Starting phenix.real_space_refine on Fri Mar 6 19:04:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xph_67098/03_2026/9xph_67098.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xph_67098/03_2026/9xph_67098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xph_67098/03_2026/9xph_67098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xph_67098/03_2026/9xph_67098.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xph_67098/03_2026/9xph_67098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xph_67098/03_2026/9xph_67098.map" } resolution = 4.02 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= 0.006 sd= 0.072 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 118 5.16 5 C 20748 2.51 5 N 5514 2.21 5 O 6352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s 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: 32732 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3489 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 18, 'TRANS': 417} Chain breaks: 6 Chain: "A" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3489 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 18, 'TRANS': 417} Chain breaks: 6 Chain: "C" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3489 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 18, 'TRANS': 417} Chain breaks: 6 Chain: "G" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2669 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 15, 'TRANS': 326} Chain breaks: 2 Chain: "D" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2408 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Chain: "J" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2669 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 15, 'TRANS': 326} Chain breaks: 2 Chain: "E" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2408 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Chain: "L" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2669 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 15, 'TRANS': 326} Chain breaks: 2 Chain: "F" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2408 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Chain: "I" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2145 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "K" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2145 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "M" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2144 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 600 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Time building chain proxies: 7.23, per 1000 atoms: 0.22 Number of scatterers: 32732 At special positions: 0 Unit cell: (194.48, 193.12, 224.4, 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 118 16.00 O 6352 8.00 N 5514 7.00 C 20748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7740 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 56 sheets defined 33.3% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 171 through 185 removed outlier: 3.848A pdb=" N LYS B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.961A pdb=" N LYS B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 369 through 379 removed outlier: 4.420A pdb=" N GLU B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 171 through 185 removed outlier: 4.087A pdb=" N LYS A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 257 through 262 removed outlier: 4.169A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 321 through 324 removed outlier: 4.391A pdb=" N LEU A 324 " --> pdb=" O ASN A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 369 through 379 removed outlier: 4.425A pdb=" N GLU A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 171 through 185 removed outlier: 4.064A pdb=" N LYS C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 257 through 262 removed outlier: 4.344A pdb=" N LYS C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 257 through 262' Processing helix chain 'C' and resid 303 through 312 Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 369 through 379 removed outlier: 4.382A pdb=" N GLU C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 44 removed outlier: 3.905A pdb=" N GLN G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 53 removed outlier: 3.651A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 81 Processing helix chain 'G' and resid 84 through 90 Processing helix chain 'G' and resid 92 through 104 removed outlier: 3.634A pdb=" N GLU G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR G 104 " --> pdb=" O PHE G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 4.535A pdb=" N ASN G 121 " --> pdb=" O ARG G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'G' and resid 164 through 182 removed outlier: 4.129A pdb=" N GLY G 173 " --> pdb=" O ALA G 169 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN G 180 " --> pdb=" O GLN G 176 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TRP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY G 182 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 192 removed outlier: 3.637A pdb=" N ILE G 187 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE G 191 " --> pdb=" O ILE G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 222 Processing helix chain 'G' and resid 222 through 227 removed outlier: 3.505A pdb=" N LEU G 226 " --> pdb=" O THR G 222 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 222 through 227' Processing helix chain 'G' and resid 231 through 242 Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.563A pdb=" N LEU G 247 " --> pdb=" O ALA G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 261 Processing helix chain 'G' and resid 269 through 271 No H-bonds generated for 'chain 'G' and resid 269 through 271' Processing helix chain 'G' and resid 272 through 288 removed outlier: 3.868A pdb=" N ILE G 276 " --> pdb=" O ASP G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.899A pdb=" N ASN G 321 " --> pdb=" O LEU G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 331 removed outlier: 3.595A pdb=" N VAL G 330 " --> pdb=" O THR G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 347 removed outlier: 3.664A pdb=" N MET G 346 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR G 347 " --> pdb=" O PHE G 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 69 through 82 removed outlier: 4.222A pdb=" N LYS D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 removed outlier: 3.903A pdb=" N GLN D 89 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 117 through 121 removed outlier: 4.227A pdb=" N ASN D 121 " --> pdb=" O ARG D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.633A pdb=" N ASP D 151 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 182 removed outlier: 3.857A pdb=" N GLY D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TRP D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 removed outlier: 3.946A pdb=" N PHE D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 227 removed outlier: 3.659A pdb=" N ARG D 215 " --> pdb=" O ASN D 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.511A pdb=" N ILE D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.503A pdb=" N ALA D 249 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 261 Processing helix chain 'D' and resid 269 through 272 Processing helix chain 'D' and resid 273 through 288 removed outlier: 3.539A pdb=" N LYS D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 330 through 334 Processing helix chain 'D' and resid 339 through 347 Processing helix chain 'J' and resid 21 through 25 removed outlier: 3.515A pdb=" N THR J 24 " --> pdb=" O ASP J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 44 removed outlier: 3.750A pdb=" N GLN J 43 " --> pdb=" O SER J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 54 removed outlier: 3.648A pdb=" N LYS J 54 " --> pdb=" O ASN J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 81 Processing helix chain 'J' and resid 84 through 90 removed outlier: 3.640A pdb=" N GLN J 89 " --> pdb=" O SER J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 104 removed outlier: 3.642A pdb=" N GLU J 96 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU J 103 " --> pdb=" O ILE J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 152 removed outlier: 3.642A pdb=" N MET J 152 " --> pdb=" O PHE J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 182 removed outlier: 4.053A pdb=" N GLY J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN J 180 " --> pdb=" O GLN J 176 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP J 181 " --> pdb=" O GLU J 177 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY J 182 " --> pdb=" O VAL J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 192 removed outlier: 3.561A pdb=" N ILE J 187 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE J 191 " --> pdb=" O ILE J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'J' and resid 222 through 227 removed outlier: 3.885A pdb=" N GLY J 227 " --> pdb=" O ALA J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 242 Processing helix chain 'J' and resid 244 through 249 removed outlier: 3.620A pdb=" N LEU J 247 " --> pdb=" O ALA J 244 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 261 Processing helix chain 'J' and resid 269 through 271 No H-bonds generated for 'chain 'J' and resid 269 through 271' Processing helix chain 'J' and resid 272 through 288 removed outlier: 3.898A pdb=" N ILE J 276 " --> pdb=" O ASP J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 321 removed outlier: 3.821A pdb=" N ASN J 321 " --> pdb=" O LEU J 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 331 removed outlier: 3.578A pdb=" N VAL J 330 " --> pdb=" O THR J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 347 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 69 through 81 Processing helix chain 'E' and resid 84 through 89 removed outlier: 3.685A pdb=" N GLN E 89 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.547A pdb=" N ASP E 151 