Starting phenix.real_space_refine on Thu Mar 5 13:51:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xou_67094/03_2026/9xou_67094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xou_67094/03_2026/9xou_67094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xou_67094/03_2026/9xou_67094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xou_67094/03_2026/9xou_67094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xou_67094/03_2026/9xou_67094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xou_67094/03_2026/9xou_67094.map" } resolution = 2.5 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= -0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 14711 2.51 5 N 3611 2.21 5 O 3973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22382 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2424 Classifications: {'peptide': 319} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 305} Chain: "B" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2417 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 304} Chain: "C" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2424 Classifications: {'peptide': 319} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 305} Chain: "D" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1920 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Chain: "E" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1920 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Chain: "F" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1920 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Chain: "G" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3119 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Chain: "H" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3119 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Chain: "I" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3119 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N PHE G 27 " occ=0.80 ... (9 atoms not shown) pdb=" CZ PHE G 27 " occ=0.80 residue: pdb=" N PHE H 27 " occ=0.80 ... (9 atoms not shown) pdb=" CZ PHE H 27 " occ=0.80 residue: pdb=" N PHE I 27 " occ=0.80 ... (9 atoms not shown) pdb=" CZ PHE I 27 " occ=0.80 Time building chain proxies: 4.81, per 1000 atoms: 0.21 Number of scatterers: 22382 At special positions: 0 Unit cell: (167.4, 172.05, 145.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3973 8.00 N 3611 7.00 C 14711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 319 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5278 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 18 sheets defined 72.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 2 through 24 Processing helix chain 'A' and resid 28 through 42 removed outlier: 3.694A pdb=" N ILE A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 59 through 72 Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.529A pdb=" N ASP A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 127 Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 229 through 239 removed outlier: 3.579A pdb=" N LEU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.906A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.535A pdb=" N GLY A 287 " --> pdb=" O TRP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 301 through 320 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 59 through 71 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 93 through 127 removed outlier: 3.778A pdb=" N ALA B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 173 through 178 removed outlier: 4.358A pdb=" N GLU B 176 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 253 through 261 removed outlier: 3.861A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.510A pdb=" N GLY B 287 " --> pdb=" O TRP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 319 Processing helix chain 'C' and resid 3 through 24 Processing helix chain 'C' and resid 28 through 42 Processing helix chain 'C' and resid 43 through 57 Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 94 through 127 removed outlier: 3.595A pdb=" N MET C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 229 through 239 Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.931A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 301 through 320 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 131 through 145 Processing helix chain 'D' and resid 149 through 157 Processing helix chain 'D' and resid 161 through 174 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 195 through 210 Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.784A pdb=" N GLY D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 249 removed outlier: 3.774A pdb=" N LYS D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 131 through 145 Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 161 through 174 Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 195 through 210 Processing helix chain 'E' and resid 210 through 225 removed outlier: 3.784A pdb=" N GLY E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 249 removed outlier: 3.774A pdb=" N LYS E 230 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP E 249 " --> pdb=" O LYS E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 131 through 145 Processing helix chain 'F' and resid 149 through 157 Processing helix chain 'F' and resid 161 through 174 Processing helix chain 'F' and resid 179 through 194 Processing helix chain 'F' and resid 195 through 210 Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.784A pdb=" N GLY F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 249 removed outlier: 3.774A pdb=" N LYS F 230 " --> pdb=" O THR F 226 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 37 removed outlier: 3.834A pdb=" N PHE G 16 " --> pdb=" O PHE G 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE G 22 " --> pdb=" O PHE G 18 " (cutoff:3.500A) Proline residue: G 28 - end of helix Proline residue: G 31 - end of helix Processing helix chain 'G' and resid 41 through 44 Processing helix chain 'G' and resid 45 through 71 Proline residue: G 61 - end of helix Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 86 through 94 Processing helix chain 'G' and resid 95 through 101 Processing helix chain 'G' and resid 102 through 118 Processing helix chain 'G' and resid 120 through 137 removed outlier: 3.580A pdb=" N ALA G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 163 removed outlier: 4.043A pdb=" N GLY G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA G 152 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLY G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE G 160 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR G 163 " --> pdb=" O GLY G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 185 Processing helix chain 'G' and resid 209 through 215 Processing helix chain 'G' and resid 216 through 218 No H-bonds generated for 'chain 'G' and resid 216 through 218' Processing helix chain 'G' and resid 219 through 232 removed outlier: 4.050A pdb=" N TRP G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 241 Processing helix chain 'G' and resid 242 through 248 Processing helix chain 'G' and resid 249 through 251 No H-bonds generated for 'chain 'G' and resid 249 through 251' Processing helix chain 'G' and resid 253 through 278 removed outlier: 3.533A pdb=" N LEU G 270 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 287 removed outlier: 3.553A pdb=" N ILE G 282 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG G 285 " --> pdb=" O LEU G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 309 Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.514A pdb=" N VAL G 315 " --> pdb=" O SER G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 341 removed outlier: 3.682A pdb=" N GLY G 332 " --> pdb=" O PHE G 328 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER G 333 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS G 335 " --> pdb=" O VAL G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 344 No H-bonds generated for 'chain 'G' and resid 342 through 344' Processing helix chain 'G' and resid 345 through 354 Processing helix chain 'G' and resid 355 through 376 removed outlier: 3.899A pdb=" N VAL G 367 " --> pdb=" O ILE G 363 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU G 368 " --> pdb=" O PHE G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 400 removed outlier: 3.630A pdb=" N GLY G 386 " --> pdb=" O TYR G 382 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE G 398 " --> pdb=" O LEU G 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 37 removed outlier: 3.834A pdb=" N PHE H 16 " --> pdb=" O PHE H 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE H 22 " --> pdb=" O PHE H 18 " (cutoff:3.500A) Proline residue: H 28 - end of helix Proline residue: H 31 - end of helix Processing helix chain 'H' and resid 41 through 44 Processing helix chain 'H' and resid 45 through 71 Proline residue: H 61 - end of helix Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 86 through 94 Processing helix chain 'H' and resid 95 through 101 Processing helix chain 'H' and resid 102 through 118 Processing helix chain 'H' and resid 120 through 137 removed outlier: 3.580A pdb=" N ALA H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 