Starting phenix.real_space_refine on Sun Sep 13 03:44:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z6h_14527/09_2026/7z6h_14527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z6h_14527/09_2026/7z6h_14527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z6h_14527/09_2026/7z6h_14527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z6h_14527/09_2026/7z6h_14527.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z6h_14527/09_2026/7z6h_14527.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z6h_14527/09_2026/7z6h_14527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z6h_14527/09_2026/7z6h_14527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z6h_14527/09_2026/7z6h_14527.map" } resolution = 3.59 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= 0.003 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 137 5.16 5 C 12953 2.51 5 N 3561 2.21 5 O 3932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20629 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1911 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 4 Chain: "B" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2049 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 250} Chain: "C" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2171 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 2 Chain: "D" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2499 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2671 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2480 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 12, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2523 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 304} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3518 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 414} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "Y" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 198 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.98, per 1000 atoms: 0.19 Number of scatterers: 20629 At special positions: 0 Unit cell: (146.2, 117.82, 130.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 137 16.00 P 46 15.00 O 3932 8.00 N 3561 7.00 C 12953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 272 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 657.5 milliseconds 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4780 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 18 sheets defined 49.3% alpha, 13.6% beta 0 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 8 through 24 removed outlier: 3.915A pdb=" N VAL A 12 " --> pdb=" O GLY A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 219 through 230 Processing helix chain 'B' and resid 24 through 33 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 230 through 237 removed outlier: 4.393A pdb=" N ALA B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 27 Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.958A pdb=" N THR C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 removed outlier: 4.594A pdb=" N LYS C 144 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 146 " --> pdb=" O TRP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 4.248A pdb=" N ASN C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 244 removed outlier: 3.566A pdb=" N PHE C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.525A pdb=" N VAL D 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 67 removed outlier: 3.609A pdb=" N GLU D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 Processing helix chain 'D' and resid 115 through 128 removed outlier: 4.107A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.560A pdb=" N MET D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 167 removed outlier: 3.651A pdb=" N ALA D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.674A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 203 through 219 Processing helix chain 'D' and resid 223 through 234 removed outlier: 3.712A pdb=" N ALA D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.753A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.607A pdb=" N GLY D 276 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 removed outlier: 3.709A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 344 through 360 Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 47 through 60 removed outlier: 3.691A pdb=" N ARG E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 118 removed outlier: 4.037A pdb=" N GLN E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 155 removed outlier: 4.021A pdb=" N GLN E 145 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.779A pdb=" N VAL E 253 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 263 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.553A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 301 Processing helix chain 'E' and resid 305 through 325 removed outlier: 3.920A pdb=" N GLY E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.154A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 42 removed outlier: 3.878A pdb=" N TYR F 42 " --> pdb=" O TRP F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 67 removed outlier: 3.554A pdb=" N SER F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 95 Processing helix chain 'F' and resid 113 through 126 Processing helix chain 'F' and resid 143 through 146 Processing helix chain 'F' and resid 147 through 158 removed outlier: 4.510A pdb=" N ARG F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 163 removed outlier: 4.467A pdb=" N LYS F 163 " --> pdb=" O ILE F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 163' Processing helix chain 'F' and resid 178 through 183 Processing helix chain 'F' and resid 194 through 210 removed outlier: 3.720A pdb=" N ILE F 198 " --> pdb=" O THR F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.518A pdb=" N GLN F 226 " --> pdb=" O ILE F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 242 removed outlier: 3.834A pdb=" N ALA F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 254 Processing helix chain 'F' and resid 259 through 272 removed outlier: 3.872A pdb=" N VAL F 263 " --> pdb=" O HIS F 259 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN F 272 " --> pdb=" O GLN F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 289 removed outlier: 3.933A pdb=" N LYS F 280 " --> pdb=" O ASP F 276 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 305 removed outlier: 3.855A pdb=" N THR F 305 " --> pdb=" O ARG F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 330 removed