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 180 removed outlier: 3.700A pdb=" N GLY E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN E 180 " --> pdb=" O GLN E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 removed outlier: 3.936A pdb=" N PHE E 191 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 4.089A pdb=" N GLY E 201 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 227 removed outlier: 3.657A pdb=" N ARG E 215 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 242 removed outlier: 3.508A pdb=" N ILE E 235 " --> pdb=" O ASP E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 253 through 261 Processing helix chain 'E' and resid 269 through 272 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 311 through 319 Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 324 through 329 removed outlier: 3.774A pdb=" N MET E 328 " --> pdb=" O TYR E 324 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 324 through 329' Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 339 through 347 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 37 through 44 removed outlier: 3.791A pdb=" N GLN L 43 " --> pdb=" O SER L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 54 removed outlier: 3.712A pdb=" N LYS L 54 " --> pdb=" O ASN L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 81 Processing helix chain 'L' and resid 84 through 90 removed outlier: 3.563A pdb=" N GLN L 89 " --> pdb=" O SER L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 104 removed outlier: 3.661A pdb=" N GLU L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU L 103 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR L 104 " --> pdb=" O PHE L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 151 Processing helix chain 'L' and resid 164 through 179 removed outlier: 4.137A pdb=" N GLY L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 192 removed outlier: 3.575A pdb=" N ILE L 187 " --> pdb=" O ILE L 183 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE L 191 " --> pdb=" O ILE L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 222 Processing helix chain 'L' and resid 222 through 227 removed outlier: 3.834A pdb=" N GLY L 227 " --> pdb=" O ALA L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 242 Processing helix chain 'L' and resid 244 through 249 removed outlier: 3.575A pdb=" N LEU L 247 " --> pdb=" O ALA L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 253 through 261 Processing helix chain 'L' and resid 269 through 271 No H-bonds generated for 'chain 'L' and resid 269 through 271' Processing helix chain 'L' and resid 272 through 288 removed outlier: 3.848A pdb=" N ILE L 276 " --> pdb=" O ASP L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 321 removed outlier: 4.007A pdb=" N ASN L 321 " --> pdb=" O LEU L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 331 removed outlier: 3.549A pdb=" N VAL L 330 " --> pdb=" O THR L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 347 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 69 through 81 Processing helix chain 'F' and resid 84 through 90 removed outlier: 3.682A pdb=" N ASP F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN F 89 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 102 Processing helix chain 'F' and resid 138 through 151 removed outlier: 3.568A pdb=" N ASP F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 179 removed outlier: 3.862A pdb=" N GLY F 173 " --> pdb=" O ALA F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 191 removed outlier: 3.964A pdb=" N PHE F 191 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 227 removed outlier: 3.704A pdb=" N ARG F 215 " --> pdb=" O ASN F 211 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER F 225 " --> pdb=" O ARG F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 253 through 261 Processing helix chain 'F' and resid 269 through 272 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 311 through 319 Processing helix chain 'F' and resid 321 through 323 No H-bonds generated for 'chain 'F' and resid 321 through 323' Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.947A pdb=" N MET F 328 " --> pdb=" O TYR F 324 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 329' Processing helix chain 'F' and resid 330 through 334 Processing helix chain 'F' and resid 339 through 347 Processing helix chain 'H' and resid 43 through 48 Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 28 removed outlier: 4.632A pdb=" N ALA B 24 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 107 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.214A pdb=" N ARG B 147 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 146 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE B 62 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.214A pdb=" N ARG B 147 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 146 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE B 62 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA B 445 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 422 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR B 443 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU B 424 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 441 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE B 426 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL B 439 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 299 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 161 through 162 removed outlier: 3.541A pdb=" N THR B 218 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 209 through 211 removed outlier: 3.792A pdb=" N ASN B 166 " --> pdb=" O SER M 81 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER M 81 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 168 " --> pdb=" O SER M 79 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER M 79 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL B 170 " --> pdb=" O LYS M 77 " (cutoff:3.500A) removed outlier: 11.121A pdb=" N LYS M 77 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 200 Processing sheet with id=AA7, first strand: chain 'B' and resid 358 through 366 removed outlier: 6.301A pdb=" N GLY B 314 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR B 361 " --> pdb=" O GLY B 314 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ARG B 316 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLN B 363 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ALA B 318 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B 365 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA J 18 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 347 " --> pdb=" O ALA J 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 25 through 28 Processing sheet with id=AA9, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AB1, first strand: chain 'A' and resid 111 through 116 removed outlier: 4.223A pdb=" N ARG A 147 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 62 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A 266 " --> pdb=" O LYS A 403 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN A 405 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A 268 " --> pdb=" O GLN A 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 111 through 116 removed outlier: 4.223A pdb=" N ARG A 147 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 62 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU A 419 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE A 447 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 439 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 161 through 162 removed outlier: 3.521A pdb=" N THR A 218 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 168 through 170 removed outlier: 6.937A pdb=" N THR A 168 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 211 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AB6, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.268A pdb=" N GLY A 314 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR A 361 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ARG A 316 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLN A 363 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA A 318 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A 365 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AB8, first strand: chain 'C' and resid 24 through 28 removed outlier: 4.609A pdb=" N ALA C 24 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS C 86 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 109 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG C 147 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 62 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU C 266 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLN C 405 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 268 " --> pdb=" O GLN C 405 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.752A pdb=" N CYS C 86 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 109 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG C 147 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 62 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 445 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 422 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR C 443 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU C 424 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 441 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE C 426 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL C 439 " --> pdb=" O PHE C 426 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.612A pdb=" N VAL C 211 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR C 168 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C 166 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 166 " --> pdb=" O SER K 81 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER K 79 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL C 170 " --> pdb=" O LYS K 77 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N