163 removed outlier: 4.042A pdb=" N GLY H 147 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA H 152 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLY H 159 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR H 163 " --> pdb=" O GLY H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 185 Processing helix chain 'H' and resid 209 through 215 Processing helix chain 'H' and resid 216 through 218 No H-bonds generated for 'chain 'H' and resid 216 through 218' Processing helix chain 'H' and resid 219 through 232 removed outlier: 4.051A pdb=" N TRP H 223 " --> pdb=" O GLN H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 241 Processing helix chain 'H' and resid 242 through 248 Processing helix chain 'H' and resid 249 through 251 No H-bonds generated for 'chain 'H' and resid 249 through 251' Processing helix chain 'H' and resid 253 through 278 removed outlier: 3.533A pdb=" N LEU H 270 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE H 278 " --> pdb=" O SER H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 287 removed outlier: 3.553A pdb=" N ILE H 282 " --> pdb=" O PHE H 278 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG H 285 " --> pdb=" O LEU H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 309 Processing helix chain 'H' and resid 311 through 321 removed outlier: 3.515A pdb=" N VAL H 315 " --> pdb=" O SER H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 341 removed outlier: 3.682A pdb=" N GLY H 332 " --> pdb=" O PHE H 328 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER H 333 " --> pdb=" O LEU H 329 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS H 335 " --> pdb=" O VAL H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 344 No H-bonds generated for 'chain 'H' and resid 342 through 344' Processing helix chain 'H' and resid 345 through 354 Processing helix chain 'H' and resid 355 through 376 removed outlier: 3.899A pdb=" N VAL H 367 " --> pdb=" O ILE H 363 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU H 368 " --> pdb=" O PHE H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 400 removed outlier: 3.631A pdb=" N GLY H 386 " --> pdb=" O TYR H 382 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE H 398 " --> pdb=" O LEU H 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 37 removed outlier: 3.834A pdb=" N PHE I 16 " --> pdb=" O PHE I 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 22 " --> pdb=" O PHE I 18 " (cutoff:3.500A) Proline residue: I 28 - end of helix Proline residue: I 31 - end of helix Processing helix chain 'I' and resid 41 through 44 Processing helix chain 'I' and resid 45 through 71 Proline residue: I 61 - end of helix Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 86 through 94 Processing helix chain 'I' and resid 95 through 101 Processing helix chain 'I' and resid 102 through 118 Processing helix chain 'I' and resid 120 through 137 removed outlier: 3.579A pdb=" N ALA I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG I 135 " --> pdb=" O LYS I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 163 removed outlier: 4.044A pdb=" N GLY I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA I 152 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLY I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE I 160 " --> pdb=" O SER I 156 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR I 163 " --> pdb=" O GLY I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 185 Processing helix chain 'I' and resid 209 through 215 Processing helix chain 'I' and resid 216 through 218 No H-bonds generated for 'chain 'I' and resid 216 through 218' Processing helix chain 'I' and resid 219 through 232 removed outlier: 4.051A pdb=" N TRP I 223 " --> pdb=" O GLN I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 241 Processing helix chain 'I' and resid 242 through 248 Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'I' and resid 253 through 278 removed outlier: 3.533A pdb=" N LEU I 270 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE I 278 " --> pdb=" O SER I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 287 removed outlier: 3.554A pdb=" N ILE I 282 " --> pdb=" O PHE I 278 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG I 285 " --> pdb=" O LEU I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 309 Processing helix chain 'I' and resid 311 through 321 removed outlier: 3.514A pdb=" N VAL I 315 " --> pdb=" O SER I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 341 removed outlier: 3.681A pdb=" N GLY I 332 " --> pdb=" O PHE I 328 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER I 333 " --> pdb=" O LEU I 329 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE I 334 " --> pdb=" O LEU I 330 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS I 335 " --> pdb=" O VAL I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 344 No H-bonds generated for 'chain 'I' and resid 342 through 344' Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 355 through 376 removed outlier: 3.899A pdb=" N VAL I 367 " --> pdb=" O ILE I 363 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU I 368 " --> pdb=" O PHE I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 400 removed outlier: 3.630A pdb=" N GLY I 386 " --> pdb=" O TYR I 382 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE I 398 " --> pdb=" O LEU I 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 184 removed outlier: 6.690A pdb=" N ILE A 128 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLU A 156 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA A 130 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 158 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 129 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.640A pdb=" N ILE A 203 " --> pdb=" O MET A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA4, first strand: chain 'B' and resid 180 through 184 Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 204 removed outlier: 6.791A pdb=" N ILE B 203 " --> pdb=" O MET B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AA7, first strand: chain 'C' and resid 180 through 184 removed outlier: 6.106A pdb=" N ALA C 130 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C 158 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU C 132 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 202 through 204 removed outlier: 6.894A pdb=" N ILE C 203 " --> pdb=" O MET C 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 226 through 227 removed outlier: 3.587A pdb=" N LEU C 246 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.769A pdb=" N LEU D 34 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG D 39 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N PHE D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 8 Processing sheet with id=AB5, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.769A pdb=" N LEU E 34 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG E 39 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AB8, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.769A pdb=" N LEU F 34 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 12 through 13 1541 hydrogen bonds defined for protein. 4536 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: 4.07 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6940 1.34 - 1.46: 4985 1.46 - 1.58: 10805 1.58 - 1.70: 0 1.70 - 1.81: 156 Bond restraints: 22886 Sorted by residual: bond pdb=" N ILE C 128 " pdb=" CA ILE C 128 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.26e+00 bond pdb=" CA ALA H 187 " pdb=" CB ALA H 187 " ideal model delta sigma weight residual 1.530 1.484 0.045 1.55e-02 4.16e+03 8.56e+00 bond pdb=" N VAL C 129 " pdb=" CA VAL C 129 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.28e-02 6.10e+03 8.46e+00 bond pdb=" C ARG F 102 " pdb=" N PRO F 103 " ideal model delta sigma weight residual 1.333 1.366 -0.033 1.17e-02 7.31e+03 7.92e+00 bond pdb=" C ARG E 102 " pdb=" N PRO E 103 " ideal model delta sigma weight residual 1.333 1.365 -0.033 1.17e-02 7.31e+03 7.73e+00 ... (remaining 22881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 29993 1.60 - 3.20: 730 3.20 - 4.79: 170 4.79 - 6.39: 32 6.39 - 7.99: 7 Bond angle restraints: 30932 Sorted by residual: angle pdb=" N ASP C 26 " pdb=" CA ASP C 26 " pdb=" CB ASP C 26 " ideal model delta sigma weight residual 111.43 104.88 6.55 1.48e+00 4.57e-01 1.96e+01 angle pdb=" N ARG E 102 " pdb=" CA ARG E 102 " pdb=" C ARG E 102 " ideal model delta sigma weight residual 109.82 117.08 -7.26 1.68e+00 3.54e-01 1.87e+01 angle pdb=" N ARG F 102 " pdb=" CA ARG F 102 " pdb=" C ARG F 102 " ideal model delta sigma weight residual 109.82 117.07 -7.25 1.68e+00 3.54e-01 1.86e+01 angle pdb=" N ARG D 102 " pdb=" CA ARG D 102 " pdb=" C ARG D 102 " ideal model delta sigma weight residual 109.82 117.07 -7.25 1.68e+00 3.54e-01 1.86e+01 angle pdb=" N TYR E 119 " pdb=" CA TYR E 119 " pdb=" CB TYR E 119 " ideal model delta sigma weight residual 109.85 103.68 6.17 1.49e+00 4.50e-01 1.72e+01 ... (remaining 30927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 11372 17.88 - 35.76: 1427 35.76 - 53.64: 503 53.64 - 71.51: 110 71.51 - 89.39: 48 Dihedral angle restraints: 13460 sinusoidal: 5237 harmonic: 8223 Sorted by residual: dihedral pdb=" CA