outlier: 3.800A pdb=" N LYS F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY F 330 " --> pdb=" O LYS F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 349 removed outlier: 3.838A pdb=" N MET F 337 " --> pdb=" O SER F 333 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 347 " --> pdb=" O ARG F 343 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET F 349 " --> pdb=" O CYS F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 26 Processing helix chain 'G' and resid 30 through 34 removed outlier: 3.503A pdb=" N ASP G 33 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU G 34 " --> pdb=" O LEU G 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 30 through 34' Processing helix chain 'G' and resid 38 through 50 Processing helix chain 'G' and resid 65 through 78 Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 127 through 130 removed outlier: 3.871A pdb=" N MET G 130 " --> pdb=" O ALA G 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 127 through 130' Processing helix chain 'G' and resid 131 through 145 removed outlier: 3.907A pdb=" N PHE G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.718A pdb=" N SER G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG G 168 " --> pdb=" O LEU G 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 164 through 168' Processing helix chain 'G' and resid 178 through 193 Proline residue: G 184 - end of helix removed outlier: 3.519A pdb=" N GLU G 193 " --> pdb=" O VAL G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 208 removed outlier: 3.632A pdb=" N MET G 202 " --> pdb=" O SER G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 225 removed outlier: 4.271A pdb=" N ILE G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU G 220 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 240 Processing helix chain 'G' and resid 243 through 257 Processing helix chain 'G' and resid 258 through 273 removed outlier: 3.577A pdb=" N ALA G 262 " --> pdb=" O ASP G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 291 Processing helix chain 'G' and resid 295 through 311 Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 317 through 336 removed outlier: 3.540A pdb=" N GLN G 321 " --> pdb=" O ASN G 317 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL G 331 " --> pdb=" O ALA G 327 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR G 332 " --> pdb=" O ALA G 328 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG G 333 " --> pdb=" O PHE G 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 95 Processing helix chain 'K' and resid 99 through 103 Processing helix chain 'K' and resid 106 through 123 Processing helix chain 'K' and resid 142 through 154 removed outlier: 3.563A pdb=" N THR K 146 " --> pdb=" O GLY K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 206 Processing helix chain 'K' and resid 229 through 236 removed outlier: 3.595A pdb=" N TYR K 233 " --> pdb=" O PRO K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 250 removed outlier: 3.779A pdb=" N GLU K 241 " --> pdb=" O HIS K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 272 removed outlier: 3.535A pdb=" N ARG K 269 " --> pdb=" O ASP K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 281 Processing helix chain 'K' and resid 291 through 309 Processing helix chain 'K' and resid 318 through 328 removed outlier: 3.622A pdb=" N GLU K 323 " --> pdb=" O LYS K 319 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU K 324 " --> pdb=" O THR K 320 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS K 326 " --> pdb=" O LEU K 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 344 Processing helix chain 'K' and resid 395 through 406 removed outlier: 3.654A pdb=" N ALA K 399 " --> pdb=" O PHE K 395 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY K 401 " --> pdb=" O PHE K 397 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS K 406 " --> pdb=" O LYS K 402 " (cutoff:3.500A) Processing helix chain 'K' and resid 423 through 427 removed outlier: 3.571A pdb=" N TYR K 426 " --> pdb=" O LEU K 423 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU K 427 " --> pdb=" O SER K 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 423 through 427' Processing helix chain 'K' and resid 434 through 442 Processing helix chain 'K' and resid 445 through 457 Processing helix chain 'K' and resid 463 through 480 removed outlier: 3.758A pdb=" N ILE K 467 " --> pdb=" O GLU K 463 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU K 480 " --> pdb=" O PHE K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 491 through 506 removed outlier: 3.908A pdb=" N ASN K 506 " --> pdb=" O VAL K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 545 removed outlier: 3.677A pdb=" N ILE K 532 " --> pdb=" O GLN K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 556 through 560 Processing helix chain 'K' and resid 560 through 567 removed outlier: 3.686A pdb=" N TYR K 564 " --> pdb=" O GLN K 560 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 584 removed outlier: 4.489A pdb=" N SER K 579 " --> pdb=" O GLN K 575 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE K 580 " --> pdb=" O ALA K 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 3.642A pdb=" N VAL A 109 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 108 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 6 removed outlier: 3.642A pdb=" N VAL A 109 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 108 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 119 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 removed outlier: 5.247A pdb=" N GLU A 26 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL A 41 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 35 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 36 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 248 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 237 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS A 252 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASN A 235 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 147 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 206 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 198 removed outlier: 3.837A pdb=" N THR A 167 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 72 through 74 removed outlier: 3.782A pdb=" N GLU B 72 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 17 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B 111 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 129 