LYS K 77 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL K 60 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AC3, first strand: chain 'C' and resid 345 through 347 removed outlier: 6.238A pdb=" N GLY C 314 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C 361 " --> pdb=" O GLY C 314 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG C 316 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN C 363 " --> pdb=" O ARG C 316 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA C 318 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER C 365 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 329 through 330 removed outlier: 3.694A pdb=" N ILE C 329 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 131 through 134 Processing sheet with id=AC6, first strand: chain 'G' and resid 193 through 194 removed outlier: 3.609A pdb=" N THR G 194 " --> pdb=" O ASP G 207 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 294 through 295 removed outlier: 3.572A pdb=" N VAL G 301 " --> pdb=" O THR G 294 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 130 through 134 removed outlier: 3.561A pdb=" N LYS D 134 " --> pdb=" O VAL D 123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 194 through 195 Processing sheet with id=AD1, first strand: chain 'D' and resid 293 through 295 removed outlier: 3.742A pdb=" N VAL D 301 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 131 through 134 Processing sheet with id=AD3, first strand: chain 'J' and resid 193 through 194 Processing sheet with id=AD4, first strand: chain 'J' and resid 294 through 295 removed outlier: 3.650A pdb=" N VAL J 301 " --> pdb=" O THR J 294 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 134 removed outlier: 3.628A pdb=" N LYS E 134 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 194 through 195 Processing sheet with id=AD7, first strand: chain 'E' and resid 293 through 295 Processing sheet with id=AD8, first strand: chain 'L' and resid 131 through 134 Processing sheet with id=AD9, first strand: chain 'L' and resid 294 through 295 removed outlier: 3.520A pdb=" N VAL L 301 " --> pdb=" O THR L 294 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 130 through 134 Processing sheet with id=AE2, first strand: chain 'F' and resid 194 through 195 Processing sheet with id=AE3, first strand: chain 'F' and resid 293 through 295 removed outlier: 3.565A pdb=" N VAL F 301 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 21 through 23 removed outlier: 3.882A pdb=" N ARG I 22 " --> pdb=" O ARG I 111 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE I 118 " --> pdb=" O PRO I 85 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS I 86 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU I 40 " --> pdb=" O CYS I 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 60 through 66 removed outlier: 3.522A pdb=" N VAL I 60 " --> pdb=" O VAL I 80 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY I 66 " --> pdb=" O TYR I 74 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR I 74 " --> pdb=" O GLY I 66 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 136 through 140 removed outlier: 4.143A pdb=" N PHE I 157 " --> pdb=" O GLY I 170 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL I 167 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 221 through 224 removed outlier: 3.607A pdb=" N ALA I 227 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR K 239 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU I 230 " --> pdb=" O THR K 239 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 238 through 239 Processing sheet with id=AE9, first strand: chain 'I' and resid 244 through 248 removed outlier: 6.092A pdb=" N PHE I 252 " --> pdb=" O THR K 260 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LYS K 262 " --> pdb=" O PHE I 252 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL I 254 " --> pdb=" O LYS K 262 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 259 through 263 removed outlier: 3.818A pdb=" N THR M 256 " --> pdb=" O LYS I 262 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 266 through 267 removed outlier: 4.010A pdb=" N HIS M 267 " --> pdb=" O THR I 274 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET I 275 " --> pdb=" O ASN K 282 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU K 284 " --> pdb=" O MET I 275 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR K 286 " --> pdb=" O HIS I 277 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET K 283 " --> pdb=" O ASP M 291 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR M 290 " --> pdb=" O THR H 85 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 266 through 267 removed outlier: 6.094A pdb=" N HIS K 267 " --> pdb=" O THR M 276 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LYS M 278 " --> pdb=" O HIS K 267 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASN I 282 " --> pdb=" O MET M 275 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N HIS M 277 " --> pdb=" O ASN I 282 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU I 284 " --> pdb=" O HIS M 277 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET I 283 " --> pdb=" O ASP K 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'I' and resid 290 through 291 removed outlier: 4.084A pdb=" N PHE M 285 " --> pdb=" O ASP I 291 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR M 286 " --> pdb=" O HIS K 277 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 21 through 23 removed outlier: 3.744A pdb=" N ARG K 22 " --> pdb=" O ARG K 111 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N PHE K 118 " --> pdb=" O PRO K 85 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS K 86 " --> pdb=" O LEU K 40 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU K 40 " --> pdb=" O CYS K 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 136 through 140 removed outlier: 4.109A pdb=" N PHE K 157 " --> pdb=" O GLY K 170 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL K 167 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 221 through 224 removed outlier: 3.541A pdb=" N ALA K 227 " --> pdb=" O GLU K 224 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR M 239 " --> pdb=" O ILE K 228 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU K 230 " --> pdb=" O THR M 239 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 244 through 247 removed outlier: 6.230A pdb=" N PHE K 252 " --> pdb=" O THR M 260 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LYS M 262 " --> pdb=" O PHE K 252 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL K 254 " --> pdb=" O LYS M 262 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 21 through 29 removed outlier: 3.538A pdb=" N LEU M 40 " --> pdb=" O CYS M 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS M 86 " --> pdb=" O LEU M 40 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE M 118 " --> pdb=" O PRO M 85 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE M 107 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE M 26 " --> pdb=" O ILE M 107 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE M 109 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG M 22 " --> pdb=" O ARG M 111 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 136 through 140 removed outlier: 4.167A pdb=" N PHE M 157 " --> pdb=" O GLY M 170 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL M 167 " --> pdb=" O ILE M 185 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 59 through 60 1180 hydrogen bonds defined for protein. 3192 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: 7.26 Time building geometry restraints manager: 3.43 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: 10774 1.34 - 1.46: 6799 1.46 - 1.58: 15583 1.58 - 1.70: 0 1.70 - 1.81: 215 Bond restraints: 33371 Sorted by residual: bond pdb=" C TYR E 273 " pdb=" N PRO E 274 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.30e+00 bond pdb=" C TYR F 273 " pdb=" N PRO F 274 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.19e-02 7.06e+03 2.24e+00 bond pdb=" CB LYS D 82 " pdb=" CG LYS D 82 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CA GLY M 147 " pdb=" C GLY M 147 " ideal model delta sigma weight residual 1.511 1.527 -0.016 1.25e-02 6.40e+03 1.56e+00 bond pdb=" CB LYS E 82 " pdb=" CG LYS E 82 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.51e+00 ... (remaining 33366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 44581 2.07 - 4.14: 557 4.14 - 6.21: 84 6.21 - 8.28: 25 8.28 - 10.34: 3 Bond angle restraints: 45250 Sorted by residual: angle pdb=" C GLU C 120 " pdb=" CA GLU C 120 " pdb=" CB GLU C 120 " ideal model delta sigma weight residual 116.54 111.19 5.35 1.15e+00 7.56e-01 2.16e+01 angle pdb=" CA LYS D 82 " pdb=" CB LYS D 82 " pdb=" CG LYS D 82 " ideal model delta sigma weight residual 114.10 122.34 -8.24 2.00e+00 2.50e-01 1.70e+01 angle pdb=" CA LYS E 82 " pdb=" CB LYS E 82 " pdb=" CG LYS E 82 " ideal model delta sigma weight residual 114.10 121.95 -7.85 2.00e+00 2.50e-01 1.54e+01 angle pdb=" N ASP J 253 " pdb=" CA ASP J 253 " pdb=" C ASP J 253 " ideal model delta sigma weight residual 114.64 109.08 5.56 1.52e+00 4.33e-01 1.34e+01 angle pdb=" C PRO M 44 " pdb=" N ILE M 45 " pdb=" CA ILE M 45 " ideal model delta sigma weight residual 122.66 119.31 3.35 9.70e-01 1.06e+00 1.19e+01 ... (remaining 45245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 18046 17.72 - 35.45: 1658 35.45 - 53.17: 223 53.17 - 70.89: 36 70.89 - 88.62: 24 Dihedral angle restraints: 19987 sinusoidal: 7930 harmonic: 12057 Sorted by residual: dihedral pdb=" CA LYS B 221 " pdb=" C LYS B 221 " pdb=" N ASP B 222 " pdb=" CA ASP B 222 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LYS A 221 " pdb=" C LYS A 221 " pdb=" N ASP A 222 " pdb=" CA ASP A 222 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA LYS F 82 " pdb=" C LYS F 82 " pdb=" N GLY F 83 " pdb=" CA GLY F 83 " ideal model delta harmonic sigma weight residual 180.00 163.32 16.68 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 