LEU G 400 " pdb=" C LEU G 400 " pdb=" N SER G 401 " pdb=" CA SER G 401 " ideal model delta harmonic sigma weight residual -180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA LEU I 400 " pdb=" C LEU I 400 " pdb=" N SER I 401 " pdb=" CA SER I 401 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LEU H 400 " pdb=" C LEU H 400 " pdb=" N SER H 401 " pdb=" CA SER H 401 " ideal model delta harmonic sigma weight residual 180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 13457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2722 0.050 - 0.101: 634 0.101 - 0.151: 134 0.151 - 0.202: 8 0.202 - 0.252: 4 Chirality restraints: 3502 Sorted by residual: chirality pdb=" CA HIS C 126 " pdb=" N HIS C 126 " pdb=" C HIS C 126 " pdb=" CB HIS C 126 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU H 180 " pdb=" CB LEU H 180 " pdb=" CD1 LEU H 180 " pdb=" CD2 LEU H 180 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CG LEU G 180 " pdb=" CB LEU G 180 " pdb=" CD1 LEU G 180 " pdb=" CD2 LEU G 180 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3499 not shown) Planarity restraints: 3869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 81 " -0.272 9.50e-02 1.11e+02 1.22e-01 9.86e+00 pdb=" NE ARG C 81 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 81 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 81 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 81 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 301 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO A 302 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 301 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.69e+00 pdb=" N PRO C 302 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.033 5.00e-02 4.00e+02 ... (remaining 3866 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3814 2.76 - 3.29: 21621 3.29 - 3.83: 38565 3.83 - 4.36: 45916 4.36 - 4.90: 78634 Nonbonded interactions: 188550 Sorted by model distance: nonbonded pdb=" O LYS A 194 " pdb=" OG SER A 198 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR H 228 " pdb=" O LEU H 292 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR G 228 " pdb=" O LEU G 292 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR I 228 " pdb=" O LEU I 292 " model vdw 2.226 3.040 nonbonded pdb=" N GLU C 210 " pdb=" OE1 GLU C 210 " model vdw 2.232 3.120 ... (remaining 188545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 319) selection = chain 'B' selection = (chain 'C' and resid 2 through 319) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.500 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22892 Z= 0.261 Angle : 0.633 7.988 30944 Z= 0.374 Chirality : 0.045 0.252 3502 Planarity : 0.005 0.122 3869 Dihedral : 18.829 89.393 8164 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.91 % Allowed : 32.36 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.29 (0.15), residues: 2846 helix: 0.30 (0.12), residues: 1918 sheet: -0.26 (0.30), residues: 284 loop : -1.33 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 81 TYR 0.023 0.002 TYR D 61 PHE 0.032 0.002 PHE G 18 TRP 0.008 0.001 TRP H 171 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00525 (22886) covalent geometry : angle 0.63263 (30932) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.45099 ( 12) hydrogen bonds : bond 0.21372 ( 1526) hydrogen bonds : angle 7.39933 ( 4536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 709 time to evaluate : 0.833 Fit side-chains REVERT: B 10 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5975 (mm-30) REVERT: B 13 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7363 (mtt90) REVERT: B 217 LYS cc_start: 0.7893 (ttpp) cc_final: 0.7662 (ttpp) REVERT: E 44 LYS cc_start: 0.7047 (ptmm) cc_final: 0.6514 (ptmm) REVERT: E 45 GLU cc_start: 0.6804 (pm20) cc_final: 0.6519 (pm20) REVERT: E 117 TYR cc_start: 0.7829 (m-80) cc_final: 0.7402 (m-80) REVERT: E 133 GLU cc_start: 0.7233 (mp0) cc_final: 0.6994 (mp0) REVERT: E 159 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7451 (mmmt) REVERT: E 228 GLU cc_start: 0.7432 (mp0) cc_final: 0.6708 (mp0) REVERT: E 243 TYR cc_start: 0.7563 (t80) cc_final: 0.7266 (t80) REVERT: F 22 SER cc_start: 0.7985 (t) cc_final: 0.7678 (p) REVERT: F 60 TYR cc_start: 0.8515 (m-80) cc_final: 0.8270 (m-80) REVERT: F 61 TYR cc_start: 0.8289 (m-80) cc_final: 0.8076 (m-80) REVERT: F 119 TYR cc_start: 0.8307 (m-80) cc_final: 0.8065 (m-80) REVERT: F 133 GLU cc_start: 0.7252 (mp0) cc_final: 0.7048 (mp0) REVERT: F 227 GLU cc_start: 0.6252 (mp0) cc_final: 0.5961 (mp0) REVERT: G 392 PHE cc_start: 0.7792 (m-80) cc_final: 0.7365 (m-80) REVERT: H 19 TYR cc_start: 0.8033 (t80) cc_final: 0.7756 (t80) REVERT: H 26 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.6368 (t80) REVERT: H 32 ILE cc_start: 0.7905 (pt) cc_final: 0.7591 (mp) REVERT: H 114 LEU cc_start: 0.8197 (mm) cc_final: 0.7811 (mp) REVERT: H 217 PHE cc_start: 0.7967 (m-80) cc_final: 0.7730 (m-80) REVERT: H 228 TYR cc_start: 0.8126 (t80) cc_final: 0.7804 (t80) REVERT: H 263 TYR cc_start: 0.7881 (m-10) cc_final: 0.7452 (m-10) REVERT: H 277 PHE cc_start: 0.8389 (t80) cc_final: 0.8092 (t80) REVERT: H 313 LEU cc_start: 0.8486 (tp) cc_final: 0.8279 (tt) REVERT: H 365 MET cc_start: 0.8093 (ttp) cc_final: 0.7887 (ttm) REVERT: H 375 SER cc_start: 0.8288 (m) cc_final: 0.8077 (t) REVERT: I 2 TYR cc_start: 0.7653 (p90) cc_final: 0.7337 (p90) REVERT: I 57 LEU cc_start: 0.8272 (mt) cc_final: 0.8060 (mp) REVERT: I 83 MET cc_start: 0.7711 (mtm) cc_final: 0.7309 (mtp) REVERT: I 95 PHE cc_start: 0.6942 (t80) cc_final: 0.6638 (t80) REVERT: I 118 PHE cc_start: 0.8341 (m-80) cc_final: 0.8060 (m-80) REVERT: I 323 MET cc_start: 0.8239 (mmt) cc_final: 0.7944 (mpm) REVERT: I 357 PHE cc_start: 0.8209 (m-80) cc_final: 0.7842 (m-80) outliers start: 21 outliers final: 8 residues processed: 725 average time/residue: 0.5944 time to fit residues: 489.1338 Evaluate side-chains 670 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 661 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain I residue 26 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN E 177 HIS F 14 GLN F 40 GLN G 245 ASN G 284 ASN G 340 GLN H 137 ASN H 284 ASN H 371 ASN I 245 ASN I 290 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.141818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132199 restraints weight = 31838.915| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.27 r_work: 0.3762 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22892 Z= 0.203 Angle : 0.577 9.113 30944 Z= 0.304 Chirality : 0.043 0.187 3502 Planarity : 0.005 0.066 3869 Dihedral : 5.010 57.747 3061 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.87 % Allowed : 28.00 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.66 (0.16), residues: 2846 helix: 1.15 (0.12), residues: 1920 sheet: -0.24 (0.30), residues: 275 loop : -1.25 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 81 TYR 0.016 0.002 TYR I 236 PHE 0.025 0.002 PHE G 18 TRP 0.009 0.001 TRP I 262 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00483 (22886) covalent geometry : angle 0.57686 (30932) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.68123 ( 12) hydrogen bonds : bond 0.04703 ( 1526) hydrogen bonds : angle 4.95724 ( 4536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 671 time to evaluate : 0.798 Fit side-chains REVERT: A 29 GLU cc_start: 0.6623 (pm20) cc_final: 0.6391 (pm20) REVERT: A 80 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7605 (mttp) REVERT: A 210 GLU cc_start: 0.7096 (pm20) cc_final: 0.6842 (pm20) REVERT: B 23 LYS cc_start: 0.7918 (mttt) cc_final: 0.7627 (mtpt) REVERT: B 25 ARG cc_start: 0.7164 (ptt90) cc_final: 0.6778 (ptt90) REVERT: B 48 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.6841 (ttm-80) REVERT: C 7 ILE cc_start: 0.7738 (mm) cc_final: 0.7536 (mt) REVERT: C 48 ARG cc_start: 0.6916 (ttm-80) cc_final: 0.6514 (ttm-80) REVERT: D 21 LEU cc_start: 0.7766 (mt) cc_final: 0.7540 (mt) REVERT: D 22 SER cc_start: 0.7994 (m) cc_final: 0.7729 (p) REVERT: E 45 GLU cc_start: 0.7434 (pm20) cc_final: 0.7056 (pm20) REVERT: E 159 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7509 (mmmt) REVERT: E 207 LEU cc_start: 0.8532 (mt) cc_final: 0.8249 (mp) REVERT: E 228 GLU cc_start: 0.7452 (mp0) cc_final: 0.6775 (mp0) REVERT: E 240 TYR cc_start: 0.7928 (t80) cc_final: 0.7720 (t80) REVERT: E 243 TYR cc_start: 0.7631 (t80) cc_final: 0.7301 (t80) REVERT: F 60 TYR cc_start: 0.8403 (m-80) cc_final: 0.8057 (m-80) REVERT: F 61 TYR cc_start: 0.8360 (m-80) cc_final: 0.8103 (m-80) REVERT: F 119 TYR cc_start: 0.8333 (m-80) cc_final: 0.7766 (m-80) REVERT: F 130 LYS cc_start: 0.7523 (tptt) cc_final: 0.7271 (tppt) REVERT: F 195 SER cc_start: 0.7338 (m) cc_final: 0.6969 (p) REVERT: F 227 GLU cc_start: 0.6622 (mp0) cc_final: 0.6311 (mp0) REVERT: F 245 LYS cc_start: 0.7803 (ttpp) cc_final: 0.7433 (ttpp) REVERT: G 69 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7821 (ttmm) REVERT: G 161 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5979 (ptt) REVERT: G 235 THR cc_start: 0.7897 (m) cc_final: 0.7616 (p) REVERT: G 294 LEU cc_start: 0.8323 (tp) cc_final: 0.8084 (tt) REVERT: H 19 TYR cc_start: 0.8126 (t80) cc_final: 0.7663 (t80) REVERT: H 26 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6714 (t80) REVERT: H 69 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8054 (tttp) REVERT: H 77 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7976 (mt) REVERT: H 114 LEU cc_start: 0.8177 (mm) cc_final: 0.7957 (mp) REVERT: H 182 VAL cc_start: 0.7598 (OUTLIER) cc_final: 0.7392 (p) REVERT: H 217 PHE cc_start: 0.7838 (m-80) cc_final: 0.7599 (m-80) REVERT: H 228 TYR cc_start: 0.8148 (t80) cc_final: 0.7875 (t80) REVERT: H 263 TYR cc_start: 0.8158 (m-10) cc_final: 0.7640 (m-10) REVERT: H 277 PHE cc_start: 0.8407 (t80) cc_final: 0.8088 (t80) REVERT: H 383 LEU cc_start: 0.8066 (tp) cc_final: 0.7815 (tt) REVERT: I 2 TYR cc_start: 0.7605 (p90) cc_final: 0.7394 (p90) REVERT: I 75 TYR cc_start: 0.7435 (m-10) cc_final: 0.7144 (m-10) REVERT: I 77 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7860 (mt) REVERT: I 92 ILE cc_start: 0.7637 (pt) cc_final: 0.7352 (mm) REVERT: I 95 PHE cc_start: 0.7020 (t80) cc_final: 0.6765 (t80) REVERT: I 160 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7204 (tt) REVERT: I 323 MET cc_start: 0.8228 (mmt) cc_final: 0.7918 (mpm) REVERT: I 330 LEU cc_start: 0.7600 (tt) cc_final: 0.7341 (tp) REVERT: I 331 VAL cc_start: 0.7815 (p) cc_final: 0.7578 (m) REVERT: I 357 PHE cc_start: 0.7681 (m-80) cc_final: 0.7408 (m-80) outliers start: 136 outliers final: 54 residues processed: 734 average time/residue: 0.5862 time to fit residues: 489.0545 Evaluate side-chains 694 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 632 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 252 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 249 optimal weight: 0.5980 chunk 269 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 273 optimal weight: 0.6980 chunk 275 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 HIS G 340 GLN H 137 ASN H 272 ASN H 284 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.150024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.140812 restraints weight = 31691.716| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.26 r_work: 0.3731 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22892 Z= 0.182 Angle : 0.541 8.831 30944 Z= 0.283 Chirality : 0.042 0.181 3502 Planarity : 0.004 0.063 3869 Dihedral : 4.513 53.209 3049 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.22 % Allowed : 29.29 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.95 (0.16), residues: 2846 helix: 1.43 (0.12), residues: 1922 sheet: -0.40 (0.30), residues: 267 loop : -1.22 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 81 TYR 0.015 0.001 TYR G 236 PHE 0.022 0.002 PHE G 18 TRP 0.010 0.001 TRP G 171 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00431 (22886) covalent geometry : angle 0.54105 (30932) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.64535 ( 12) hydrogen bonds : bond 0.04228 ( 1526) hydrogen bonds : angle 4.65254 ( 4536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 666 time to evaluate : 0.690 Fit side-chains REVERT: A 29 GLU cc_start: 0.6550 (pm20) cc_final: 0.6238 (pm20) REVERT: A 113 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7129 (tm-30) REVERT: B 10 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6472 (mm-30) REVERT: B 23 LYS cc_start: 0.7903 (mttt) cc_final: 0.7584 (mtpt) REVERT: B 25 ARG cc_start: 0.7185 (ptt90) cc_final: 0.6762 (ptt90) REVERT: B 46 ASP cc_start: 0.7262 (m-30) cc_final: 0.7007 (m-30) REVERT: B 48 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.6843 (ttm-80) REVERT: B 217 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7748 (ttpp) REVERT: C 48 ARG cc_start: 0.6938 (ttm-80) cc_final: 0.6653 (ttm-80) REVERT: C 201 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: C 214 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: C 224 MET cc_start: 0.8274 (ttm) cc_final: 0.8012 (ttt) REVERT: D 21 LEU cc_start: 0.7762 (mt) cc_final: 0.7552 (mt) REVERT: E 207 LEU cc_start: 0.8568 (mt) cc_final: 0.8301 (mp) REVERT: E 228 GLU cc_start: 0.7433 (mp0) cc_final: 0.6779 (mp0) REVERT: F 14 GLN cc_start: 0.7829 (mt0) cc_final: 0.7419 (mt0) REVERT: F 60 TYR cc_start: 0.8381 (m-80) cc_final: 0.8027 (m-80) REVERT: F 61 TYR cc_start: 0.8352 (m-80) cc_final: 0.8089 (m-80) REVERT: F 130 LYS cc_start: 0.7513 (tptt) cc_final: 0.7037 (tppt) REVERT: F 149 GLN cc_start: 0.6972 (mp10) cc_final: 0.6651 (mp10) REVERT: F 195 SER cc_start: 0.7390 (m) cc_final: 0.7030 (p) REVERT: F 227 GLU cc_start: 0.6664 (mp0) cc_final: 0.6351 (mp0) REVERT: F 245 LYS cc_start: 0.7864 (ttpp) cc_final: 0.7521 (ttpp) REVERT: G 1 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7775 (mtt) REVERT: G 161 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5888 (ptt) REVERT: G 294 LEU cc_start: 0.8300 (tp) cc_final: 0.8084 (tt) REVERT: G 392 PHE cc_start: 0.7611 (m-80) cc_final: 0.7095 (m-80) REVERT: H 1 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7508 (mtp) REVERT: H 17 PHE cc_start: 0.8318 (t80) cc_final: 0.8080 (t80) REVERT: H 26 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.6864 (t80) REVERT: H 32 ILE cc_start: 0.7896 (pt) cc_final: 0.7582 (mt) REVERT: H 69 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8182 (tptp) REVERT: H 92 ILE cc_start: 0.7583 (pp) cc_final: 0.7268 (mp) REVERT: H 114 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7911 (mp) REVERT: H 182 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7431 (p) REVERT: H 217 PHE cc_start: 0.7929 (m-80) cc_final: 0.7673 (m-80) REVERT: H 277 PHE cc_start: 0.8421 (t80) cc_final: 0.8139 (t80) REVERT: H 316 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7910 (t) REVERT: H 383 LEU cc_start: 0.8074 (tp) cc_final: 0.7829 (tp) REVERT: I 75 TYR cc_start: 0.7429 (m-10) cc_final: 0.7098 (m-10) REVERT: I 95 PHE cc_start: 0.7120 (t80) cc_final: 0.6858 (t80) REVERT: I 323 MET cc_start: 0.8189 (mmt) cc_final: 0.7886 (mpm) REVERT: I 357 PHE cc_start: 0.7645 (m-80) cc_final: 0.7376 (m-80) outliers start: 121 outliers final: 66 residues processed: 724 average time/residue: 0.6003 time to fit residues: 492.3523 Evaluate side-chains 724 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 648 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 26 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 343 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 226 optimal weight: 0.3980 chunk 208 optimal weight: 0.2980 chunk 206 optimal weight: 0.7980 chunk 252 optimal weight: 0.1980 chunk 232 optimal weight: 0.5980 chunk 259 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 HIS F 182 GLN G 340 GLN H 245 ASN H 272 ASN H 284 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.141926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132215 restraints weight = 31980.109| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.27 r_work: 0.3735 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22892 Z= 0.147 Angle : 0.516 6.406 30944 Z= 0.269 Chirality : 0.041 0.168 3502 Planarity : 0.004 0.059 3869 Dihedral : 4.438 52.855 3049 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.57 % Allowed : 29.64 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.17 (0.16), residues: 2846 helix: 1.59 (0.12), residues: 1921 sheet: -0.32 (0.30), residues: 264 loop : -1.10 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 81 TYR 0.017 0.001 TYR G 236 PHE 0.023 0.001 PHE G 18 TRP 0.009 0.001 TRP G 171 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00345 (22886) covalent geometry : angle 0.51602 (30932) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.56817 ( 12) hydrogen bonds : bond 0.03784 ( 1526) hydrogen bonds : angle 4.49760 ( 4536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 663 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6604 (mm-30) REVERT: A 29 GLU cc_start: 0.6554 (pm20) cc_final: 0.6202 (pm20) REVERT: A 80 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7543 (mttp) REVERT: A 113 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7103 (tm-30) REVERT: B 10 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6487 (mm-30) REVERT: B 23 LYS cc_start: 0.7904 (mttt) cc_final: 0.7606 (mtpt) REVERT: B 95 LYS cc_start: 0.8002 (tmmm) cc_final: 0.7783 (tmmm) REVERT: B 217 LYS cc_start: 0.7938 (ttpp) cc_final: 0.7722 (ttpp) REVERT: C 39 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7140 (mm-30) REVERT: C 48 ARG cc_start: 0.6953 (ttm-80) cc_final: 0.6630 (ttm-80) REVERT: C 214 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: D 22 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7738 (p) REVERT: D 61 TYR cc_start: 0.8448 (m-80) cc_final: 0.7671 (m-80) REVERT: E 207 LEU cc_start: 0.8572 (mt) cc_final: 0.8318 (mp) REVERT: E 226 THR cc_start: 0.7172 (OUTLIER) cc_final: 0.6953 (m) REVERT: E 228 GLU cc_start: 0.7429 (mp0) cc_final: 0.6661 (mp0) REVERT: E 244 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7119 (mtmm) REVERT: F 60 TYR cc_start: 0.8378 (m-80) cc_final: 0.8033 (m-80) REVERT: F 66 LYS cc_start: 0.8308 (tttt) cc_final: 0.8085 (tttt) REVERT: F 130 LYS cc_start: 0.7531 (tptt) cc_final: 0.7314 (tppt) REVERT: F 227 GLU cc_start: 0.6659 (mp0) cc_final: 0.6325 (mp0) REVERT: F 245 LYS cc_start: 0.7903 (ttpp) cc_final: 0.7584 (ttpp) REVERT: G 1 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7772 (mtt) REVERT: G 69 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7813 (ttmm) REVERT: G 160 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.6924 (pp) REVERT: G 161 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5860 (ptt) REVERT: G 294 LEU cc_start: 0.8317 (tp) cc_final: 0.8102 (tt) REVERT: G 325 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6540 (tp30) REVERT: G 392 PHE cc_start: 0.7620 (m-80) cc_final: 0.7346 (m-80) REVERT: H 17 PHE cc_start: 0.8313 (t80) cc_final: 0.8051 (t80) REVERT: H 26 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.6931 (t80) REVERT: H 69 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8090 (tptp) REVERT: H 92 ILE cc_start: 0.7548 (pp) cc_final: 0.7273 (mp) REVERT: H 95 PHE cc_start: 0.7473 (t80) cc_final: 0.7198 (t80) REVERT: H 114 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7891 (mp) REVERT: H 182 VAL cc_start: 0.7651 (OUTLIER) cc_final: 0.7441 (p) REVERT: H 277 PHE cc_start: 0.8424 (t80) cc_final: 0.8159 (t80) REVERT: H 316 VAL cc_start: 0.8158 (t) cc_final: 0.7908 (t) REVERT: H 383 LEU cc_start: 0.8025 (tp) cc_final: 0.7754 (tp) REVERT: H 392 PHE cc_start: 0.7757 (m-80) cc_final: 0.7555 (m-80) REVERT: I 75 TYR cc_start: 0.7456 (m-10) cc_final: 0.7154 (m-10) REVERT: I 95 PHE cc_start: 0.7127 (t80) cc_final: 0.6817 (t80) REVERT: I 103 ILE cc_start: 0.6655 (tt) cc_final: 0.6414 (tt) REVERT: I 160 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7243 (tt) REVERT: I 323 MET cc_start: 0.8258 (mmt) cc_final: 0.7958 (mpm) REVERT: I 357 PHE cc_start: 0.7631 (m-80) cc_final: 0.7270 (m-80) outliers start: 129 outliers final: 73 residues processed: 723 average time/residue: 0.5865 time to fit residues: 481.8417 Evaluate side-chains 728 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 641 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 26 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 69 LYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 94 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 279 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 278 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.0570 chunk 187 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 HIS F 145 HIS G 245 ASN G 340 GLN H 245 ASN H 272 ASN H 284 ASN H 290 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.145788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136264 restraints weight = 31700.206| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.31 r_work: 0.3718 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22892 Z= 0.197 Angle : 0.542 6.998 30944 Z= 0.282 Chirality : 0.043 0.160 3502 Planarity : 0.004 0.065 3869 Dihedral : 4.414 53.555 3047 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.21 % Allowed : 29.25 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.16), residues: 2846 helix: 1.66 (0.12), residues: 1923 sheet: -0.26 (0.29), residues: 283 loop : -1.12 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 81 TYR 0.022 0.001 TYR G 228 PHE 0.028 0.002 PHE G 18 TRP 0.009 0.001 TRP G 171 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00474 (22886) covalent geometry : angle 0.54158 (30932) SS BOND : bond 0.00263 ( 6) SS BOND : angle 0.66987 ( 12) hydrogen bonds : bond 0.04008 ( 1526) hydrogen bonds : angle 4.47726 ( 4536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 664 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6621 (mm-30) REVERT: A 29 GLU cc_start: 0.6558 (pm20) cc_final: 0.6164 (pm20) REVERT: A 80 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7520 (mttp) REVERT: A 113 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7142 (tm-30) REVERT: A 307 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7356 (tp30) REVERT: B 10 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6397 (mm-30) REVERT: B 23 LYS cc_start: 0.7894 (mttt) cc_final: 0.7579 (mtpt) REVERT: B 75 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7411 (mp) REVERT: B 95 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7686 (tmmm) REVERT: B 214 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7142 (tm130) REVERT: B 217 LYS cc_start: 0.7963 (ttpp) cc_final: 0.7750 (ttpp) REVERT: C 214 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6843 (tm-30) REVERT: D 22 SER cc_start: 0.7976 (OUTLIER) cc_final: 0.7721 (p) REVERT: D 61 TYR cc_start: 0.8473 (m-80) cc_final: 0.7744 (m-80) REVERT: E 207 LEU cc_start: 0.8599 (mt) cc_final: 0.8346 (mp) REVERT: E 218 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6767 (mm) REVERT: E 226 THR cc_start: 0.7281 (OUTLIER) cc_final: 0.7032 (m) REVERT: E 228 GLU cc_start: 0.7453 (mp0) cc_final: 0.6654 (mp0) REVERT: E 244 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7208 (mtmm) REVERT: F 14 GLN cc_start: 0.7909 (mt0) cc_final: 0.7455 (mt0) REVERT: F 60 TYR cc_start: 0.8405 (m-80) cc_final: 0.8056 (m-80) REVERT: F 130 LYS cc_start: 0.7482 (tptt) cc_final: 0.7053 (tppt) REVERT: F 149 GLN cc_start: 0.7177 (mp10) cc_final: 0.6843 (mp10) REVERT: F 198 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6547 (mt-10) REVERT: F 227 GLU cc_start: 0.6731 (mp0) cc_final: 0.6379 (mp0) REVERT: F 245 LYS cc_start: 0.7921 (ttpp) cc_final: 0.7585 (ttpp) REVERT: G 1 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7796 (mtt) REVERT: G 160 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.6929 (pp) REVERT: G 161 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5899 (ptt) REVERT: G 294 LEU cc_start: 0.8359 (tp) cc_final: 0.8150 (tt) REVERT: G 325 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6585 (tp30) REVERT: H 17 PHE cc_start: 0.8319 (t80) cc_final: 0.8066 (t80) REVERT: H 19 TYR cc_start: 0.8139 (t80) cc_final: 0.7600 (t80) REVERT: H 26 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6991 (t80) REVERT: H 32 ILE cc_start: 0.7931 (pt) cc_final: 0.7650 (mp) REVERT: H 69 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8088 (tttp) REVERT: H 95 PHE cc_start: 0.7500 (t80) cc_final: 0.7223 (t80) REVERT: H 114 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7906 (mp) REVERT: H 182 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7464 (p) REVERT: H 183 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7689 (mp) REVERT: H 263 TYR cc_start: 0.8057 (m-10) cc_final: 0.7478 (m-10) REVERT: H 277 PHE cc_start: 0.8459 (t80) cc_final: 0.8154 (t80) REVERT: H 316 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7934 (t) REVERT: H 344 ARG cc_start: 0.8224 (ptp-170) cc_final: 0.7988 (ptp-170) REVERT: H 383 LEU cc_start: 0.8042 (tp) cc_final: 0.7758 (tp) REVERT: I 18 PHE cc_start: 0.7985 (m-80) cc_final: 0.7647 (m-80) REVERT: I 75 TYR cc_start: 0.7518 (m-10) cc_final: 0.7243 (m-10) REVERT: I 95 PHE cc_start: 0.7112 (t80) cc_final: 0.6841 (t80) REVERT: I 103 ILE cc_start: 0.6755 (tt) cc_final: 0.6525 (tt) REVERT: I 299 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6115 (mmt) REVERT: I 331 VAL cc_start: 0.8103 (m) cc_final: 0.7882 (m) REVERT: I 357 PHE cc_start: 0.7705 (m-80) cc_final: 0.7348 (m-80) outliers start: 144 outliers final: 86 residues processed: 732 average time/residue: 0.5902 time to fit residues: 490.0827 Evaluate side-chains 753 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 648 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 26 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 270 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN F 182 GLN G 340 GLN H 245 ASN H 272 ASN H 284 ASN H 290 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.148949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139677 restraints weight = 31849.163| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.28 r_work: 0.3716 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22892 Z= 0.213 Angle : 0.557 6.860 30944 Z= 0.289 Chirality : 0.043 0.163 3502 Planarity : 0.004 0.068 3869 Dihedral : 4.469 54.293 3047 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.56 % Allowed : 28.65 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.29 (0.16), residues: 2846 helix: 1.64 (0.12), residues: 1945 sheet: -0.21 (0.30), residues: 276 loop : -1.07 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 81 TYR 0.014 0.001 TYR G 3 PHE 0.033 0.002 PHE G 18 TRP 0.009 0.001 TRP G 171 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00514 (22886) covalent geometry : angle 0.55663 (30932) SS BOND : bond 0.00287 ( 6) SS BOND : angle 0.70916 ( 12) hydrogen bonds : bond 0.04030 ( 1526) hydrogen bonds : angle 4.49434 ( 4536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 648 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6654 (mm-30) REVERT: A 29 GLU cc_start: 0.6590 (pm20) cc_final: 0.6230 (pm20) REVERT: A 32 GLU cc_start: 0.7209 (tp30) cc_final: 0.7004 (tp30) REVERT: A 80 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7521 (mttp) REVERT: A 113 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7117 (tm-30) REVERT: A 307 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7344 (tp30) REVERT: B 23 LYS cc_start: 0.7920 (mttt) cc_final: 0.7606 (mtpt) REVERT: B 75 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7428 (mp) REVERT: B 95 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7656 (tmmm) REVERT: B 96 GLU cc_start: 0.8280 (mp0) cc_final: 0.7910 (mp0) REVERT: B 214 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7129 (tm130) REVERT: B 217 