( 2106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.804 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 126 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: K 304 ASN cc_start: 0.7941 (p0) cc_final: 0.7670 (p0) REVERT: C 287 TYR cc_start: 0.8577 (t80) cc_final: 0.8346 (t80) REVERT: I 287 TYR cc_start: 0.8583 (t80) cc_final: 0.8350 (t80) REVERT: A 304 ASN cc_start: 0.7924 (p0) cc_final: 0.7624 (p0) outliers start: 25 outliers final: 22 residues processed: 158 average time/residue: 0.2409 time to fit residues: 59.5181 Evaluate side-chains 149 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 339 TRP Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 343 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 378 ASN ** K 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 ASN C 158 GLN E 378 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064906 restraints weight = 171572.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067720 restraints weight = 70914.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069607 restraints weight = 37269.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070828 restraints weight = 22457.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.071648 restraints weight = 14845.825| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15972 Z= 0.258 Angle : 0.645 6.572 21654 Z= 0.329 Chirality : 0.042 0.137 2406 Planarity : 0.005 0.054 2802 Dihedral : 9.164 146.531 2214 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.36 % Allowed : 12.20 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.93 (0.18), residues: 2004 helix: 0.48 (0.18), residues: 768 sheet: -0.77 (0.24), residues: 432 loop : -1.54 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 161 TYR 0.022 0.002 TYR A 197 PHE 0.013 0.002 PHE G 153 TRP 0.008 0.002 TRP C 97 HIS 0.010 0.002 HIS K 354 Details of bonding type rmsd covalent geometry : bond 0.00527 (15972) covalent geometry : angle 0.64477 (21654) hydrogen bonds : bond 0.03515 ( 780) hydrogen bonds : angle 6.10854 ( 2106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.702 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 126 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: K 304 ASN cc_start: 0.8015 (p0) cc_final: 0.7740 (p0) REVERT: C 323 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: I 193 MET cc_start: 0.8679 (ptp) cc_final: 0.8461 (ptp) REVERT: A 304 ASN cc_start: 0.8077 (p0) cc_final: 0.7744 (p0) outliers start: 39 outliers final: 27 residues processed: 165 average time/residue: 0.2290 time to fit residues: 60.4660 Evaluate side-chains 146 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 246 SER Chi-restraints excluded: chain K residue 339 TRP Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain K residue 348 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 195 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 182 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 206 GLN C 158 GLN A 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066259 restraints weight = 169510.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069151 restraints weight = 69441.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.071072 restraints weight = 36310.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072286 restraints weight = 21821.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073143 restraints weight = 14509.404| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15972 Z= 0.146 Angle : 0.574 7.509 21654 Z= 0.282 Chirality : 0.041 0.135 2406 Planarity : 0.005 0.062 2802 Dihedral : 8.880 144.535 2214 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.15 % Allowed : 13.53 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.67 (0.18), residues: 2004 helix: 0.78 (0.18), residues: 768 sheet: -0.73 (0.24), residues: 432 loop : -1.41 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.016 0.001 TYR A 197 PHE 0.032 0.001 PHE K 85 TRP 0.012 0.001 TRP I 191 HIS 0.005 0.001 HIS K 354 Details of bonding type rmsd covalent geometry : bond 0.00301 (15972) covalent geometry : angle 0.57395 (21654) hydrogen bonds : bond 0.03018 ( 780) hydrogen bonds : angle 5.60164 ( 2106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.947 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 126 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: K 304 ASN cc_start: 0.7962 (p0) cc_final: 0.7712 (p0) REVERT: A 304 ASN cc_start: 0.8010 (p0) cc_final: 0.7682 (p0) outliers start: 19 outliers final: 14 residues processed: 144 average time/residue: 0.2304 time to fit residues: 53.1190 Evaluate side-chains 137 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 339 TRP Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 129 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.065588 restraints weight = 171904.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068396 restraints weight = 71957.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070247 restraints weight = 38089.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.071437 restraints weight = 23088.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.072256 restraints weight = 15474.190| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15972 Z= 0.187 Angle : 0.594 6.694 21654 Z= 0.296 Chirality : 0.042 0.138 2406 Planarity : 0.005 0.047 2802 Dihedral : 8.838 145.267 2214 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.39 % Allowed : 13.53 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.65 (0.18), residues: 2004 helix: 0.88 (0.18), residues: 732 sheet: -0.64 (0.25), residues: 402 loop : -1.45 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.019 0.002 TYR K 197 PHE 0.026 0.002 PHE K 85 TRP 0.008 0.001 TRP I 191 HIS 0.007 0.001 HIS K 354 Details of bonding type rmsd covalent geometry : bond 0.00385 (15972) covalent geometry : angle 0.59427 (21654) hydrogen bonds : bond 0.03157 ( 780) hydrogen bonds : angle 5.71445 ( 2106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.822 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 126 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: K 304 ASN cc_start: 0.7976 (p0) cc_final: 0.7721 (p0) REVERT: I 323 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: A 304 ASN cc_start: 0.8014 (p0) cc_final: 0.7701 (p0) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.2258 time to fit residues: 52.8800 Evaluate side-chains 141 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 246 SER Chi-restraints excluded: chain K residue 339 TRP Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 323 GLU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 142 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.076643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.066768 restraints weight = 169168.