19984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3508 0.038 - 0.077: 1011 0.077 - 0.115: 481 0.115 - 0.153: 82 0.153 - 0.192: 5 Chirality restraints: 5087 Sorted by residual: chirality pdb=" CB ILE I 268 " pdb=" CA ILE I 268 " pdb=" CG1 ILE I 268 " pdb=" CG2 ILE I 268 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CB ILE M 194 " pdb=" CA ILE M 194 " pdb=" CG1 ILE M 194 " pdb=" CG2 ILE M 194 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CB VAL I 67 " pdb=" CA VAL I 67 " pdb=" CG1 VAL I 67 " pdb=" CG2 VAL I 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 5084 not shown) Planarity restraints: 5876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 40 " 0.054 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO C 41 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 40 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO B 41 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 40 " 0.052 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 41 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.042 5.00e-02 4.00e+02 ... (remaining 5873 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 13665 2.91 - 3.41: 30669 3.41 - 3.91: 49151 3.91 - 4.40: 52329 4.40 - 4.90: 89003 Nonbonded interactions: 234817 Sorted by model distance: nonbonded pdb=" O ILE G 38 " pdb=" OE1 GLU G 42 " model vdw 2.415 3.040 nonbonded pdb=" O ASN C 273 " pdb=" ND2 ASN C 273 " model vdw 2.458 3.120 nonbonded pdb=" N GLU M 61 " pdb=" OE1 GLU M 61 " model vdw 2.528 3.120 nonbonded pdb=" OD1 ASP K 68 " pdb=" N ALA K 69 " model vdw 2.540 3.120 nonbonded pdb=" N GLU B 83 " pdb=" OE1 GLU B 83 " model vdw 2.546 3.120 ... (remaining 234812 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 45 through 195 or resid 202 through 353)) selection = (chain 'E' and (resid 45 through 195 or resid 202 through 353)) selection = (chain 'F' and (resid 45 through 195 or resid 202 through 353)) selection = (chain 'G' and (resid 45 through 103 or resid 106 through 353)) selection = (chain 'J' and (resid 45 through 103 or resid 106 through 353)) selection = (chain 'L' and (resid 45 through 103 or resid 106 through 353)) } ncs_group { reference = (chain 'I' and (resid 18 through 147 or (resid 148 through 149 and (name N or na \ me CA or name C or name O )) or resid 150 through 293)) selection = (chain 'K' and (resid 18 through 147 or (resid 148 through 149 and (name N or na \ me CA or name C or name O )) or resid 150 through 293)) selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.870 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.003 0.040 33371 Z= 0.124 Angle : 0.609 10.344 45250 Z= 0.315 Chirality : 0.045 0.192 5087 Planarity : 0.004 0.083 5876 Dihedral : 13.451 88.618 12247 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.09 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 4090 helix: 1.12 (0.16), residues: 1102 sheet: -0.41 (0.20), residues: 723 loop : -2.17 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 177 TYR 0.023 0.001 TYR I 74 PHE 0.027 0.001 PHE C 179 TRP 0.020 0.001 TRP A 360 HIS 0.003 0.001 HIS M 267 Details of bonding type rmsd covalent geometry : bond 0.00263 (33371) covalent geometry : angle 0.60860 (45250) hydrogen bonds : bond 0.20807 ( 1123) hydrogen bonds : angle 7.09773 ( 3192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 TYR cc_start: 0.8219 (m-10) cc_final: 0.7868 (m-10) REVERT: B 222 ASP cc_start: 0.8281 (p0) cc_final: 0.8046 (p0) REVERT: B 302 ASP cc_start: 0.8695 (t0) cc_final: 0.8463 (t0) REVERT: B 335 MET cc_start: 0.9034 (mmm) cc_final: 0.8271 (tpp) REVERT: A 82 ASP cc_start: 0.8843 (m-30) cc_final: 0.7798 (t70) REVERT: A 160 MET cc_start: 0.8618 (pmm) cc_final: 0.8294 (pmm) REVERT: A 195 VAL cc_start: 0.9315 (m) cc_final: 0.8946 (p) REVERT: A 207 GLU cc_start: 0.8584 (tt0) cc_final: 0.8157 (tm-30) REVERT: A 308 MET cc_start: 0.8455 (ttm) cc_final: 0.8139 (ttm) REVERT: A 335 MET cc_start: 0.8807 (ptp) cc_final: 0.8496 (ptp) REVERT: C 58 TYR cc_start: 0.8581 (t80) cc_final: 0.8365 (t80) REVERT: C 138 MET cc_start: 0.9241 (mmt) cc_final: 0.8955 (mmm) REVERT: C 302 ASP cc_start: 0.8573 (t70) cc_final: 0.8162 (t0) REVERT: C 310 ASP cc_start: 0.8496 (t0) cc_final: 0.8202 (t0) REVERT: G 49 LEU cc_start: 0.9580 (tp) cc_final: 0.9300 (tp) REVERT: G 54 LYS cc_start: 0.8792 (mttt) cc_final: 0.8368 (mttm) REVERT: G 72 ASP cc_start: 0.8716 (t0) cc_final: 0.8432 (t70) REVERT: G 142 MET cc_start: 0.8800 (tpp) cc_final: 0.8339 (tpp) REVERT: G 328 MET cc_start: 0.9158 (tpp) cc_final: 0.8749 (tpp) REVERT: D 96 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8122 (mt-10) REVERT: D 142 MET cc_start: 0.8754 (ttt) cc_final: 0.8362 (ttm) REVERT: D 150 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8174 (tm-30) REVERT: D 185 ASP cc_start: 0.8953 (t70) cc_final: 0.8411 (t0) REVERT: J 119 MET cc_start: 0.8846 (mmm) cc_final: 0.8485 (mmm) REVERT: J 328 MET cc_start: 0.9046 (tpp) cc_final: 0.8678 (tpp) REVERT: J 346 MET cc_start: 0.8868 (tpp) cc_final: 0.8239 (ttp) REVERT: E 69 ASN cc_start: 0.9084 (t0) cc_final: 0.8843 (t0) REVERT: L 54 LYS cc_start: 0.9000 (mttt) cc_final: 0.8730 (mttp) REVERT: L 312 ASP cc_start: 0.8508 (p0) cc_final: 0.8196 (p0) REVERT: L 328 MET cc_start: 0.9031 (tpp) cc_final: 0.8444 (tpp) REVERT: F 132 VAL cc_start: 0.9137 (t) cc_final: 0.8853 (m) REVERT: F 152 MET cc_start: 0.6988 (mmm) cc_final: 0.5880 (mmm) REVERT: I 31 GLU cc_start: 0.8500 (pp20) cc_final: 0.8170 (pp20) REVERT: I 74 TYR cc_start: 0.7343 (p90) cc_final: 0.7065 (p90) REVERT: I 269 GLN cc_start: 0.8951 (pt0) cc_final: 0.8582 (pp30) REVERT: I 275 MET cc_start: 0.8166 (tmm) cc_final: 0.7415 (tmm) REVERT: I 284 LEU cc_start: 0.8890 (mt) cc_final: 0.8612 (tp) REVERT: K 41 MET cc_start: 0.9048 (mmp) cc_final: 0.8671 (mmm) REVERT: K 158 MET cc_start: 0.8866 (ttt) cc_final: 0.8569 (ttt) REVERT: K 284 LEU cc_start: 0.8989 (mt) cc_final: 0.8641 (tp) REVERT: M 129 LEU cc_start: 0.8518 (tp) cc_final: 0.8125 (tp) REVERT: M 214 MET cc_start: 0.8732 (tpt) cc_final: 0.8276 (tpt) REVERT: M 246 GLU cc_start: 0.7303 (tt0) cc_final: 0.7101 (tt0) REVERT: M 275 MET cc_start: 0.7622 (ttp) cc_final: 0.7132 (tmm) REVERT: M 284 LEU cc_start: 0.8929 (mt) cc_final: 0.8305 (tp) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.1831 time to fit residues: 129.1081 Evaluate side-chains 352 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.0170 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 overall best weight: 4.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN ** M 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.070099 restraints weight = 114017.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071788 restraints weight = 59488.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.072940 restraints weight = 36493.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.073730 restraints weight = 24717.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.074293 restraints weight = 18051.635| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33371 Z= 0.132 Angle : 0.554 9.503 45250 Z= 0.287 Chirality : 0.045 0.162 5087 Planarity : 0.004 0.065 5876 Dihedral : 4.441 58.343 4519 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.58 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 4090 helix: 1.17 (0.16), residues: 1149 sheet: -0.46 (0.20), residues: 690 loop : -2.16 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 215 TYR 0.010 0.001 TYR C 46 PHE 0.016 0.001 PHE C 47 TRP 0.011 0.001 TRP E 181 HIS 0.002 0.000 HIS M 267 Details of bonding type rmsd covalent geometry : bond 0.00295 (33371) covalent geometry : angle 0.55379 (45250) hydrogen bonds : bond 0.04716 ( 1123) hydrogen bonds : angle 5.31140 ( 3192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 TYR cc_start: 0.8612 (p90) cc_final: 0.8393 (p90) REVERT: B 222 ASP cc_start: 0.8339 (p0) cc_final: 0.8081 (p0) REVERT: B 302 ASP cc_start: 0.8625 (t0) cc_final: 0.8311 (t0) REVERT: B 335 MET cc_start: 0.9068 (mmm) cc_final: 0.8389 (tpp) REVERT: A 82 ASP cc_start: 0.8687 (m-30) cc_final: 0.8003 (t0) REVERT: A 160 MET cc_start: 0.8449 (pmm) cc_final: 0.8168 (pmm) REVERT: A 207 GLU cc_start: 0.8574 (tt0) cc_final: 0.8100 (tm-30) REVERT: C 58 TYR cc_start: 0.8831 (t80) cc_final: 0.8379 (t80) REVERT: C 302 ASP cc_start: 0.8689 (t70) cc_final: 0.8162 (t0) REVERT: C 310 ASP cc_start: 0.8502 (t0) cc_final: 0.8269 (t0) REVERT: G 49 LEU cc_start: 0.9576 (tp) cc_final: 0.9258 (tp) REVERT: G 54 LYS cc_start: 0.8816 (mttt) cc_final: 0.8400 (mttm) REVERT: G 72 ASP cc_start: 0.8715 (t0) cc_final: 0.8393 (t70) REVERT: G 328 MET cc_start: 0.9176 (tpp) cc_final: 0.8830 (tpp) REVERT: D 96 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8032 (mt-10) REVERT: D 142 MET cc_start: 0.8654 (ttt) cc_final: 0.8283 (ttm) REVERT: D 185 ASP cc_start: 0.8920 (t70) cc_final: 0.8393 (t0) REVERT: D 222 THR cc_start: 0.9082 (m) cc_final: 0.8798 (t) REVERT: J 119 MET cc_start: 0.8774 (mmm) cc_final: 0.8391 (mmm) REVERT: J 328 MET cc_start: 0.9220 (tpp) cc_final: 0.8792 (tpp) REVERT: E 69 ASN cc_start: 0.8952 (t0) cc_final: 0.8639 (t0) REVERT: E 152 MET cc_start: 0.7945 (mmm) cc_final: 0.7632 (mmm) REVERT: L 54 LYS cc_start: 0.8940 (mttt) cc_final: 0.8624 (mttp) REVERT: L 72 ASP cc_start: 0.8316 (t70) cc_final: 0.8048 (t70) REVERT: L 328 MET cc_start: 0.9154 (tpp) cc_final: 0.8568 (tpp) REVERT: I 31 GLU cc_start: 0.8559 (pp20) cc_final: 0.8153 (pp20) REVERT: I 74 TYR cc_start: 0.7373 (p90) cc_final: 0.7160 (p90) REVERT: I 166 HIS cc_start: 0.8212 (p90) cc_final: 0.7616 (p90) REVERT: I 268 ILE cc_start: 0.9121 (mt) cc_final: 0.8854 (tt) REVERT: I 269 GLN cc_start: 0.8983 (pt0) cc_final: 0.8646 (pp30) REVERT: I 284 LEU cc_start: 0.8924 (mt) cc_final: 0.8579 (tp) REVERT: K 102 MET cc_start: 0.7628 (mtp) cc_final: 0.7255 (mtp) REVERT: K 158 MET cc_start: 0.8708 (ttt) cc_final: 0.8312 (ttt) REVERT: K 275 MET cc_start: 0.8312 (ppp) cc_final: 0.8063 (ppp) REVERT: K 284 LEU cc_start: 0.8796 (mt) cc_final: 0.8417 (tp) REVERT: M 129 LEU cc_start: 0.8652 (tp) cc_final: 0.8261 (tp) REVERT: M 166 HIS cc_start: 0.7735 (p90) cc_final: 0.7148 (p90) REVERT: M 275 MET cc_start: 0.7544 (ttp) cc_final: 0.7098 (tmm) REVERT: M 284 LEU cc_start: 0.8755 (mt) cc_final: 0.8087 (tp) REVERT: H 71 MET cc_start: 0.7688 (mmp) cc_final: 0.7307 (mmm) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.1776 time to fit residues: 130.0813 Evaluate side-chains 366 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 409 optimal weight: 50.0000 chunk 62 optimal weight: 30.0000 chunk 303 optimal weight: 20.0000 chunk 399 optimal weight: 30.0000 chunk 355 optimal weight: 7.9990 chunk 363 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 78 GLN D 241 HIS ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 HIS ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.068020 restraints weight = 115342.