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7747 (ttpp) REVERT: C 39 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7039 (mm-30) REVERT: C 214 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: D 22 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7725 (p) REVERT: D 61 TYR cc_start: 0.8456 (m-80) cc_final: 0.7745 (m-80) REVERT: D 153 LEU cc_start: 0.7907 (tp) cc_final: 0.7686 (tp) REVERT: E 44 LYS cc_start: 0.7614 (ptmm) cc_final: 0.7413 (ptmm) REVERT: E 156 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8165 (tt) REVERT: E 177 HIS cc_start: 0.8056 (t70) cc_final: 0.7846 (t70) REVERT: E 207 LEU cc_start: 0.8617 (mt) cc_final: 0.8374 (mp) REVERT: E 218 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6828 (mm) REVERT: E 226 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.7103 (m) REVERT: E 228 GLU cc_start: 0.7464 (mp0) cc_final: 0.6686 (mp0) REVERT: E 244 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7284 (mtmm) REVERT: F 14 GLN cc_start: 0.7872 (mt0) cc_final: 0.7457 (mt0) REVERT: F 66 LYS cc_start: 0.8352 (tttt) cc_final: 0.8103 (tttt) REVERT: F 130 LYS cc_start: 0.7455 (tptt) cc_final: 0.7046 (tppt) REVERT: F 149 GLN cc_start: 0.7208 (mp10) cc_final: 0.6882 (mp10) REVERT: F 198 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6542 (mt-10) REVERT: F 207 LEU cc_start: 0.8149 (mt) cc_final: 0.7939 (mp) REVERT: F 227 GLU cc_start: 0.6662 (mp0) cc_final: 0.6328 (mp0) REVERT: F 245 LYS cc_start: 0.7955 (ttpp) cc_final: 0.7641 (ttpp) REVERT: G 1 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7809 (mtt) REVERT: G 81 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7579 (m) REVERT: G 116 PHE cc_start: 0.8048 (t80) cc_final: 0.7683 (t80) REVERT: G 156 SER cc_start: 0.7469 (m) cc_final: 0.7240 (p) REVERT: G 160 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.6947 (pp) REVERT: G 161 MET cc_start: 0.6198 (OUTLIER) cc_final: 0.5897 (ptt) REVERT: G 294 LEU cc_start: 0.8383 (tp) cc_final: 0.8181 (tt) REVERT: G 299 MET cc_start: 0.6948 (mmt) cc_final: 0.5937 (mmt) REVERT: G 378 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: H 17 PHE cc_start: 0.8285 (t80) cc_final: 0.8055 (t80) REVERT: H 26 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.6983 (t80) REVERT: H 32 ILE cc_start: 0.7967 (pt) cc_final: 0.7706 (mp) REVERT: H 69 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8070 (tptp) REVERT: H 95 PHE cc_start: 0.7487 (t80) cc_final: 0.7254 (t80) REVERT: H 114 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7933 (mp) REVERT: H 182 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7496 (p) REVERT: H 263 TYR cc_start: 0.8034 (m-10) cc_final: 0.7474 (m-10) REVERT: H 316 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7940 (t) REVERT: H 340 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7880 (mm-40) REVERT: H 383 LEU cc_start: 0.7998 (tp) cc_final: 0.7730 (tp) REVERT: I 95 PHE cc_start: 0.7094 (t80) cc_final: 0.6812 (t80) REVERT: I 103 ILE cc_start: 0.6878 (tt) cc_final: 0.6678 (tt) REVERT: I 299 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6118 (mmt) REVERT: I 357 PHE cc_start: 0.7706 (m-80) cc_final: 0.7390 (m-80) outliers start: 152 outliers final: 95 residues processed: 729 average time/residue: 0.6090 time to fit residues: 502.6160 Evaluate side-chains 758 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 643 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 182 GLN Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain G residue 378 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 26 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 248 optimal weight: 0.6980 chunk 252 optimal weight: 0.3980 chunk 125 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 238 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 HIS F 164 GLN G 340 GLN H 245 ASN H 272 ASN H 284 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140044 restraints weight = 31688.288| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.28 r_work: 0.3722 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22892 Z= 0.186 Angle : 0.558 10.671 30944 Z= 0.287 Chirality : 0.043 0.180 3502 Planarity : 0.004 0.070 3869 Dihedral : 4.449 54.457 3047 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 6.21 % Allowed : 29.21 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.30 (0.16), residues: 2846 helix: 1.69 (0.12), residues: 1926 sheet: -0.27 (0.30), residues: 273 loop : -1.10 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 81 TYR 0.015 0.001 TYR D 240 PHE 0.030 0.001 PHE G 18 TRP 0.009 0.001 TRP G 171 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00449 (22886) covalent geometry : angle 0.55761 (30932) SS BOND : bond 0.00258 ( 6) SS BOND : angle 0.63598 ( 12) hydrogen bonds : bond 0.03877 ( 1526) hydrogen bonds : angle 4.46657 ( 4536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 639 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7793 (ttmt) cc_final: 0.7507 (mttp) REVERT: A 113 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7109 (tm-30) REVERT: A 307 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7340 (tp30) REVERT: B 10 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6382 (mm-30) REVERT: B 23 LYS cc_start: 0.7931 (mttt) cc_final: 0.7576 (mtpt) REVERT: B 25 ARG cc_start: 0.7182 (ptt90) cc_final: 0.6725 (ptt90) REVERT: B 75 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7400 (mp) REVERT: B 95 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7569 (tmmm) REVERT: B 96 GLU cc_start: 0.8275 (mp0) cc_final: 0.7913 (mp0) REVERT: B 214 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7148 (tm130) REVERT: B 217 LYS cc_start: 0.7959 (ttpp) cc_final: 0.7748 (ttpp) REVERT: C 4 ILE cc_start: 0.7527 (mp) cc_final: 0.7326 (OUTLIER) REVERT: C 39 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7068 (mm-30) REVERT: C 48 ARG cc_start: 0.7153 (ttm-80) cc_final: 0.6383 (ttt-90) REVERT: C 214 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6826 (tm-30) REVERT: D 22 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.7724 (p) REVERT: D 61 TYR cc_start: 0.8448 (m-80) cc_final: 0.7731 (m-80) REVERT: E 156 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8148 (tt) REVERT: E 207 LEU cc_start: 0.8631 (mt) cc_final: 0.8390 (mp) REVERT: E 218 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6807 (mm) REVERT: E 226 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.7101 (m) REVERT: E 228 GLU cc_start: 0.7456 (mp0) cc_final: 0.6677 (mp0) REVERT: E 244 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7289 (mtmm) REVERT: F 14 GLN cc_start: 0.7885 (mt0) cc_final: 0.7455 (mt0) REVERT: F 66 LYS cc_start: 0.8340 (tttt) cc_final: 0.8092 (tttt) REVERT: F 130 LYS cc_start: 0.7467 (tptt) cc_final: 0.7041 (tppt) REVERT: F 149 GLN cc_start: 0.7190 (mp10) cc_final: 0.6855 (mp10) REVERT: F 198 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6688 (mt-10) REVERT: F 207 LEU cc_start: 0.8147 (mt) cc_final: 0.7936 (mp) REVERT: F 227 GLU cc_start: 0.6714 (mp0) cc_final: 0.6383 (mp0) REVERT: F 245 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7611 (ttpp) REVERT: G 1 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7788 (mtt) REVERT: G 81 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7575 (m) REVERT: G 86 MET cc_start: 0.6672 (mmm) cc_final: 0.6365 (mmm) REVERT: G 116 PHE cc_start: 0.8054 (t80) cc_final: 0.7688 (t80) REVERT: G 156 SER cc_start: 0.7433 (m) cc_final: 0.7197 (p) REVERT: G 160 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.6939 (pp) REVERT: G 161 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5893 (ptt) REVERT: G 294 LEU cc_start: 0.8371 (tp) cc_final: 0.8166 (tt) REVERT: G 325 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6583 (tp30) REVERT: G 378 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: H 17 PHE cc_start: 0.8269 (t80) cc_final: 0.8012 (t80) REVERT: H 26 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6997 (t80) REVERT: H 32 ILE cc_start: 0.7971 (pt) cc_final: 0.7710 (mp) REVERT: H 69 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8111 (tptp) REVERT: H 114 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7959 (mp) REVERT: H 160 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7268 (pt) REVERT: H 316 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7828 (p) REVERT: H 323 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7696 (mpp) REVERT: H 383 LEU cc_start: 0.7985 (tp) cc_final: 0.7712 (tp) REVERT: I 18 PHE cc_start: 0.8046 (m-80) cc_final: 0.7816 (m-80) REVERT: I 95 PHE cc_start: 0.7093 (t80) cc_final: 0.6821 (t80) REVERT: I 103 ILE cc_start: 0.6717 (tt) cc_final: 0.6488 (tt) REVERT: I 299 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.6132 (mmt) REVERT: I 392 PHE cc_start: 0.7844 (m-80) cc_final: 0.7598 (m-80) outliers start: 144 outliers final: 101 residues processed: 707 average time/residue: 0.6221 time to fit residues: 498.4391 Evaluate side-chains 750 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 628 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 182 GLN Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain G residue 378 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 26 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 248 