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS C 200 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.510A pdb=" N ILE B 65 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.982A pdb=" N VAL B 267 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 157 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 212 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 188 through 192 Processing sheet with id=AB1, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 70 removed outlier: 4.011A pdb=" N GLU C 66 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N PHE C 3 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 100 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 133 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.554A pdb=" N SER C 53 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.066A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 149 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 179 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 93 through 95 removed outlier: 6.791A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 70 through 75 Processing sheet with id=AB7, first strand: chain 'F' and resid 102 through 105 removed outlier: 6.492A pdb=" N LEU F 103 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP F 141 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU F 105 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS F 136 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA F 168 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE F 138 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA F 170 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU F 140 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 72 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE F 73 " --> pdb=" O LEU F 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 56 through 59 removed outlier: 5.890A pdb=" N LEU G 56 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N CYS G 155 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU G 58 " --> pdb=" O CYS G 155 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL G 122 " --> pdb=" O ARG G 150 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS G 152 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 154 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU G 88 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASP G 125 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU G 90 " --> pdb=" O ASP G 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 157 through 159 removed outlier: 6.479A pdb=" N GLN K 157 " --> pdb=" O ILE K 222 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU K 224 " --> pdb=" O GLN K 157 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN K 159 " --> pdb=" O LEU K 224 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ILE K 255 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE K 223 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE K 257 " --> pdb=" O ILE K 223 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL K 225 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU K 133 " --> pdb=" O PHE K 256 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6777 1.36 - 1.51: 5449 1.51 - 1.66: 8624 1.66 - 1.80: 110 1.80 - 1.95: 88 Bond restraints: 21048 Sorted by residual: bond pdb=" C3' DC Y 2 " pdb=" C2' DC Y 2 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.60e+00 bond pdb=" CB PRO F 77 " pdb=" CG PRO F 77 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.91e+00 bond pdb=" N PRO F 77 " pdb=" CA PRO F 77 " ideal model delta sigma weight residual 1.465 1.408 0.057 2.03e-02 2.43e+03 7.90e+00 bond pdb=" C3' DC X 55 " pdb=" C2' DC X 55 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.65e+00 bond pdb=" C3' DC Y 1 " pdb=" C2' DC Y 1 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.61e+00 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 28437 3.13 - 6.27: 128 6.27 - 9.40: 17 9.40 - 12.53: 3 12.53 - 15.67: 1 Bond angle restraints: 28586 Sorted by residual: angle pdb=" CA PRO F 77 " pdb=" N PRO F 77 " pdb=" CD PRO F 77 " ideal model delta sigma weight residual 112.00 96.33 15.67 1.40e+00 5.10e-01 1.25e+02 angle pdb=" N PRO G 21 " pdb=" CA PRO G 21 " pdb=" CB PRO G 21 " ideal model delta sigma weight residual 103.25 110.80 -7.55 1.05e+00 9.07e-01 5.18e+01 angle pdb=" N PRO F 77 " pdb=" CD PRO F 77 " pdb=" CG PRO F 77 " ideal model delta sigma weight residual 103.20 96.45 6.75 1.50e+00 4.44e-01 2.02e+01 angle pdb=" N3 DT Y 5 " pdb=" C4 DT Y 5 " pdb=" O4 DT Y 5 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT Y 9 " pdb=" C4 DT Y 9 " pdb=" O4 DT Y 9 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 28581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.47: 11737 30.47 - 60.94: 1018 60.94 - 91.40: 38 91.40 - 121.87: 2 121.87 - 152.34: 1 Dihedral angle restraints: 12796 sinusoidal: 5465 harmonic: 7331 Sorted by residual: dihedral pdb=" CB CYS B 58 " pdb=" SG CYS B 58 " pdb=" SG CYS B 272 " pdb=" CB CYS B 272 " ideal model delta sinusoidal sigma weight residual -86.00 -131.69 45.69 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CA PHE A 58 " pdb=" C PHE A 58 " pdb=" N GLN A 59 " pdb=" CA GLN A 59 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" O1A AGS E 401 " pdb=" O3A AGS E 401 " pdb=" PA AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sinusoidal sigma weight residual -67.73 84.61 -152.34 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 12793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2713 0.051 - 0.103: 520 0.103 - 0.154: 83 0.154 - 0.205: 2 0.205 - 0.257: 2 Chirality restraints: 3320 Sorted by residual: chirality pdb=" CA PRO G 21 " pdb=" N PRO G 21 " pdb=" C PRO G 21 " pdb=" CB PRO G 21 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU K 567 " pdb=" CB LEU K 567 " pdb=" CD1 LEU K 567 " pdb=" CD2 LEU K 567 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO K 420 " pdb=" N PRO K 420 " pdb=" C PRO K 420 " pdb=" CB PRO K 420 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 3317 not shown) Planarity restraints: 3509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 76 " 0.124 5.00e-02 4.00e+02 1.75e-01 4.91e+01 pdb=" N PRO F 77 " -0.302 5.00e-02 4.00e+02 pdb=" CA PRO F 77 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO F 77 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 562 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO K 563 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO K 563 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO K 563 