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.069665 restraints weight = 60723.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070794 restraints weight = 37544.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.071566 restraints weight = 25651.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072090 restraints weight = 18836.343| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33371 Z= 0.198 Angle : 0.606 12.088 45250 Z= 0.312 Chirality : 0.046 0.150 5087 Planarity : 0.004 0.075 5876 Dihedral : 4.697 61.071 4519 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.17 % Favored : 89.73 % Rotamer: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 4090 helix: 1.14 (0.16), residues: 1131 sheet: -0.34 (0.20), residues: 708 loop : -2.25 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 215 TYR 0.015 0.001 TYR A 416 PHE 0.015 0.001 PHE A 47 TRP 0.012 0.001 TRP E 181 HIS 0.004 0.001 HIS K 166 Details of bonding type rmsd covalent geometry : bond 0.00455 (33371) covalent geometry : angle 0.60551 (45250) hydrogen bonds : bond 0.04515 ( 1123) hydrogen bonds : angle 5.06596 ( 3192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 435 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 TYR cc_start: 0.8708 (p90) cc_final: 0.8467 (p90) REVERT: B 302 ASP cc_start: 0.8727 (t0) cc_final: 0.8392 (t0) REVERT: A 82 ASP cc_start: 0.8778 (m-30) cc_final: 0.8091 (t0) REVERT: A 160 MET cc_start: 0.8339 (pmm) cc_final: 0.8060 (pmm) REVERT: A 195 VAL cc_start: 0.9391 (m) cc_final: 0.9015 (p) REVERT: A 207 GLU cc_start: 0.8415 (tt0) cc_final: 0.8120 (tm-30) REVERT: A 380 GLN cc_start: 0.8694 (mt0) cc_final: 0.8454 (mt0) REVERT: C 82 ASP cc_start: 0.9052 (m-30) cc_final: 0.7995 (t70) REVERT: C 310 ASP cc_start: 0.8470 (t0) cc_final: 0.8206 (t0) REVERT: C 311 ASN cc_start: 0.9172 (m110) cc_final: 0.8687 (m110) REVERT: C 380 GLN cc_start: 0.8864 (mt0) cc_final: 0.8596 (mt0) REVERT: G 54 LYS cc_start: 0.8917 (mttt) cc_final: 0.8478 (mttm) REVERT: G 328 MET cc_start: 0.9262 (tpp) cc_final: 0.8873 (tpp) REVERT: D 96 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8168 (mt-10) REVERT: D 142 MET cc_start: 0.8674 (ttt) cc_final: 0.8295 (ttm) REVERT: D 185 ASP cc_start: 0.8872 (t70) cc_final: 0.8303 (t0) REVERT: J 119 MET cc_start: 0.8848 (mmm) cc_final: 0.8476 (mmm) REVERT: J 328 MET cc_start: 0.9285 (tpp) cc_final: 0.8854 (tpp) REVERT: E 69 ASN cc_start: 0.8968 (t0) cc_final: 0.8641 (t0) REVERT: E 152 MET cc_start: 0.8398 (mmm) cc_final: 0.7605 (mmm) REVERT: L 54 LYS cc_start: 0.8978 (mttt) cc_final: 0.8599 (mttp) REVERT: L 72 ASP cc_start: 0.8447 (t70) cc_final: 0.8220 (t70) REVERT: L 171 LEU cc_start: 0.9460 (mt) cc_final: 0.9206 (mm) REVERT: L 328 MET cc_start: 0.9169 (tpp) cc_final: 0.8610 (tpp) REVERT: F 122 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8177 (tp30) REVERT: I 31 GLU cc_start: 0.8483 (pp20) cc_final: 0.7806 (pp20) REVERT: I 41 MET cc_start: 0.8883 (mmp) cc_final: 0.8620 (mmp) REVERT: I 79 SER cc_start: 0.9305 (m) cc_final: 0.8873 (p) REVERT: I 269 GLN cc_start: 0.8909 (pt0) cc_final: 0.8519 (pp30) REVERT: I 275 MET cc_start: 0.7894 (tmm) cc_final: 0.7404 (tmm) REVERT: I 284 LEU cc_start: 0.8938 (mt) cc_final: 0.8556 (tp) REVERT: K 31 GLU cc_start: 0.9130 (pm20) cc_final: 0.8712 (pm20) REVERT: K 275 MET cc_start: 0.7892 (ppp) cc_final: 0.7643 (ppp) REVERT: K 284 LEU cc_start: 0.8889 (mt) cc_final: 0.8494 (tp) REVERT: M 165 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8079 (mtmt) REVERT: M 253 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8715 (mppt) REVERT: M 275 MET cc_start: 0.7494 (ttp) cc_final: 0.7044 (tmm) REVERT: M 284 LEU cc_start: 0.8801 (mt) cc_final: 0.8103 (tp) REVERT: H 71 MET cc_start: 0.7783 (mmp) cc_final: 0.7261 (mmm) outliers start: 1 outliers final: 0 residues processed: 436 average time/residue: 0.1820 time to fit residues: 131.7281 Evaluate side-chains 353 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 191 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 319 optimal weight: 50.0000 chunk 316 optimal weight: 8.9990 chunk 373 optimal weight: 30.0000 chunk 260 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 400 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 overall best weight: 5.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.076832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.069322 restraints weight = 113621.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.070991 restraints weight = 59152.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072131 restraints weight = 36288.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072911 restraints weight = 24579.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073452 restraints weight = 17929.232| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33371 Z= 0.160 Angle : 0.577 11.151 45250 Z= 0.297 Chirality : 0.045 0.190 5087 Planarity : 0.004 0.075 5876 Dihedral : 4.671 61.050 4519 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.00 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4090 helix: 1.19 (0.16), residues: 1128 sheet: -0.29 (0.20), residues: 702 loop : -2.24 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 237 TYR 0.019 0.001 TYR A 416 PHE 0.015 0.001 PHE A 179 TRP 0.031 0.001 TRP A 360 HIS 0.006 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00367 (33371) covalent geometry : angle 0.57716 (45250) hydrogen bonds : bond 0.03923 ( 1123) hydrogen bonds : angle 4.88534 ( 3192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 TYR cc_start: 0.8387 (m-10) cc_final: 0.8070 (m-10) REVERT: B 28 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 46 TYR cc_start: 0.8680 (p90) cc_final: 0.8396 (p90) REVERT: B 207 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7299 (tm-30) REVERT: B 222 ASP cc_start: 0.8414 (p0) cc_final: 0.8136 (p0) REVERT: B 302 ASP cc_start: 0.8693 (t0) cc_final: 0.8362 (t0) REVERT: B 416 TYR cc_start: 0.8611 (m-80) cc_final: 0.8381 (m-80) REVERT: A 25 TYR cc_start: 0.8423 (m-80) cc_final: 0.8126 (m-10) REVERT: A 82 ASP cc_start: 0.8699 (m-30) cc_final: 0.8027 (t0) REVERT: A 160 MET cc_start: 0.8320 (pmm) cc_final: 0.8054 (pmm) REVERT: A 195 VAL cc_start: 0.9353 (m) cc_final: 0.8995 (p) REVERT: A 207 GLU cc_start: 0.8373 (tt0) cc_final: 0.8124 (tm-30) REVERT: C 82 ASP cc_start: 0.8995 (m-30) cc_final: 0.7942 (t70) REVERT: C 310 ASP cc_start: 0.8394 (t0) cc_final: 0.8155 (t0) REVERT: C 311 ASN cc_start: 0.9392 (m110) cc_final: 0.9087 (m110) REVERT: G 32 ASN cc_start: 0.8590 (m-40) cc_final: 0.7531 (p0) REVERT: G 54 LYS cc_start: 0.8877 (mttt) cc_final: 0.8424 (mttm) REVERT: G 328 MET cc_start: 0.9235 (tpp) cc_final: 0.8893 (tpp) REVERT: D 96 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8077 (mt-10) REVERT: D 142 MET cc_start: 0.8629 (ttt) cc_final: 0.8220 (ttm) REVERT: D 185 ASP cc_start: 0.8886 (t70) cc_final: 0.8317 (t0) REVERT: D 349 MET cc_start: 0.7928 (ttt) cc_final: 0.7571 (ttt) REVERT: J 119 MET cc_start: 0.8809 (mmm) cc_final: 0.8442 (mmm) REVERT: J 328 MET cc_start: 0.9246 (tpp) cc_final: 0.8842 (tpp) REVERT: J 344 ARG cc_start: 0.9202 (tpp80) cc_final: 0.8880 (tpt170) REVERT: E 69 ASN cc_start: 0.8936 (t0) cc_final: 0.8640 (t0) REVERT: E 152 MET cc_start: 0.8416 (mmm) cc_final: 0.7389 (mmm) REVERT: L 54 LYS cc_start: 0.8973 (mttt) cc_final: 0.8599 (mttp) REVERT: L 72 ASP cc_start: 0.8455 (t70) cc_final: 0.8197 (t70) REVERT: L 171 LEU cc_start: 0.9460 (mt) cc_final: 0.9201 (mm) REVERT: L 312 ASP cc_start: 0.8605 (p0) cc_final: 0.8357 (p0) REVERT: L 328 MET cc_start: 0.9145 (tpp) cc_final: 0.8604 (tpp) REVERT: F 122 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7900 (tp30) REVERT: I 31 GLU cc_start: 0.8474 (pp20) cc_final: 0.7854 (pp20) REVERT: I 79 SER cc_start: 0.9317 (m) cc_final: 0.8896 (p) REVERT: I 180 ARG cc_start: 0.9022 (mtm180) cc_final: 0.8723 (mtm110) REVERT: I 246 GLU cc_start: 0.7480 (tt0) cc_final: 0.7239 (tt0) REVERT: I 269 GLN cc_start: 0.8836 (pt0) cc_final: 0.8461 (pp30) REVERT: I 275 MET cc_start: 0.7860 (tmm) cc_final: 0.7219 (tmm) REVERT: I 284 LEU cc_start: 0.8930 (mt) cc_final: 0.8568 (tp) REVERT: K 102 MET cc_start: 0.7793 (mtp) cc_final: 0.7497 (mtp) REVERT: K 284 LEU cc_start: 0.8874 (mt) cc_final: 0.8422 (tp) REVERT: M 165 LYS cc_start: 0.8294 (mtmt) cc_final: 0.8041 (mtmt) REVERT: M 166 HIS cc_start: 0.8018 (p90) cc_final: 0.7814 (p90) REVERT: M 275 MET cc_start: 0.7581 (ttp) cc_final: 0.7165 (tmm) REVERT: M 284 LEU cc_start: 0.8762 (mt) cc_final: 0.8104 (tp) REVERT: H 71 MET cc_start: 0.7772 (mmp) cc_final: 0.7252 (mmm) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1809 time to fit residues: 133.1976 Evaluate side-chains 356 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 288 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 0.0670 chunk 276 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 chunk 266 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 380 GLN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.077382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.069815 restraints weight = 113575.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.071506 restraints weight = 59216.