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 250 optimal weight: 0.1980 chunk 212 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 240 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 64 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN G 340 GLN H 245 ASN H 272 ASN H 284 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.149935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140493 restraints weight = 31558.829| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.33 r_work: 0.3728 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22892 Z= 0.144 Angle : 0.539 8.814 30944 Z= 0.277 Chirality : 0.041 0.195 3502 Planarity : 0.004 0.083 3869 Dihedral : 4.381 53.958 3047 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.69 % Allowed : 30.11 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.43 (0.16), residues: 2846 helix: 1.78 (0.12), residues: 1929 sheet: -0.28 (0.30), residues: 271 loop : -1.01 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 81 TYR 0.013 0.001 TYR G 228 PHE 0.025 0.001 PHE G 18 TRP 0.009 0.001 TRP H 171 HIS 0.006 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00341 (22886) covalent geometry : angle 0.53920 (30932) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.52357 ( 12) hydrogen bonds : bond 0.03590 ( 1526) hydrogen bonds : angle 4.40469 ( 4536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 662 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6672 (mm-30) REVERT: A 80 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7500 (mttp) REVERT: A 113 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 307 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7361 (tp30) REVERT: B 23 LYS cc_start: 0.7910 (mttt) cc_final: 0.7563 (mtpt) REVERT: B 25 ARG cc_start: 0.7145 (ptt90) cc_final: 0.6687 (ptt90) REVERT: B 75 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7332 (mp) REVERT: B 95 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7565 (tmmm) REVERT: B 96 GLU cc_start: 0.8304 (mp0) cc_final: 0.7965 (mp0) REVERT: B 214 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7151 (tm130) REVERT: B 217 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7727 (ttpp) REVERT: C 39 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7059 (mm-30) REVERT: C 142 GLU cc_start: 0.7737 (tp30) cc_final: 0.7346 (tp30) REVERT: C 214 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: D 61 TYR cc_start: 0.8455 (m-80) cc_final: 0.7718 (m-80) REVERT: E 124 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7940 (m) REVERT: E 156 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8169 (tt) REVERT: E 207 LEU cc_start: 0.8599 (mt) cc_final: 0.8356 (mp) REVERT: E 218 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6742 (mm) REVERT: E 226 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.7048 (m) REVERT: E 228 GLU cc_start: 0.7432 (mp0) cc_final: 0.6624 (mp0) REVERT: E 244 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7304 (mtmm) REVERT: F 14 GLN cc_start: 0.7905 (mt0) cc_final: 0.7487 (mt0) REVERT: F 66 LYS cc_start: 0.8450 (tttt) cc_final: 0.8177 (tttt) REVERT: F 130 LYS cc_start: 0.7497 (tptt) cc_final: 0.7068 (tppt) REVERT: F 149 GLN cc_start: 0.7177 (mp10) cc_final: 0.6825 (mp10) REVERT: F 198 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6709 (mt-10) REVERT: F 207 LEU cc_start: 0.8130 (mt) cc_final: 0.7927 (mp) REVERT: F 227 GLU cc_start: 0.6722 (mp0) cc_final: 0.6371 (mp0) REVERT: G 1 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7818 (mtt) REVERT: G 81 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7574 (m) REVERT: G 86 MET cc_start: 0.6694 (mmm) cc_final: 0.6370 (mmm) REVERT: G 116 PHE cc_start: 0.8061 (t80) cc_final: 0.7630 (t80) REVERT: G 156 SER cc_start: 0.7447 (m) cc_final: 0.7208 (p) REVERT: G 160 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.6940 (pp) REVERT: G 161 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5883 (ptt) REVERT: G 294 LEU cc_start: 0.8358 (tp) cc_final: 0.8157 (tt) REVERT: G 299 MET cc_start: 0.6877 (mmt) cc_final: 0.5944 (mmt) REVERT: H 17 PHE cc_start: 0.8270 (t80) cc_final: 0.8026 (t80) REVERT: H 19 TYR cc_start: 0.8130 (t80) cc_final: 0.7547 (t80) REVERT: H 26 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7050 (t80) REVERT: H 32 ILE cc_start: 0.7975 (pt) cc_final: 0.7705 (mp) REVERT: H 69 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8128 (tptm) REVERT: H 114 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7918 (mp) REVERT: H 160 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7244 (pt) REVERT: H 263 TYR cc_start: 0.8031 (m-10) cc_final: 0.7487 (m-10) REVERT: H 316 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7901 (t) REVERT: H 323 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7704 (mpp) REVERT: H 340 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7922 (mm-40) REVERT: H 383 LEU cc_start: 0.8007 (tp) cc_final: 0.7711 (tp) REVERT: I 95 PHE cc_start: 0.7093 (t80) cc_final: 0.6835 (t80) REVERT: I 103 ILE cc_start: 0.6609 (tt) cc_final: 0.6347 (tt) REVERT: I 160 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7278 (tt) REVERT: I 299 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6176 (mmt) REVERT: I 325 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: I 392 PHE cc_start: 0.7845 (m-80) cc_final: 0.7526 (m-80) outliers start: 132 outliers final: 86 residues processed: 724 average time/residue: 0.6206 time to fit residues: 507.7050 Evaluate side-chains 758 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 650 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 182 GLN Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 26 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 55 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 103 optimal weight: 0.0000 chunk 79 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 256 optimal weight: 0.3980 chunk 188 optimal weight: 0.1980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN F 164 GLN G 340 GLN H 38 ASN H 245 ASN H 272 ASN H 284 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140849 restraints weight = 31765.485| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.34 r_work: 0.3731 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22892 Z= 0.138 Angle : 0.542 8.762 30944 Z= 0.277 Chirality : 0.041 0.198 3502 Planarity : 0.004 0.075 3869 Dihedral : 4.335 53.551 3047 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.05 % Allowed : 30.93 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.50 (0.16), residues: 2846 helix: 1.83 (0.12), residues: 1929 sheet: -0.24 (0.30), residues: 271 loop : -0.96 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 81 TYR 0.013 0.001 TYR G 228 PHE 0.024 0.001 PHE G 18 TRP 0.010 0.001 TRP F 220 HIS 0.010 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00323 (22886) covalent geometry : angle 0.54163 (30932) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.46653 ( 12) hydrogen bonds : bond 0.03507 ( 1526) hydrogen bonds : angle 4.37274 ( 4536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 663 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7497 (mttp) REVERT: A 113 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 10 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6556 (tm-30) REVERT: B 23 LYS cc_start: 0.7907 (mttt) cc_final: 0.7552 (mtpt) REVERT: B 25 ARG cc_start: 0.7148 (ptt90) cc_final: 0.6679 (ptt90) REVERT: B 75 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7332 (mp) REVERT: B 95 LYS cc_start: 0.8019 (tmmm) cc_final: 0.7503 (tmmm) REVERT: B 96 GLU cc_start: 0.8302 (mp0) cc_final: 0.7984 (mp0) REVERT: B 210 GLU cc_start: 0.7172 (pm20) cc_final: 0.6819 (pm20) REVERT: C 39 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7042 (mm-30) REVERT: C 142 GLU cc_start: 0.7723 (tp30) cc_final: 0.7327 (tp30) REVERT: C 214 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: C 250 GLU cc_start: 0.7369 (tt0) cc_final: 0.7106 (tt0) REVERT: D 61 TYR cc_start: 0.8451 (m-80) cc_final: 0.7687 (m-80) REVERT: E 124 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7919 (m) REVERT: E 156 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8156 (tt) REVERT: E 207 LEU cc_start: 0.8600 (mt) cc_final: 0.8357 (mp) REVERT: E 218 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6722 (mm) REVERT: E 226 THR cc_start: 0.7273 (OUTLIER) cc_final: 0.7069 (m) REVERT: E 227 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: E 228 GLU cc_start: 0.7390 (mp0) cc_final: 0.6679 (mp0) REVERT: E 244 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7319 (mtmm) REVERT: F 14 GLN cc_start: 0.7917 (mt0) cc_final: 0.7498 (mt0) REVERT: F 66 LYS cc_start: 0.8434 (tttt) cc_final: 0.8175 (tttt) REVERT: F 130 LYS cc_start: 0.7516 (tptt) cc_final: 0.6979 (tppt) REVERT: F 149 GLN cc_start: 0.7212 (mp10) cc_final: 0.6867 (mp10) REVERT: F 198 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6718 (mt-10) REVERT: F 215 LYS cc_start: 0.7309 (mmmt) cc_final: 0.7022 (mmmt) REVERT: F 227 GLU cc_start: 0.6726 (mp0) cc_final: 0.6368 (mp0) REVERT: G 1 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7811 (mtt) REVERT: G 69 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7835 (ttmm) REVERT: G 81 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7570 (m) REVERT: G 86 MET cc_start: 0.6702 (mmm) cc_final: 0.6381 (mmm) REVERT: G 156 SER cc_start: 0.7422 (m) cc_final: 0.7178 (p) REVERT: G 161 MET cc_start: 0.6226 (OUTLIER) cc_final: 0.5955 (ptt) REVERT: G 299 MET cc_start: 0.6849 (mmt) cc_final: 0.5901 (mmt) REVERT: H 17 PHE cc_start: 0.8259 (t80) cc_final: 0.8038 (t80) REVERT: H 19 TYR cc_start: 0.8139 (t80) cc_final: 0.7586 (t80) REVERT: H 26 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7024 (t80) REVERT: H 32 ILE cc_start: 0.7979 (pt) cc_final: 0.7711 (mp) REVERT: H 69 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8124 (tttp) REVERT: H 109 VAL cc_start: 0.7643 (t) cc_final: 0.7437 (p) REVERT: H 114 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7859 (mp) REVERT: H 160 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7229 (pt) REVERT: H 263 TYR cc_start: 0.8016 (m-10) cc_final: 0.7553 (m-10) REVERT: H 299 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.6484 (mmt) REVERT: H 316 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7915 (t) REVERT: H 323 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7695 (mpp) REVERT: H 340 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7879 (mm-40) REVERT: I 95 PHE cc_start: 0.7049 (t80) cc_final: 0.6787 (t80) REVERT: I 103 ILE cc_start: 0.6579 (tt) cc_final: 0.6298 (tt) REVERT: I 160 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7271 (tt) REVERT: I 299 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6190 (mmt) REVERT: I 325 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6766 (tp30) outliers start: 117 outliers final: 80 residues processed: 720 average time/residue: 0.6231 time to fit residues: 507.0610 Evaluate side-chains 757 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 655 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 182 GLN Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain H residue 16 PHE Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 299 MET Chi-restraints excluded: chain H residue 311 SER Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 26 TYR Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 280 optimal weight: 0.9980 chunk 131 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 189 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 187 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN G 340 GLN H 245 ASN ** H 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.149289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139880 restraints weight = 31789.760| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.33 r_work: 0.3721 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22892 Z= 0.189 Angle : 0.578 9.488 30944 Z= 0.295 Chirality : 0.043 0.216 3502 Planarity : 0.004 0.069 3869 Dihedral : 4.293 46.259 3045 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.49 % Allowed : 31.75 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.43 (0.16), residues: 2846 helix: 1.79 (0.12), residues: 1923 sheet: -0.35 (0.29), residues: 280 loop : -0.98 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 81 TYR 0.023 0.002 TYR I 228 PHE 0.031 0.001 PHE G 18 TRP 0.011 0.001 TRP E 54 HIS 0.009 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00457 (22886) covalent geometry : angle 0.57756 (30932) SS BOND : bond 0.00257 ( 6) SS BOND : angle 0.60302 ( 12) hydrogen bonds : bond 0.03806 ( 1526) hydrogen bonds : angle 4.42812 ( 4536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5692 Ramachandran restraints generated. 2846 Oldfield, 0 Emsley, 2846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 642 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7131 (tm-30) REVERT: B 10 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6604 (tm-30) REVERT: B 23 LYS cc_start: 0.7910 (mttt) cc_final: 0.7578 (mtpt) REVERT: B 25 ARG cc_start: 0.7177 (ptt90) cc_final: 0.6723 (ptt90) REVERT: B 75 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7389 (mp) REVERT: B 95 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7496 (tmmm) REVERT: B 96 GLU cc_start: 0.8303 (mp0) cc_final: 0.7992 (mp0) REVERT: C 39 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7120 (mm-30) REVERT: C 142 GLU cc_start: 0.7649 (tp30) cc_final: 0.7252 (tp30) REVERT: C 214 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: C 250 GLU cc_start: 0.7410 (tt0) cc_final: 0.7152 (tt0) REVERT: D 61 TYR cc_start: 0.8467 (m-80) cc_final: 0.7723 (m-80) REVERT: E 124 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7941 (m) REVERT: E 156 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8178 (tt) REVERT: E 207 LEU cc_start: 0.8579 (mt) cc_final: 0.8352 (mp) REVERT: E 218 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6773 (mm) REVERT: E 226 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.7082 (m) REVERT: E 227 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: E 228 GLU cc_start: 0.7386 (mp0) cc_final: 0.6684 (mp0) REVERT: E 240 TYR cc_start: 0.8259 (t80) cc_final: 0.7889 (t80) REVERT: E 244 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7294 (mtmm) REVERT: F 14 GLN cc_start: 0.7901 (mt0) cc_final: 0.7521 (mt0) REVERT: F 66 LYS cc_start: 0.8463 (tttt) cc_final: 0.8221 (tttt) REVERT: F 130 LYS cc_start: 0.7559 (tptt) cc_final: 0.7039 (tppt) REVERT: F 149 GLN cc_start: 0.7238 (mp10) cc_final: 0.6887 (mp10) REVERT: F 198 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6777 (mt-10) REVERT: F 215 LYS cc_start: 0.7293 (mmmt) cc_final: 0.7009 (mmmt) REVERT: F 227 GLU cc_start: 0.6722 (mp0) cc_final: 0.6377 (mp0) REVERT: G 1 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7790 (mtt) REVERT: G 81 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7608 (m) REVERT: G 86 MET cc_start: 0.6745 (mmm) cc_final: 0.6387 (mmm) REVERT: G 156 SER cc_start: 0.7459 (m) cc_final: 0.7248 (p) REVERT: G 161 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.6046 (ptt) REVERT: G 299 MET cc_start: 0.6965 (mmt) cc_final: 0.5991 (mmt) REVERT: G 378 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: H 17 PHE cc_start: 0.8287 (t80) cc_final: 0.8056 (t80) REVERT: H 26 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7008 (t80) REVERT: H 32 ILE cc_start: 0.7998 (pt) cc_final: 0.7751 (mp) REVERT: H 69 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8129 (tptp) REVERT: H 114 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7851 (mp) REVERT: H 160 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7258 (pt) REVERT: H 263 TYR cc_start: 0.8027 (m-10) cc_final: 0.7593 (m-10) REVERT: H 276 MET cc_start: 0.8449 (ttm) cc_final: 0.8204 (mtp) REVERT: H 299 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.6472 (mmt) REVERT: H 316 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7825 (p) REVERT: H 323 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7753 (mpp) REVERT: H 340 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7932 (mm-40) REVERT: I 95 PHE cc_start: 0.7102 (t80) cc_final: 0.6845 (t80) REVERT: I 103 ILE cc_start: 0.6616 (tt) cc_final: 0.6403 (tt) REVERT: I 299 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6138 (mmt) REVERT: I 310 THR cc_start: 0.8030 (p) cc_final: 0.7702 (m) REVERT: I 325 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6778 (tp30) REVERT: I 331 VAL cc_start: 0.8188 (m) cc_final: 0.7969 (m) outliers start: 104 outliers final: 74 residues processed: 695 average time/residue: 0.6163 time to fit residues: 484.2864 Evaluate side-chains 736 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 640 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 182 GLN Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain G residue 378 PHE Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 299 MET Chi-restraints excluded: chain H residue 311 SER Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 26 TYR Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 343 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 179 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 266 optimal weight: 0.0970 chunk 89 optimal weight: 0.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN G 340 GLN H 245 ASN ** H 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.149947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.140566 restraints weight = 31622.580| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.33 r_work: 0.3762 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22892 Z= 0.144 Angle : 0.555 9.236 30944 Z= 0.284 Chirality : 0.041 0.202 3502 Planarity : 0.004 0.066 3869 Dihedral : 4.240 45.812 3045 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.27 % Allowed : 32.10 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.52 (0.16), residues: 2846 helix: 1.82 (0.12), residues: 1932 sheet: -0.24 (0.30), residues: 273 loop : -0.89 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 81 TYR 0.015 0.001 TYR F 240 PHE 0.026 0.001 PHE G 18 TRP 0.015 0.001 TRP F 220 HIS 0.009 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00342 (22886) covalent geometry : angle 0.55481 (30932) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.49628 ( 12) hydrogen bonds : bond 0.03530 ( 1526) hydrogen bonds : angle 4.38175 ( 4536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12680.00 seconds wall clock time: 215 minutes 12.08 seconds (12912.08 seconds total)