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 185 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO B 186 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 186 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 186 " -0.028 5.00e-02 4.00e+02 ... (remaining 3506 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 155 2.62 - 3.19: 16752 3.19 - 3.76: 29589 3.76 - 4.33: 37979 4.33 - 4.90: 65458 Nonbonded interactions: 149933 Sorted by model distance: nonbonded pdb=" OG SER B 16 " pdb=" O TYR B 112 " model vdw 2.045 3.040 nonbonded pdb=" O PHE G 108 " pdb=" OG1 THR G 111 " model vdw 2.119 3.040 nonbonded pdb=" OH TYR E 60 " pdb=" O PHE E 129 " model vdw 2.183 3.040 nonbonded pdb=" NE2 GLN C 244 " pdb=" OH TYR C 274 " model vdw 2.184 3.120 nonbonded pdb=" OG SER B 231 " pdb=" OH TYR B 255 " model vdw 2.202 3.040 ... (remaining 149928 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.940 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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 0.141 21054 Z= 0.179 Angle : 0.631 15.668 28588 Z= 0.364 Chirality : 0.041 0.257 3320 Planarity : 0.005 0.175 3509 Dihedral : 19.721 152.340 8013 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.36 % Favored : 93.44 % Rotamer: Outliers : 0.68 % Allowed : 35.48 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.18), residues: 2469 helix: 1.27 (0.16), residues: 1112 sheet: -0.24 (0.24), residues: 494 loop : -2.08 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 102 TYR 0.015 0.001 TYR A 181 PHE 0.016 0.001 PHE G 145 TRP 0.008 0.001 TRP K 161 HIS 0.008 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.18 (21048) covalent geometry : angle 0.63133 / 0.36 (28586) SS BOND : bond 0.00090 / 0.05 ( 1) SS BOND : angle 0.83011 / 0.48 ( 2) hydrogen bonds : bond 0.15852 / 10.51 ( 955) hydrogen bonds : angle 5.04354 / 3.40 ( 2766) Misc. bond : bond 0.00085 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 355 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 193 ARG cc_start: 0.8148 (ptp-110) cc_final: 0.7171 (ptp90) REVERT: F 267 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6148 (mt) REVERT: K 268 GLN cc_start: 0.7176 (tm-30) cc_final: 0.6673 (tm-30) REVERT: K 327 GLN cc_start: 0.7565 (tt0) cc_final: 0.7249 (tt0) outliers start: 15 outliers final: 8 residues processed: 364 average time/residue: 0.1844 time to fit residues: 98.0242 Evaluate side-chains 358 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 349 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 127 LYS Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain K residue 400 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.149229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133125 restraints weight = 27982.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136056 restraints weight = 17491.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138252 restraints weight = 11639.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140456 restraints weight = 7720.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140743 restraints weight = 5738.141| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21054 Z= 0.153 Angle : 0.594 9.935 28588 Z= 0.312 Chirality : 0.041 0.201 3320 Planarity : 0.005 0.087 3509 Dihedral : 13.183 158.519 3088 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.53 % Favored : 92.26 % Rotamer: Outliers : 4.28 % Allowed : 31.83 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2469 helix: 1.20 (0.16), residues: 1137 sheet: -0.12 (0.24), residues: 496 loop : -2.21 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 334 TYR 0.016 0.001 TYR D 77 PHE 0.020 0.001 PHE B 36 TRP 0.006 0.001 TRP F 286 HIS 0.011 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (21048) covalent geometry : angle 0.59428 / 0.31 (28586) SS BOND : bond 0.00052 / 0.03 ( 1) SS BOND : angle 1.14941 / 0.67 ( 2) hydrogen bonds : bond 0.05466 / 3.65 ( 955) hydrogen bonds : angle 4.26212 / 2.91 ( 2766) Misc. bond : bond 0.00432 / 0.35 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 356 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7678 (tmm) cc_final: 0.7334 (tpp) REVERT: C 173 MET cc_start: 0.7193 (tpp) cc_final: 0.6941 (mtt) REVERT: D 124 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.6028 (ttpt) REVERT: E 16 LEU cc_start: 0.4619 (OUTLIER) cc_final: 0.4394 (mp) REVERT: F 40 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: F 267 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6021 (mt) REVERT: F 349 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6986 (tmt) REVERT: G 24 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: G 98 ILE cc_start: 0.8194 (mt) cc_final: 0.7855 (mt) REVERT: G 145 PHE cc_start: 0.5760 (OUTLIER) cc_final: 0.5211 (p90) outliers start: 95 outliers final: 51 residues processed: 419 average time/residue: 0.1769 time to fit residues: 108.4042 Evaluate side-chains 404 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 441 MET Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 49 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 164 optimal weight: 0.0980 chunk 173 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 239 GLN C 244 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN K 159 GLN K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 GLN ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.149929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133840 restraints weight = 28178.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136731 restraints weight = 17338.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138777 restraints weight = 11786.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141046 restraints weight = 7854.