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.072641 restraints weight = 36246.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.073422 restraints weight = 24667.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.073977 restraints weight = 17966.007| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33371 Z= 0.137 Angle : 0.568 10.727 45250 Z= 0.290 Chirality : 0.045 0.145 5087 Planarity : 0.004 0.074 5876 Dihedral : 4.587 60.488 4519 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.22 % Favored : 90.73 % Rotamer: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.13), residues: 4090 helix: 1.25 (0.16), residues: 1128 sheet: -0.26 (0.20), residues: 708 loop : -2.23 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 215 TYR 0.013 0.001 TYR C 416 PHE 0.017 0.001 PHE B 179 TRP 0.023 0.001 TRP A 360 HIS 0.002 0.001 HIS K 163 Details of bonding type rmsd covalent geometry : bond 0.00315 (33371) covalent geometry : angle 0.56820 (45250) hydrogen bonds : bond 0.03660 ( 1123) hydrogen bonds : angle 4.74389 ( 3192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 ASP cc_start: 0.8370 (p0) cc_final: 0.8101 (p0) REVERT: B 302 ASP cc_start: 0.8697 (t0) cc_final: 0.8374 (t0) REVERT: A 25 TYR cc_start: 0.8466 (m-80) cc_final: 0.8246 (m-80) REVERT: A 82 ASP cc_start: 0.8692 (m-30) cc_final: 0.8011 (t0) REVERT: A 160 MET cc_start: 0.8341 (pmm) cc_final: 0.8054 (pmm) REVERT: A 195 VAL cc_start: 0.9344 (m) cc_final: 0.9002 (p) REVERT: A 207 GLU cc_start: 0.8323 (tt0) cc_final: 0.8046 (tm-30) REVERT: C 82 ASP cc_start: 0.8985 (m-30) cc_final: 0.7971 (t70) REVERT: C 105 LYS cc_start: 0.8209 (mttp) cc_final: 0.7497 (tptt) REVERT: C 310 ASP cc_start: 0.8395 (t0) cc_final: 0.8173 (t0) REVERT: C 311 ASN cc_start: 0.9391 (m110) cc_final: 0.9078 (m110) REVERT: C 413 LYS cc_start: 0.6679 (mptt) cc_final: 0.6430 (mptt) REVERT: G 32 ASN cc_start: 0.7854 (m-40) cc_final: 0.7649 (p0) REVERT: G 54 LYS cc_start: 0.8932 (mttt) cc_final: 0.8475 (mttm) REVERT: G 142 MET cc_start: 0.8972 (tpp) cc_final: 0.8699 (tpp) REVERT: G 328 MET cc_start: 0.9233 (tpp) cc_final: 0.8901 (tpp) REVERT: D 96 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8158 (mt-10) REVERT: D 142 MET cc_start: 0.8625 (ttt) cc_final: 0.8216 (ttm) REVERT: D 185 ASP cc_start: 0.8888 (t70) cc_final: 0.8324 (t0) REVERT: J 54 LYS cc_start: 0.9096 (mttp) cc_final: 0.8848 (mtpt) REVERT: J 119 MET cc_start: 0.8797 (mmm) cc_final: 0.8427 (mmm) REVERT: J 312 ASP cc_start: 0.8358 (p0) cc_final: 0.8145 (p0) REVERT: J 328 MET cc_start: 0.9236 (tpp) cc_final: 0.8840 (tpp) REVERT: J 344 ARG cc_start: 0.9235 (tpp80) cc_final: 0.8939 (tpt170) REVERT: E 69 ASN cc_start: 0.8878 (t0) cc_final: 0.8581 (t0) REVERT: E 150 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7771 (tm-30) REVERT: E 152 MET cc_start: 0.8399 (mmm) cc_final: 0.7270 (mmm) REVERT: L 54 LYS cc_start: 0.8965 (mttt) cc_final: 0.8588 (mttp) REVERT: L 72 ASP cc_start: 0.8423 (t70) cc_final: 0.8157 (t70) REVERT: L 171 LEU cc_start: 0.9449 (mt) cc_final: 0.9178 (mm) REVERT: L 312 ASP cc_start: 0.8585 (p0) cc_final: 0.8333 (p0) REVERT: L 328 MET cc_start: 0.9130 (tpp) cc_final: 0.8610 (tpp) REVERT: F 122 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8090 (mm-30) REVERT: I 31 GLU cc_start: 0.8491 (pp20) cc_final: 0.7891 (pp20) REVERT: I 41 MET cc_start: 0.8783 (mmp) cc_final: 0.8402 (mmp) REVERT: I 246 GLU cc_start: 0.7426 (tt0) cc_final: 0.7217 (tt0) REVERT: I 269 GLN cc_start: 0.8827 (pt0) cc_final: 0.8454 (pp30) REVERT: I 275 MET cc_start: 0.7937 (tmm) cc_final: 0.7275 (tmm) REVERT: I 284 LEU cc_start: 0.8859 (mt) cc_final: 0.8525 (tp) REVERT: K 31 GLU cc_start: 0.8789 (pm20) cc_final: 0.8585 (pm20) REVERT: K 41 MET cc_start: 0.9122 (mmp) cc_final: 0.8842 (mmm) REVERT: K 46 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8464 (tm-30) REVERT: K 102 MET cc_start: 0.7813 (mtp) cc_final: 0.7444 (mtp) REVERT: K 284 LEU cc_start: 0.8760 (mt) cc_final: 0.8324 (tp) REVERT: M 165 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8035 (mtmt) REVERT: M 166 HIS cc_start: 0.8006 (p90) cc_final: 0.7779 (p90) REVERT: M 253 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8193 (mppt) REVERT: M 275 MET cc_start: 0.7583 (ttp) cc_final: 0.7136 (tmm) REVERT: M 284 LEU cc_start: 0.8881 (mt) cc_final: 0.8225 (tp) REVERT: H 71 MET cc_start: 0.7816 (mmp) cc_final: 0.7270 (mmm) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.1869 time to fit residues: 140.1142 Evaluate side-chains 365 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 99 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 401 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 316 optimal weight: 9.9990 chunk 256 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.077860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070319 restraints weight = 112808.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072008 restraints weight = 58738.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073153 restraints weight = 35978.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.073917 restraints weight = 24352.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.074496 restraints weight = 17840.693| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33371 Z= 0.126 Angle : 0.560 10.618 45250 Z= 0.285 Chirality : 0.045 0.174 5087 Planarity : 0.004 0.076 5876 Dihedral : 4.530 60.396 4519 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.00 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 4090 helix: 1.30 (0.16), residues: 1128 sheet: -0.24 (0.21), residues: 669 loop : -2.19 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 215 TYR 0.018 0.001 TYR B 416 PHE 0.028 0.001 PHE C 179 TRP 0.018 0.001 TRP A 360 HIS 0.006 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00288 (33371) covalent geometry : angle 0.56043 (45250) hydrogen bonds : bond 0.03500 ( 1123) hydrogen bonds : angle 4.63418 ( 3192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8952 (mmt) cc_final: 0.8518 (mmm) REVERT: A 25 TYR cc_start: 0.8525 (m-80) cc_final: 0.8322 (m-80) REVERT: A 82 ASP cc_start: 0.8643 (m-30) cc_final: 0.7893 (t0) REVERT: A 160 MET cc_start: 0.8379 (pmm) cc_final: 0.8106 (pmm) REVERT: A 195 VAL cc_start: 0.9375 (m) cc_final: 0.9028 (p) REVERT: A 207 GLU cc_start: 0.8367 (tt0) cc_final: 0.8041 (tm-30) REVERT: A 380 GLN cc_start: 0.8709 (mt0) cc_final: 0.8461 (mt0) REVERT: C 58 TYR cc_start: 0.8854 (t80) cc_final: 0.8333 (t80) REVERT: C 82 ASP cc_start: 0.8984 (m-30) cc_final: 0.7889 (t70) REVERT: C 105 LYS cc_start: 0.8236 (mttp) cc_final: 0.7467 (tptt) REVERT: C 251 TYR cc_start: 0.8679 (p90) cc_final: 0.8298 (p90) REVERT: C 310 ASP cc_start: 0.8411 (t0) cc_final: 0.8194 (t0) REVERT: C 311 ASN cc_start: 0.9399 (m110) cc_final: 0.9041 (m110) REVERT: C 413 LYS cc_start: 0.6755 (mptt) cc_final: 0.6497 (mptt) REVERT: G 54 LYS cc_start: 0.8909 (mttt) cc_final: 0.8454 (mttm) REVERT: G 167 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8682 (mm-30) REVERT: D 78 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8390 (tp-100) REVERT: D 96 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8098 (mt-10) REVERT: D 142 MET cc_start: 0.8641 (ttt) cc_final: 0.8251 (ttm) REVERT: D 185 ASP cc_start: 0.8920 (t70) cc_final: 0.8358 (t0) REVERT: D 349 MET cc_start: 0.7920 (ttt) cc_final: 0.7543 (ttt) REVERT: J 54 LYS cc_start: 0.9006 (mttp) cc_final: 0.8716 (mtpt) REVERT: J 119 MET cc_start: 0.8837 (mmm) cc_final: 0.8470 (mmm) REVERT: J 312 ASP cc_start: 0.8343 (p0) cc_final: 0.8040 (p0) REVERT: J 328 MET cc_start: 0.9270 (tpp) cc_final: 0.8864 (tpp) REVERT: J 344 ARG cc_start: 0.9234 (tpp80) cc_final: 0.8929 (tpt170) REVERT: E 69 ASN cc_start: 0.8911 (t0) cc_final: 0.8541 (t0) REVERT: E 150 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7806 (tm-30) REVERT: E 152 MET cc_start: 0.8347 (mmm) cc_final: 0.7246 (mmm) REVERT: L 54 LYS cc_start: 0.8916 (mttt) cc_final: 0.8555 (mttp) REVERT: L 171 LEU cc_start: 0.9444 (mt) cc_final: 0.9162 (mm) REVERT: L 312 ASP cc_start: 0.8619 (p0) cc_final: 0.8381 (p0) REVERT: L 328 MET cc_start: 0.9157 (tpp) cc_final: 0.8624 (tpp) REVERT: F 122 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7783 (tp30) REVERT: I 31 GLU cc_start: 0.8544 (pp20) cc_final: 0.7939 (pp20) REVERT: I 79 SER cc_start: 0.9316 (m) cc_final: 0.8946 (p) REVERT: I 246 GLU cc_start: 0.7483 (tt0) cc_final: 0.7247 (tt0) REVERT: I 269 GLN cc_start: 0.8897 (pt0) cc_final: 0.8426 (pp30) REVERT: I 275 MET cc_start: 0.7883 (tmm) cc_final: 0.7207 (tmm) REVERT: I 284 LEU cc_start: 0.8790 (mt) cc_final: 0.8489 (tp) REVERT: K 46 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8460 (tm-30) REVERT: K 284 LEU cc_start: 0.8727 (mt) cc_final: 0.8279 (tp) REVERT: M 102 MET cc_start: 0.7780 (mtp) cc_final: 0.7555 (mtp) REVERT: M 165 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7969 (mtmt) REVERT: M 253 LYS cc_start: 0.8542 (mtmm) cc_final: 0.7994 (mppt) REVERT: M 275 MET cc_start: 0.7525 (ttp) cc_final: 0.7148 (tmm) REVERT: M 284 LEU cc_start: 0.8842 (mt) cc_final: 0.8202 (tp) REVERT: H 71 MET cc_start: 0.7768 (mmp) cc_final: 0.7337 (mmm) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.1787 time to fit residues: 137.3927 Evaluate side-chains 371 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 151 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 chunk 397 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 351 optimal weight: 6.9990 chunk 347 optimal weight: 30.0000 chunk 161 optimal weight: 0.0050 overall best weight: 6.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN G 69 ASN D 241 HIS ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 HIS ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.076817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.069267 restraints weight = 113951.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.070947 restraints weight = 59394.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072094 restraints weight = 36409.