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069663 restraints weight = 70639.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.071570 restraints weight = 37349.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.072809 restraints weight = 22517.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073649 restraints weight = 14902.624| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15972 Z= 0.107 Angle : 0.549 6.300 21654 Z= 0.267 Chirality : 0.041 0.139 2406 Planarity : 0.005 0.049 2802 Dihedral : 8.671 143.556 2214 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.97 % Allowed : 13.77 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.41 (0.18), residues: 2004 helix: 1.09 (0.19), residues: 768 sheet: -0.41 (0.25), residues: 396 loop : -1.48 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.013 0.001 TYR K 197 PHE 0.027 0.001 PHE K 85 TRP 0.006 0.001 TRP C 339 HIS 0.003 0.001 HIS K 354 Details of bonding type rmsd covalent geometry : bond 0.00227 (15972) covalent geometry : angle 0.54914 (21654) hydrogen bonds : bond 0.02783 ( 780) hydrogen bonds : angle 5.30644 ( 2106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.769 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8126 (mm-30) REVERT: K 235 MET cc_start: 0.6512 (tpp) cc_final: 0.6070 (tpp) REVERT: K 304 ASN cc_start: 0.7950 (p0) cc_final: 0.7713 (p0) REVERT: A 235 MET cc_start: 0.6484 (tpp) cc_final: 0.6059 (tpp) REVERT: A 304 ASN cc_start: 0.7993 (p0) cc_final: 0.7682 (p0) outliers start: 16 outliers final: 10 residues processed: 143 average time/residue: 0.2311 time to fit residues: 53.3029 Evaluate side-chains 135 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain K residue 339 TRP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 3 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.075656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.065959 restraints weight = 171889.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068769 restraints weight = 72486.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070640 restraints weight = 38609.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071844 restraints weight = 23356.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.072702 restraints weight = 15579.413| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15972 Z= 0.165 Angle : 0.576 6.597 21654 Z= 0.285 Chirality : 0.041 0.156 2406 Planarity : 0.005 0.045 2802 Dihedral : 8.653 144.746 2214 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.85 % Allowed : 14.01 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 2004 helix: 1.16 (0.19), residues: 732 sheet: -0.38 (0.25), residues: 396 loop : -1.41 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 161 TYR 0.017 0.002 TYR A 197 PHE 0.024 0.001 PHE K 85 TRP 0.024 0.001 TRP G 339 HIS 0.007 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00341 (15972) covalent geometry : angle 0.57604 (21654) hydrogen bonds : bond 0.02953 ( 780) hydrogen bonds : angle 5.47442 ( 2106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.897 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8134 (mm-30) REVERT: K 304 ASN cc_start: 0.7961 (p0) cc_final: 0.7731 (p0) REVERT: E 181 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8250 (mm-30) REVERT: A 304 ASN cc_start: 0.8035 (p0) cc_final: 0.7707 (p0) outliers start: 14 outliers final: 13 residues processed: 135 average time/residue: 0.2354 time to fit residues: 50.4600 Evaluate side-chains 136 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 339 TRP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 339 TRP Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 94 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 190 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 GLN E 374 GLN A 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067380 restraints weight = 169042.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.070282 restraints weight = 71067.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.072197 restraints weight = 37631.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.073454 restraints weight = 22748.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.074303 restraints weight = 15015.290| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15972 Z= 0.105 Angle : 0.538 6.245 21654 Z= 0.260 Chirality : 0.041 0.140 2406 Planarity : 0.004 0.044 2802 Dihedral : 8.502 142.626 2214 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.72 % Allowed : 14.55 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.12 (0.18), residues: 2004 helix: 1.43 (0.19), residues: 732 sheet: -0.21 (0.26), residues: 396 loop : -1.33 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.011 0.001 TYR A 197 PHE 0.021 0.001 PHE K 85 TRP 0.016 0.001 TRP G 339 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00225 (15972) covalent geometry : angle 0.53793 (21654) hydrogen bonds : bond 0.02627 ( 780) hydrogen bonds : angle 5.10801 ( 2106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4046.85 seconds wall clock time: 70 minutes 18.00 seconds (4218.00 seconds total)