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141279 restraints weight = 5826.239| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21054 Z= 0.129 Angle : 0.562 9.606 28588 Z= 0.294 Chirality : 0.040 0.161 3320 Planarity : 0.004 0.067 3509 Dihedral : 13.125 161.072 3074 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.89 % Favored : 92.91 % Rotamer: Outliers : 4.82 % Allowed : 31.70 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2469 helix: 1.24 (0.16), residues: 1151 sheet: -0.12 (0.24), residues: 499 loop : -2.18 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 168 TYR 0.012 0.001 TYR C 274 PHE 0.016 0.001 PHE B 36 TRP 0.006 0.001 TRP E 251 HIS 0.009 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (21048) covalent geometry : angle 0.56163 / 0.29 (28586) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 1.00969 / 0.58 ( 2) hydrogen bonds : bond 0.04904 / 3.27 ( 955) hydrogen bonds : angle 4.10375 / 2.81 ( 2766) Misc. bond : bond 0.00175 / 0.13 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 353 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7651 (tmm) cc_final: 0.7340 (tpp) REVERT: C 173 MET cc_start: 0.7209 (tpp) cc_final: 0.6986 (mtt) REVERT: D 149 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7781 (pt) REVERT: F 40 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: F 256 ASP cc_start: 0.5694 (t0) cc_final: 0.5460 (t0) REVERT: F 267 ILE cc_start: 0.6848 (OUTLIER) cc_final: 0.5996 (mt) REVERT: G 24 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5878 (mp0) REVERT: G 98 ILE cc_start: 0.8126 (mt) cc_final: 0.7758 (mt) REVERT: G 145 PHE cc_start: 0.5858 (OUTLIER) cc_final: 0.5094 (p90) REVERT: G 199 GLU cc_start: 0.6146 (tp30) cc_final: 0.5749 (tp30) REVERT: G 311 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7593 (ttp-170) REVERT: K 96 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7759 (ptmm) REVERT: K 279 GLU cc_start: 0.6878 (pt0) cc_final: 0.6367 (pt0) REVERT: K 567 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.5079 (tp) outliers start: 107 outliers final: 59 residues processed: 432 average time/residue: 0.1691 time to fit residues: 108.5648 Evaluate side-chains 413 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 311 ARG Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 480 LEU Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 97 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 248 optimal weight: 10.0000 chunk 246 optimal weight: 0.0870 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 ASN ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.150400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133928 restraints weight = 28095.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137124 restraints weight = 17398.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139643 restraints weight = 11601.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141502 restraints weight = 7359.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141704 restraints weight = 5628.975| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21054 Z= 0.121 Angle : 0.548 9.681 28588 Z= 0.287 Chirality : 0.040 0.160 3320 Planarity : 0.004 0.065 3509 Dihedral : 13.141 162.627 3074 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.72 % Favored : 93.07 % Rotamer: Outliers : 4.91 % Allowed : 31.56 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2469 helix: 1.28 (0.16), residues: 1153 sheet: -0.07 (0.24), residues: 499 loop : -2.12 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 178 TYR 0.011 0.001 TYR C 274 PHE 0.018 0.001 PHE F 223 TRP 0.006 0.001 TRP K 161 HIS 0.007 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (21048) covalent geometry : angle 0.54755 / 0.29 (28586) SS BOND : bond 0.00112 / 0.06 ( 1) SS BOND : angle 0.95191 / 0.54 ( 2) hydrogen bonds : bond 0.04503 / 3.02 ( 955) hydrogen bonds : angle 3.99895 / 2.74 ( 2766) Misc. bond : bond 0.00134 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 340 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7763 (mtt90) REVERT: A 144 MET cc_start: 0.7629 (tmm) cc_final: 0.7344 (tpp) REVERT: C 173 MET cc_start: 0.7234 (tpp) cc_final: 0.7020 (mtt) REVERT: D 124 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.6034 (ttpt) REVERT: D 149 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7808 (pt) REVERT: D 237 ASP cc_start: 0.5458 (OUTLIER) cc_final: 0.5226 (m-30) REVERT: F 349 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.6911 (tmt) REVERT: G 98 ILE cc_start: 0.7991 (mt) cc_final: 0.7745 (mt) REVERT: G 145 PHE cc_start: 0.6102 (OUTLIER) cc_final: 0.5148 (p90) REVERT: G 199 GLU cc_start: 0.6117 (tp30) cc_final: 0.5727 (tp30) REVERT: G 311 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7584 (ttp-170) REVERT: K 96 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7730 (ptmm) REVERT: K 230 ASN cc_start: 0.6614 (t160) cc_final: 0.6374 (t160) REVERT: K 322 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5391 (mp) REVERT: K 567 LEU cc_start: 0.5325 (OUTLIER) cc_final: 0.5098 (tp) outliers start: 109 outliers final: 69 residues processed: 415 average time/residue: 0.1700 time to fit residues: 104.1263 Evaluate side-chains 418 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 341 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 311 ARG Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 480 LEU Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 231 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 43 optimal weight: 0.2980 chunk 78 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 204 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 HIS C 244 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 HIS K 210 GLN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 GLN K 558 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131108 restraints weight = 28134.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134104 restraints weight = 16237.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136154 restraints weight = 10736.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137617 restraints weight = 7773.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138648 restraints weight = 6052.122| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21054 Z= 0.181 Angle : 0.605 8.713 28588 Z= 0.317 Chirality : 0.042 0.168 3320 Planarity : 0.005 0.068 3509 Dihedral : 13.280 164.865 3072 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.53 % Favored : 92.26 % Rotamer: Outliers : 5.73 % Allowed : 31.47 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2469 helix: 1.14 (0.16), residues: 1150 sheet: -0.14 (0.24), residues: 491 loop : -2.15 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 178 TYR 0.018 0.001 TYR D 77 PHE 0.031 0.002 PHE F 223 TRP 0.008 0.001 TRP K 529 HIS 0.007 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (21048) covalent geometry : angle 0.60496 / 0.32 (28586) SS BOND : bond 0.00186 / 0.10 ( 1) SS BOND : angle 1.54289 / 0.90 ( 2) hydrogen bonds : bond 0.05791 / 3.87 ( 955) hydrogen bonds : angle 4.13592 / 2.83 ( 2766) Misc. bond : bond 0.00207 / 0.14 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 360 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8009 (mtt90) cc_final: 0.7756 (mtt90) REVERT: A 57 