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.072857 restraints weight = 24655.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.073407 restraints weight = 17993.521| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33371 Z= 0.178 Angle : 0.604 12.244 45250 Z= 0.307 Chirality : 0.046 0.213 5087 Planarity : 0.004 0.082 5876 Dihedral : 4.659 61.726 4519 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.88 % Favored : 90.07 % Rotamer: Outliers : 0.03 % Allowed : 1.51 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.13), residues: 4090 helix: 1.24 (0.16), residues: 1122 sheet: -0.25 (0.21), residues: 660 loop : -2.19 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 215 TYR 0.016 0.001 TYR C 46 PHE 0.030 0.001 PHE A 167 TRP 0.043 0.001 TRP A 360 HIS 0.004 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00412 (33371) covalent geometry : angle 0.60440 (45250) hydrogen bonds : bond 0.03927 ( 1123) hydrogen bonds : angle 4.74064 ( 3192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 433 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 TYR cc_start: 0.8215 (p90) cc_final: 0.7524 (p90) REVERT: B 200 MET cc_start: 0.8456 (ppp) cc_final: 0.8225 (ppp) REVERT: B 222 ASP cc_start: 0.8465 (p0) cc_final: 0.8182 (p0) REVERT: A 82 ASP cc_start: 0.8627 (m-30) cc_final: 0.7909 (t0) REVERT: A 160 MET cc_start: 0.8372 (pmm) cc_final: 0.8114 (pmm) REVERT: A 195 VAL cc_start: 0.9397 (m) cc_final: 0.9061 (p) REVERT: A 207 GLU cc_start: 0.8340 (tt0) cc_final: 0.8069 (tm-30) REVERT: A 380 GLN cc_start: 0.8701 (mt0) cc_final: 0.8403 (mt0) REVERT: A 416 TYR cc_start: 0.8832 (m-80) cc_final: 0.8311 (m-80) REVERT: C 58 TYR cc_start: 0.8808 (t80) cc_final: 0.8290 (t80) REVERT: C 82 ASP cc_start: 0.8968 (m-30) cc_final: 0.7905 (t70) REVERT: C 105 LYS cc_start: 0.8240 (mttp) cc_final: 0.7498 (tptt) REVERT: C 413 LYS cc_start: 0.6579 (mptt) cc_final: 0.6286 (mptt) REVERT: G 54 LYS cc_start: 0.8963 (mttt) cc_final: 0.8533 (mttm) REVERT: G 72 ASP cc_start: 0.8840 (t0) cc_final: 0.8513 (t70) REVERT: G 142 MET cc_start: 0.9001 (tpp) cc_final: 0.8745 (tpp) REVERT: D 96 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8084 (mt-10) REVERT: D 142 MET cc_start: 0.8618 (ttt) cc_final: 0.8214 (ttm) REVERT: D 185 ASP cc_start: 0.8884 (t70) cc_final: 0.8311 (t0) REVERT: D 349 MET cc_start: 0.7969 (ttt) cc_final: 0.7613 (ttt) REVERT: J 54 LYS cc_start: 0.9073 (mttp) cc_final: 0.8755 (mtpt) REVERT: J 119 MET cc_start: 0.8781 (mmm) cc_final: 0.8430 (mmm) REVERT: J 344 ARG cc_start: 0.9178 (tpp80) cc_final: 0.8901 (tpt170) REVERT: E 69 ASN cc_start: 0.8842 (t0) cc_final: 0.8554 (t0) REVERT: E 150 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7790 (tm-30) REVERT: L 54 LYS cc_start: 0.8981 (mttt) cc_final: 0.8602 (mttp) REVERT: L 171 LEU cc_start: 0.9456 (mt) cc_final: 0.9180 (mm) REVERT: L 312 ASP cc_start: 0.8662 (p0) cc_final: 0.8421 (p0) REVERT: L 328 MET cc_start: 0.9181 (tpp) cc_final: 0.8624 (tpp) REVERT: L 346 MET cc_start: 0.8507 (tmm) cc_final: 0.8265 (tmm) REVERT: F 122 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7775 (tp30) REVERT: I 31 GLU cc_start: 0.8544 (pp20) cc_final: 0.7985 (pp20) REVERT: I 41 MET cc_start: 0.8750 (mmp) cc_final: 0.8354 (mmp) REVERT: I 79 SER cc_start: 0.9405 (m) cc_final: 0.8940 (p) REVERT: I 246 GLU cc_start: 0.7468 (tt0) cc_final: 0.7264 (tt0) REVERT: I 269 GLN cc_start: 0.8847 (pt0) cc_final: 0.8410 (pp30) REVERT: I 275 MET cc_start: 0.7911 (tmm) cc_final: 0.7610 (tmm) REVERT: I 284 LEU cc_start: 0.8998 (mt) cc_final: 0.8563 (tp) REVERT: K 41 MET cc_start: 0.8947 (mmp) cc_final: 0.8582 (mmm) REVERT: K 46 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8505 (tm-30) REVERT: K 284 LEU cc_start: 0.8955 (mt) cc_final: 0.8495 (tp) REVERT: M 102 MET cc_start: 0.7855 (mtp) cc_final: 0.7642 (mtp) REVERT: M 165 LYS cc_start: 0.8260 (mtmt) cc_final: 0.8000 (mtmt) REVERT: M 275 MET cc_start: 0.7627 (ttp) cc_final: 0.7147 (tmm) REVERT: M 284 LEU cc_start: 0.8890 (mt) cc_final: 0.8276 (tp) REVERT: H 71 MET cc_start: 0.7828 (mmp) cc_final: 0.7385 (mmm) outliers start: 1 outliers final: 0 residues processed: 434 average time/residue: 0.1865 time to fit residues: 135.2196 Evaluate side-chains 359 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 363 optimal weight: 6.9990 chunk 326 optimal weight: 0.0970 chunk 102 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 279 optimal weight: 6.9990 chunk 380 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 373 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN D 241 HIS ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.069537 restraints weight = 113532.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.071215 restraints weight = 59211.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.072362 restraints weight = 36328.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.073140 restraints weight = 24605.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073697 restraints weight = 17941.887| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33371 Z= 0.154 Angle : 0.597 12.321 45250 Z= 0.302 Chirality : 0.045 0.173 5087 Planarity : 0.004 0.084 5876 Dihedral : 4.657 60.384 4519 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.32 % Favored : 90.66 % Rotamer: Outliers : 0.03 % Allowed : 1.23 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 4090 helix: 1.24 (0.16), residues: 1122 sheet: -0.17 (0.21), residues: 666 loop : -2.19 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 215 TYR 0.016 0.001 TYR C 416 PHE 0.031 0.001 PHE G 343 TRP 0.036 0.001 TRP A 360 HIS 0.002 0.001 HIS G 241 Details of bonding type rmsd covalent geometry : bond 0.00358 (33371) covalent geometry : angle 0.59707 (45250) hydrogen bonds : bond 0.03705 ( 1123) hydrogen bonds : angle 4.69382 ( 3192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 200 MET cc_start: 0.8487 (ppp) cc_final: 0.8199 (ppp) REVERT: B 222 ASP cc_start: 0.8482 (p0) cc_final: 0.8184 (p0) REVERT: A 25 TYR cc_start: 0.8451 (m-10) cc_final: 0.8234 (m-10) REVERT: A 82 ASP cc_start: 0.8596 (m-30) cc_final: 0.7888 (t0) REVERT: A 160 MET cc_start: 0.8385 (pmm) cc_final: 0.8100 (pmm) REVERT: A 195 VAL cc_start: 0.9408 (m) cc_final: 0.9100 (p) REVERT: A 207 GLU cc_start: 0.8358 (tt0) cc_final: 0.8076 (tm-30) REVERT: A 380 GLN cc_start: 0.8650 (mt0) cc_final: 0.8414 (mt0) REVERT: C 58 TYR cc_start: 0.8785 (t80) cc_final: 0.8260 (t80) REVERT: C 82 ASP cc_start: 0.8945 (m-30) cc_final: 0.7874 (t70) REVERT: C 105 LYS cc_start: 0.8239 (mttp) cc_final: 0.7495 (tptt) REVERT: C 413 LYS cc_start: 0.6674 (mptt) cc_final: 0.6377 (mptt) REVERT: G 54 LYS cc_start: 0.8956 (mttt) cc_final: 0.8523 (mttm) REVERT: G 72 ASP cc_start: 0.8790 (t0) cc_final: 0.8495 (t70) REVERT: D 96 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8071 (mt-10) REVERT: D 142 MET cc_start: 0.8614 (ttt) cc_final: 0.8214 (ttm) REVERT: D 185 ASP cc_start: 0.8887 (t70) cc_final: 0.8314 (t0) REVERT: J 54 LYS cc_start: 0.9095 (mttp) cc_final: 0.8719 (mtpt) REVERT: J 119 MET cc_start: 0.8775 (mmm) cc_final: 0.8423 (mmm) REVERT: J 328 MET cc_start: 0.9264 (tpp) cc_final: 0.8822 (tpp) REVERT: E 69 ASN cc_start: 0.8917 (t0) cc_final: 0.8580 (t0) REVERT: E 150 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7745 (tm-30) REVERT: L 54 LYS cc_start: 0.8976 (mttt) cc_final: 0.8596 (mttp) REVERT: L 139 TYR cc_start: 0.8665 (t80) cc_final: 0.8167 (t80) REVERT: L 171 LEU cc_start: 0.9475 (mt) cc_final: 0.9183 (mm) REVERT: L 312 ASP cc_start: 0.8654 (p0) cc_final: 0.8404 (p0) REVERT: L 328 MET cc_start: 0.9175 (tpp) cc_final: 0.8607 (tpp) REVERT: L 346 MET cc_start: 0.8625 (tmm) cc_final: 0.8322 (tmm) REVERT: F 122 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7787 (tp30) REVERT: I 31 GLU cc_start: 0.8552 (pp20) cc_final: 0.7996 (pp20) REVERT: I 41 MET cc_start: 0.8770 (mmp) cc_final: 0.8353 (mmp) REVERT: I 246 GLU cc_start: 0.7509 (tt0) cc_final: 0.7240 (tt0) REVERT: I 269 GLN cc_start: 0.8826 (pt0) cc_final: 0.8402 (pp30) REVERT: I 275 MET cc_start: 0.7848 (tmm) cc_final: 0.7445 (tmm) REVERT: I 284 LEU cc_start: 0.8939 (mt) cc_final: 0.8537 (tp) REVERT: K 46 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8491 (tm-30) REVERT: K 284 LEU cc_start: 0.8930 (mt) cc_final: 0.8423 (tp) REVERT: M 41 MET cc_start: 0.9087 (mmp) cc_final: 0.8703 (mmm) REVERT: M 102 MET cc_start: 0.8026 (mtp) cc_final: 0.7715 (mtp) REVERT: M 165 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7996 (mtmt) REVERT: M 214 MET cc_start: 0.8733 (tpt) cc_final: 0.7979 (tpt) REVERT: M 275 MET cc_start: 0.7577 (ttp) cc_final: 0.7123 (tmm) REVERT: M 284 LEU cc_start: 0.8919 (mt) cc_final: 0.8340 (tp) REVERT: H 71 MET cc_start: 0.7793 (mmp) cc_final: 0.7384 (mmm) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.1803 time to fit residues: 129.7901 Evaluate side-chains 362 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 2 optimal weight: 20.0000 chunk 373 optimal weight: 40.0000 chunk 206 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 355 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 344 optimal weight: 8.9990 chunk 317 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN G 136 ASN G 261 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 ASN M 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.067847 restraints weight = 114731.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.069496 restraints weight = 60092.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.070619 restraints weight = 36968.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.071381 restraints weight = 25157.