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.5544 (p90) REVERT: A 144 MET cc_start: 0.7592 (tmm) cc_final: 0.7365 (tpp) REVERT: B 83 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6672 (ttp80) REVERT: C 54 MET cc_start: 0.7406 (tpp) cc_final: 0.6845 (tpp) REVERT: C 173 MET cc_start: 0.7338 (tpp) cc_final: 0.7116 (mtt) REVERT: C 250 LYS cc_start: 0.7899 (tmtp) cc_final: 0.7478 (tmtp) REVERT: D 124 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.6152 (ttpt) REVERT: F 40 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: F 155 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7307 (ptt180) REVERT: F 349 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.6955 (tmt) REVERT: G 24 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5929 (mp0) REVERT: G 98 ILE cc_start: 0.7911 (mt) cc_final: 0.7661 (mt) REVERT: G 116 LYS cc_start: 0.8266 (ptmm) cc_final: 0.7887 (ttpp) REVERT: G 199 GLU cc_start: 0.6152 (tp30) cc_final: 0.5750 (tp30) REVERT: K 166 LEU cc_start: 0.5290 (OUTLIER) cc_final: 0.5030 (mt) REVERT: K 221 LYS cc_start: 0.7955 (pttm) cc_final: 0.7750 (pttm) REVERT: K 322 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5634 (mp) outliers start: 127 outliers final: 88 residues processed: 448 average time/residue: 0.1744 time to fit residues: 114.7477 Evaluate side-chains 455 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 358 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 311 ARG Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 148 optimal weight: 0.9990 chunk 242 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 323 GLN F 152 GLN K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.147683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131307 restraints weight = 28212.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134470 restraints weight = 17167.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136717 restraints weight = 11511.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138378 restraints weight = 7579.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139348 restraints weight = 5968.030| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21054 Z= 0.153 Angle : 0.588 9.890 28588 Z= 0.307 Chirality : 0.041 0.180 3320 Planarity : 0.004 0.066 3509 Dihedral : 13.290 166.208 3072 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.01 % Favored : 92.79 % Rotamer: Outliers : 5.46 % Allowed : 32.15 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2469 helix: 1.18 (0.16), residues: 1149 sheet: -0.13 (0.24), residues: 491 loop : -2.16 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 140 TYR 0.016 0.001 TYR E 41 PHE 0.020 0.001 PHE B 36 TRP 0.006 0.001 TRP K 529 HIS 0.007 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (21048) covalent geometry : angle 0.58791 / 0.31 (28586) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 1.19586 / 0.69 ( 2) hydrogen bonds : bond 0.05217 / 3.48 ( 955) hydrogen bonds : angle 4.07773 / 2.79 ( 2766) Misc. bond : bond 0.00242 / 0.18 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 361 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.5783 (OUTLIER) cc_final: 0.5393 (p90) REVERT: A 144 MET cc_start: 0.7552 (tmm) cc_final: 0.7310 (tpp) REVERT: B 83 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6673 (ttp80) REVERT: C 54 MET cc_start: 0.7266 (tpp) cc_final: 0.7031 (tpp) REVERT: C 170 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.5574 (m) REVERT: C 173 MET cc_start: 0.7358 (tpp) cc_final: 0.7117 (mtt) REVERT: C 244 GLN cc_start: 0.6970 (mm-40) cc_final: 0.6723 (mm-40) REVERT: C 250 LYS cc_start: 0.7902 (tmtp) cc_final: 0.7432 (tmtp) REVERT: D 124 LYS cc_start: 0.6404 (OUTLIER) cc_final: 0.6141 (ttpt) REVERT: D 237 ASP cc_start: 0.5530 (OUTLIER) cc_final: 0.5298 (m-30) REVERT: E 233 CYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7213 (t) REVERT: F 155 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7295 (ptt180) REVERT: F 267 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6109 (mt) REVERT: F 349 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.6930 (tmt) REVERT: G 98 ILE cc_start: 0.7849 (mt) cc_final: 0.7634 (mt) REVERT: G 145 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.4680 (p90) REVERT: G 199 GLU cc_start: 0.6098 (tp30) cc_final: 0.5712 (tp30) REVERT: K 221 LYS cc_start: 0.7965 (pttm) cc_final: 0.7748 (pttm) REVERT: K 230 ASN cc_start: 0.6775 (t160) cc_final: 0.6494 (t160) outliers start: 121 outliers final: 90 residues processed: 443 average time/residue: 0.1711 time to fit residues: 111.9549 Evaluate side-chains 458 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 358 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 171 CYS Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 311 ARG Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 326 CYS Chi-restraints excluded: chain K residue 334 ARG Chi-restraints excluded: chain K residue 392 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 240 optimal weight: 0.0570 chunk 89 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 106 ASN F 152 GLN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132731 restraints weight = 28201.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136198 restraints weight = 16893.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138488 restraints weight = 11078.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140343 restraints weight = 7237.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141075 restraints weight = 5577.728| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21054 Z= 0.118 Angle : 0.557 8.339 28588 Z= 0.292 Chirality : 0.040 0.187 3320 Planarity : 0.004 0.062 3509 Dihedral : 13.245 166.843 3072 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.44 % Favored : 93.36 % Rotamer: Outliers : 5.46 % Allowed : 32.51 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2469 helix: 1.30 (0.16), residues: 1145 sheet: -0.11 (0.24), residues: 491 loop : -2.08 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 39 TYR 0.015 0.001 TYR C 274 PHE 0.023 0.001 PHE F 223 TRP 0.015 0.001 TRP G 22 HIS 0.008 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (21048) covalent geometry : angle 0.55699 / 0.29 (28586) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 1.16732 / 0.65 ( 2) hydrogen bonds : bond 0.04409 / 2.95 ( 955) hydrogen bonds : angle 3.97743 / 2.73 ( 2766) Misc. bond : bond 0.00121 / 0.08 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 356 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7806 (mtt90) REVERT: A 144 MET cc_start: 0.7546 (tmm) cc_final: 0.7297 (tpp) REVERT: B 83 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6604 (ttp80) REVERT: C 54 MET cc_start: 0.7229 (tpp) cc_final: 0.6969 (tpp) REVERT: C 173 MET cc_start: 0.7298 (tpp) cc_final: 0.7089 (mtt) REVERT: C 250 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7421 (tmtp) REVERT: D 124 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.6069 (ttpt) REVERT: D 170 GLU cc_start: 0.6661 (mp0) cc_final: 0.6404 (mp0) REVERT: D 237 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.5218 (m-30) REVERT: E 233 CYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7211 (t) REVERT: F 155 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7135 (ptt180) REVERT: F 349 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.6901 (tmt) REVERT: G 98 ILE cc_start: 0.7852 (mt) cc_final: 0.7652 (mt) REVERT: G 145 PHE cc_start: 0.6242 (OUTLIER) cc_final: 0.4607 (p90) REVERT: G 199 GLU cc_start: 0.6086 (tp30) cc_final: 0.5685 (tp30) REVERT: G 311 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7587 (ttp-170) REVERT: K 322 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5524 (mp) outliers start: 121 outliers final: 88 residues processed: 439 average time/residue: 0.1720 time to fit residues: 112.0491 Evaluate side-chains 450 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 352 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 269 HIS Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 311 ARG Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 238 THR Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 334 ARG Chi-restraints excluded: chain K residue 392 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 480 LEU Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 130 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 106 ASN K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.149023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132637 restraints weight = 27848.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135835 restraints weight = 15824.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138034 restraints weight = 10354.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139575 restraints weight = 7448.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140581 restraints weight = 5755.118| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21054 Z= 0.131 Angle : 0.568 8.243 28588 Z= 0.297 Chirality : 0.040 0.209 3320 Planarity : 0.004 0.063 3509 Dihedral : 13.246 166.472 3072 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.80 % Favored : 92.99 % Rotamer: Outliers : 5.09 % Allowed : 33.23 % Favored : 61.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2469 helix: 1.27 (0.16), residues: 1147 sheet: -0.08 (0.24), residues: 491 loop : -2.07 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 178 TYR 0.022 0.001 TYR C 274 PHE 0.017 0.001 PHE B 36 TRP 0.023 0.001 TRP G 22 HIS 0.012 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21048) covalent geometry : angle 0.56767 / 0.30 (28586) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 1.00321 / 0.57 ( 2) hydrogen bonds : bond 0.04597 / 3.09 ( 955) hydrogen bonds : angle 3.97842 / 2.73 ( 2766) Misc. bond : bond 0.00112 / 0.07 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 355 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7783 (mtt90) REVERT: A 144 MET cc_start: 0.7506 (tmm) cc_final: 0.7236 (tpp) REVERT: B 83 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6622 (ttp80) REVERT: C 173 MET cc_start: 0.7342 (tpp) cc_final: 0.7117 (mtt) REVERT: C 250 LYS cc_start: 0.7928 (tmtp) cc_final: 0.7476 (tmtp) REVERT: D 124 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.6118 (ttpt) REVERT: D 170 GLU cc_start: 0.6646 (mp0) cc_final: 0.6398 (mp0) REVERT: D 237 ASP cc_start: 0.5456 (OUTLIER) cc_final: 0.5233 (m-30) REVERT: F 155 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7286 (ptt180) REVERT: F 267 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6097 (mt) REVERT: F 349 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.6930 (tmt) REVERT: G 145 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.4780 (p90) REVERT: K 322 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5484 (mp) outliers start: 113 outliers final: 90 residues processed: 429 average time/residue: 0.1659 time to fit residues: 105.3415 Evaluate side-chains 455 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 357 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 171 CYS Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 HIS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 311 ARG Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 238 THR Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 334 ARG Chi-restraints excluded: chain K residue 392 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 480 LEU Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 196 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 214 optimal weight: 0.2980 chunk 139 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.149962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133865 restraints weight = 27749.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136970 restraints weight = 15956.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139158 restraints weight = 10538.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140605 restraints weight = 7598.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141725 restraints weight = 5881.308| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21054 Z= 0.119 Angle : 0.557 9.476 28588 Z= 0.290 Chirality : 0.040 0.213 3320 Planarity : 0.004 0.062 3509 Dihedral : 13.233 166.211 3070 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.68 % Favored : 93.11 % Rotamer: Outliers : 4.82 % Allowed : 33.63 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2469 helix: 1.34 (0.16), residues: 1140 sheet: -0.05 (0.24), residues: 491 loop : -2.01 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 168 TYR 0.026 0.001 TYR C 274 PHE 0.014 0.001 PHE B 36 TRP 0.016 0.001 TRP G 22 HIS 0.013 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (21048) covalent geometry : angle 0.55736 / 0.29 (28586) SS BOND : bond 0.00114 / 0.06 ( 1) SS BOND : angle 0.95970 / 0.54 ( 2) hydrogen bonds : bond 0.04228 / 2.84 ( 955) hydrogen bonds : angle 3.92506 / 2.70 ( 2766) Misc. bond : bond 0.00103 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 350 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7725 (mtt90) REVERT: A 144 MET cc_start: 0.7495 (tmm) cc_final: 0.7226 (tpp) REVERT: B 83 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6598 (ttp80) REVERT: C 173 MET cc_start: 0.7295 (tpp) cc_final: 0.7091 (mtt) REVERT: C 250 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7470 (tmtp) REVERT: D 124 LYS cc_start: 0.6330 (OUTLIER) cc_final: 0.6093 (ttpt) REVERT: D 170 GLU cc_start: 0.6711 (mp0) cc_final: 0.6429 (mp0) REVERT: D 237 ASP cc_start: 0.5415 (OUTLIER) cc_final: 0.5171 (m-30) REVERT: F 155 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7094 (ptt180) REVERT: F 349 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.6925 (tmt) REVERT: G 98 ILE cc_start: 0.7699 (mt) cc_final: 0.7390 (tp) REVERT: G 145 PHE cc_start: 0.6250 (OUTLIER) cc_final: 0.4695 (p90) REVERT: G 311 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7535 (ttp-170) REVERT: K 322 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5473 (mp) outliers start: 107 outliers final: 90 residues processed: 422 average time/residue: 0.1661 time to fit residues: 103.3230 Evaluate side-chains 446 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 347 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 HIS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 311 ARG Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 208 LYS Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 238 THR Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 334 ARG Chi-restraints excluded: chain K residue 392 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 480 LEU Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 54 optimal weight: 0.4980 chunk 206 optimal weight: 0.0670 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 118 optimal weight: 0.0470 chunk 117 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 220 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 60 GLN K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.151507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135202 restraints weight = 27821.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138429 restraints weight = 16976.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140705 restraints weight = 11212.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142958 restraints weight = 7230.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143211 restraints weight = 5519.634| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21054 Z= 0.109 Angle : 0.553 9.342 28588 Z= 0.287 Chirality : 0.039 0.202 3320 Planarity : 0.004 0.060 3509 Dihedral : 13.215 165.086 3070 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.24 % Favored : 93.60 % Rotamer: Outliers : 4.06 % Allowed : 34.67 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 2469 helix: 1.42 (0.16), residues: 1142 sheet: 0.08 (0.24), residues: 500 loop : -1.98 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 166 TYR 0.020 0.001 TYR E 41 PHE 0.011 0.001 PHE C 263 TRP 0.016 0.001 TRP G 22 HIS 0.012 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (21048) covalent geometry : angle 0.55317 / 0.29 (28586) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 0.88376 / 0.51 ( 2) hydrogen bonds : bond 0.03657 / 2.46 ( 955) hydrogen bonds : angle 3.85554 / 2.65 ( 2766) Misc. bond : bond 0.00084 / 0.05 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 349 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7484 (tmm) cc_final: 0.7220 (tpp) REVERT: B 264 ILE cc_start: 0.6417 (pt) cc_final: 0.6212 (mt) REVERT: C 250 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7419 (tmtp) REVERT: D 124 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.6020 (ttpt) REVERT: D 170 GLU cc_start: 0.6715 (mp0) cc_final: 0.6457 (mp0) REVERT: D 213 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7537 (t0) REVERT: D 237 ASP cc_start: 0.5359 (OUTLIER) cc_final: 0.5101 (m-30) REVERT: E 233 CYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7120 (t) REVERT: F 349 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.6919 (tmt) REVERT: G 98 ILE cc_start: 0.7758 (mt) cc_final: 0.7440 (tp) REVERT: G 145 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.4549 (p90) REVERT: K 96 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7667 (ptmm) REVERT: K 322 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5410 (mp) outliers start: 90 outliers final: 75 residues processed: 412 average time/residue: 0.1697 time to fit residues: 103.6646 Evaluate side-chains 428 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 345 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 171 CYS Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 269 HIS Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 208 LYS Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 334 ARG Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 480 LEU Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 132 optimal weight: 0.1980 chunk 208 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 237 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 102 ASN K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134231 restraints weight = 28020.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137656 restraints weight = 15632.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139955 restraints weight = 10063.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141466 restraints weight = 7180.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.142671 restraints weight = 5529.329| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21054 Z= 0.119 Angle : 0.563 11.139 28588 Z= 0.290 Chirality : 0.040 0.244 3320 Planarity : 0.004 0.061 3509 Dihedral : 13.220 164.321 3070 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.64 % Favored : 93.20 % Rotamer: Outliers : 4.19 % Allowed : 34.17 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 2469 helix: 1.41 (0.16), residues: 1141 sheet: 0.10 (0.24), residues: 500 loop : -1.97 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 72 TYR 0.057 0.001 TYR C 274 PHE 0.014 0.001 PHE C 240 TRP 0.012 0.001 TRP G 22 HIS 0.013 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (21048) covalent geometry : angle 0.56270 / 0.29 (28586) SS BOND : bond 0.00111 / 0.06 ( 1) SS BOND : angle 0.95414 / 0.55 ( 2) hydrogen bonds : bond 0.03892 / 2.62 ( 955) hydrogen bonds : angle 3.86696 / 2.67 ( 2766) Misc. bond : bond 0.00094 / 0.06 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3400.48 seconds wall clock time: 59 minutes 45.42 seconds (3585.42 seconds total)