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.071919 restraints weight = 18424.290| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33371 Z= 0.218 Angle : 0.659 13.837 45250 Z= 0.335 Chirality : 0.047 0.186 5087 Planarity : 0.004 0.091 5876 Dihedral : 4.897 62.609 4519 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.00 % Favored : 88.97 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 4090 helix: 1.04 (0.16), residues: 1122 sheet: -0.28 (0.21), residues: 660 loop : -2.26 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 215 TYR 0.021 0.001 TYR D 208 PHE 0.041 0.002 PHE A 179 TRP 0.035 0.002 TRP A 360 HIS 0.003 0.001 HIS L 241 Details of bonding type rmsd covalent geometry : bond 0.00504 (33371) covalent geometry : angle 0.65866 (45250) hydrogen bonds : bond 0.04395 ( 1123) hydrogen bonds : angle 4.93135 ( 3192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 403 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 MET cc_start: 0.8477 (ppp) cc_final: 0.8123 (ppp) REVERT: B 222 ASP cc_start: 0.8506 (p0) cc_final: 0.8201 (p0) REVERT: A 25 TYR cc_start: 0.8500 (m-10) cc_final: 0.8293 (m-10) REVERT: A 82 ASP cc_start: 0.8696 (m-30) cc_final: 0.7962 (t0) REVERT: A 160 MET cc_start: 0.8324 (pmm) cc_final: 0.8040 (pmm) REVERT: A 195 VAL cc_start: 0.9440 (m) cc_final: 0.9123 (p) REVERT: A 207 GLU cc_start: 0.8487 (tt0) cc_final: 0.8121 (tm-30) REVERT: A 335 MET cc_start: 0.8906 (ptp) cc_final: 0.8668 (ptm) REVERT: A 416 TYR cc_start: 0.8726 (m-80) cc_final: 0.8268 (m-80) REVERT: C 58 TYR cc_start: 0.8868 (t80) cc_final: 0.8355 (t80) REVERT: C 82 ASP cc_start: 0.9002 (m-30) cc_final: 0.7910 (t70) REVERT: C 105 LYS cc_start: 0.8259 (mttp) cc_final: 0.7503 (tptt) REVERT: C 413 LYS cc_start: 0.6547 (mptt) cc_final: 0.6259 (mptt) REVERT: G 54 LYS cc_start: 0.8914 (mttt) cc_final: 0.8479 (mttm) REVERT: G 72 ASP cc_start: 0.8843 (t0) cc_final: 0.8575 (t70) REVERT: D 96 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7990 (mt-10) REVERT: D 142 MET cc_start: 0.8539 (ttt) cc_final: 0.8130 (ttm) REVERT: D 185 ASP cc_start: 0.8829 (t70) cc_final: 0.8325 (t0) REVERT: J 54 LYS cc_start: 0.9230 (mttp) cc_final: 0.8739 (mtpt) REVERT: J 119 MET cc_start: 0.8886 (mmm) cc_final: 0.8550 (mmm) REVERT: E 69 ASN cc_start: 0.8893 (t0) cc_final: 0.8631 (t0) REVERT: E 150 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7807 (tm-30) REVERT: E 152 MET cc_start: 0.8516 (mmm) cc_final: 0.7994 (mmm) REVERT: L 54 LYS cc_start: 0.8998 (mttt) cc_final: 0.8620 (mttp) REVERT: L 171 LEU cc_start: 0.9516 (mt) cc_final: 0.9236 (mm) REVERT: L 312 ASP cc_start: 0.8714 (p0) cc_final: 0.8480 (p0) REVERT: L 328 MET cc_start: 0.9182 (tpp) cc_final: 0.8615 (tpp) REVERT: L 346 MET cc_start: 0.8657 (tmm) cc_final: 0.8329 (tmm) REVERT: F 122 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7871 (tp30) REVERT: F 152 MET cc_start: 0.8357 (tpp) cc_final: 0.8055 (mmm) REVERT: I 31 GLU cc_start: 0.8589 (pp20) cc_final: 0.8042 (pp20) REVERT: I 41 MET cc_start: 0.8814 (mmp) cc_final: 0.8394 (mmp) REVERT: I 72 ARG cc_start: 0.0744 (tpm170) cc_final: 0.0374 (tpm170) REVERT: I 246 GLU cc_start: 0.7483 (tt0) cc_final: 0.7231 (tt0) REVERT: I 269 GLN cc_start: 0.8864 (pt0) cc_final: 0.8430 (pp30) REVERT: K 41 MET cc_start: 0.8790 (mmp) cc_final: 0.8532 (mmm) REVERT: K 284 LEU cc_start: 0.8813 (mt) cc_final: 0.8321 (tp) REVERT: M 41 MET cc_start: 0.9231 (mmp) cc_final: 0.8901 (mmm) REVERT: M 102 MET cc_start: 0.8135 (mtp) cc_final: 0.7925 (mtp) REVERT: M 165 LYS cc_start: 0.8281 (mtmt) cc_final: 0.8023 (mtmt) REVERT: M 166 HIS cc_start: 0.8108 (p90) cc_final: 0.7888 (p90) REVERT: M 275 MET cc_start: 0.7625 (ttp) cc_final: 0.7143 (tmm) REVERT: M 284 LEU cc_start: 0.8944 (mt) cc_final: 0.8380 (tp) REVERT: H 71 MET cc_start: 0.7845 (mmp) cc_final: 0.7456 (mmm) outliers start: 2 outliers final: 0 residues processed: 405 average time/residue: 0.1824 time to fit residues: 123.1023 Evaluate side-chains 342 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 195 optimal weight: 30.0000 chunk 223 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 288 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 396 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 380 GLN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 ASN M 234 GLN ** M 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.068948 restraints weight = 113699.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.070631 restraints weight = 59474.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.071777 restraints weight = 36488.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.072550 restraints weight = 24773.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073081 restraints weight = 18099.520| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33371 Z= 0.165 Angle : 0.626 12.849 45250 Z= 0.317 Chirality : 0.046 0.163 5087 Planarity : 0.004 0.091 5876 Dihedral : 4.825 62.047 4519 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.41 % Favored : 90.56 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 4090 helix: 1.06 (0.16), residues: 1122 sheet: -0.26 (0.21), residues: 660 loop : -2.23 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 177 TYR 0.021 0.001 TYR C 416 PHE 0.033 0.001 PHE A 179 TRP 0.030 0.001 TRP A 360 HIS 0.005 0.001 HIS L 241 Details of bonding type rmsd covalent geometry : bond 0.00385 (33371) covalent geometry : angle 0.62605 (45250) hydrogen bonds : bond 0.03942 ( 1123) hydrogen bonds : angle 4.82171 ( 3192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8180 Ramachandran restraints generated. 4090 Oldfield, 0 Emsley, 4090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 200 MET cc_start: 0.8467 (ppp) cc_final: 0.8152 (ppp) REVERT: B 222 ASP cc_start: 0.8451 (p0) cc_final: 0.8143 (p0) REVERT: A 82 ASP cc_start: 0.8617 (m-30) cc_final: 0.7877 (t0) REVERT: A 160 MET cc_start: 0.8368 (pmm) cc_final: 0.8088 (pmm) REVERT: A 195 VAL cc_start: 0.9406 (m) cc_final: 0.9088 (p) REVERT: A 207 GLU cc_start: 0.8377 (tt0) cc_final: 0.8093 (tm-30) REVERT: A 335 MET cc_start: 0.8927 (ptp) cc_final: 0.8714 (ptm) REVERT: A 416 TYR cc_start: 0.8733 (m-80) cc_final: 0.8282 (m-80) REVERT: C 58 TYR cc_start: 0.8809 (t80) cc_final: 0.8290 (t80) REVERT: C 82 ASP cc_start: 0.8996 (m-30) cc_final: 0.7922 (t70) REVERT: C 105 LYS cc_start: 0.8249 (mttp) cc_final: 0.7501 (tptt) REVERT: C 413 LYS cc_start: 0.6643 (mptt) cc_final: 0.6338 (mptt) REVERT: G 54 LYS cc_start: 0.8869 (mttt) cc_final: 0.8428 (mttm) REVERT: G 72 ASP cc_start: 0.8777 (t0) cc_final: 0.8518 (t70) REVERT: D 96 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7981 (mt-10) REVERT: D 142 MET cc_start: 0.8616 (ttt) cc_final: 0.8215 (ttm) REVERT: D 185 ASP cc_start: 0.8892 (t70) cc_final: 0.8322 (t0) REVERT: J 54 LYS cc_start: 0.9185 (mttp) cc_final: 0.8718 (mtpt) REVERT: J 119 MET cc_start: 0.8855 (mmm) cc_final: 0.8508 (mmm) REVERT: J 328 MET cc_start: 0.9270 (tpp) cc_final: 0.8859 (tpp) REVERT: E 69 ASN cc_start: 0.8948 (t0) cc_final: 0.8653 (t0) REVERT: E 150 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7737 (tm-30) REVERT: E 152 MET cc_start: 0.8518 (mmm) cc_final: 0.7944 (mmm) REVERT: L 54 LYS cc_start: 0.8982 (mttt) cc_final: 0.8609 (mttp) REVERT: L 139 TYR cc_start: 0.8668 (t80) cc_final: 0.8190 (t80) REVERT: L 171 LEU cc_start: 0.9488 (mt) cc_final: 0.9204 (mm) REVERT: L 312 ASP cc_start: 0.8675 (p0) cc_final: 0.8446 (p0) REVERT: L 328 MET cc_start: 0.9186 (tpp) cc_final: 0.8618 (tpp) REVERT: F 122 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7815 (tp30) REVERT: F 185 ASP cc_start: 0.8420 (t70) cc_final: 0.8045 (t0) REVERT: I 31 GLU cc_start: 0.8562 (pp20) cc_final: 0.8012 (pp20) REVERT: I 41 MET cc_start: 0.8802 (mmp) cc_final: 0.8376 (mmp) REVERT: I 72 ARG cc_start: 0.0594 (tpm170) cc_final: 0.0229 (tpm170) REVERT: I 246 GLU cc_start: 0.7480 (tt0) cc_final: 0.7272 (tt0) REVERT: I 269 GLN cc_start: 0.8858 (pt0) cc_final: 0.8407 (pp30) REVERT: I 284 LEU cc_start: 0.9133 (mt) cc_final: 0.8710 (tp) REVERT: K 41 MET cc_start: 0.8829 (mmp) cc_final: 0.8434 (mmm) REVERT: K 284 LEU cc_start: 0.8912 (mt) cc_final: 0.8374 (tp) REVERT: M 41 MET cc_start: 0.9144 (mmp) cc_final: 0.8776 (mmm) REVERT: M 102 MET cc_start: 0.8066 (mtp) cc_final: 0.7828 (mtp) REVERT: M 165 LYS cc_start: 0.8280 (mtmt) cc_final: 0.8020 (mtmt) REVERT: M 166 HIS cc_start: 0.8087 (p90) cc_final: 0.7879 (p90) REVERT: M 275 MET cc_start: 0.7576 (ttp) cc_final: 0.7219 (tmm) REVERT: M 284 LEU cc_start: 0.8939 (mt) cc_final: 0.8393 (tp) REVERT: H 71 MET cc_start: 0.7754 (mmp) cc_final: 0.7391 (mmm) outliers start: 1 outliers final: 0 residues processed: 406 average time/residue: 0.1858 time to fit residues: 126.5753 Evaluate side-chains 352 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 264 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 326 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 336 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 353 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 ASN M 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.077385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.069807 restraints weight = 113518.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071496 restraints weight = 59085.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.072647 restraints weight = 36213.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073416 restraints weight = 24520.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073985 restraints weight = 17893.462| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33371 Z= 0.135 Angle : 0.606 12.353 45250 Z= 0.306 Chirality : 0.046 0.216 5087 Planarity : 0.004 0.089 5876 Dihedral : 4.732 60.580 4519 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.68 % Favored : 90.29 % Rotamer: Outliers : 0.03 % Allowed : 0.20 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4090 helix: 1.15 (0.16), residues: 1119 sheet: -0.25 (0.21), residues: 672 loop : -2.19 (0.13), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 177 TYR 0.014 0.001 TYR A 416 PHE 0.026 0.001 PHE A 179 TRP 0.052 0.001 TRP D 181 HIS 0.005 0.001 HIS L 241 Details of bonding type rmsd covalent geometry : bond 0.00313 (33371) covalent geometry : angle 0.60646 (45250) hydrogen bonds : bond 0.03635 ( 1123) hydrogen bonds : angle 4.71396 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4570.13 seconds wall clock time: 80 minutes 20.96 seconds (4820.96 seconds total)