Starting phenix.real_space_refine on Thu Mar 5 23:10:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qo1_53253/03_2026/9qo1_53253.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qo1_53253/03_2026/9qo1_53253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qo1_53253/03_2026/9qo1_53253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qo1_53253/03_2026/9qo1_53253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qo1_53253/03_2026/9qo1_53253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qo1_53253/03_2026/9qo1_53253.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 6 5.49 5 S 140 5.16 5 C 16124 2.51 5 N 4306 2.21 5 O 4803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25382 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3213 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3305 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 393} Chain breaks: 1 Chain: "C" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2809 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 12, 'TRANS': 337} Chain breaks: 1 Chain: "D" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3067 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain: "E" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2228 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 2 Chain: "F" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2156 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 261} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1694 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1359 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 161} 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: "I" Number of atoms: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4073 Classifications: {'peptide': 509} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 499} Chain breaks: 5 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "J" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 661 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Chain: "P" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 179 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "K" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24268 SG CYS J 75 108.020 73.426 107.989 1.00 76.43 S ATOM 24435 SG CYS J 94 106.926 72.397 103.838 1.00 38.63 S ATOM 24081 SG CYS J 42 112.178 78.301 95.703 1.00 84.85 S ATOM 24339 SG CYS J 83 109.926 80.513 93.869 1.00 60.77 S ATOM 24167 SG CYS J 53 110.540 85.019 91.744 1.00 89.07 S ATOM 24190 SG CYS J 56 110.607 88.751 90.813 1.00101.80 S ATOM 24218 SG CYS J 68 112.247 87.505 94.053 1.00 77.04 S Time building chain proxies: 5.04, per 1000 atoms: 0.20 Number of scatterers: 25382 At special positions: 0 Unit cell: (181.44, 163.08, 182.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 140 16.00 P 6 15.00 O 4803 8.00 N 4306 7.00 C 16124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 77 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 94 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 75 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 83 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 80 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 42 " pdb=" ZN J 203 " pdb="ZN ZN J 203 " - pdb=" ND1 HIS J 82 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 68 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 53 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 56 " Number of angles added : 3 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 10 sheets defined 65.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.758A pdb=" N SER A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.858A pdb=" N TYR A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 155 Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.783A pdb=" N ILE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 removed outlier: 4.385A pdb=" N SER A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 197 through 213 removed outlier: 4.049A pdb=" N MET A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.690A pdb=" N LEU A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 225 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.768A pdb=" N ALA A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.708A pdb=" N VAL A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 313 through 322 removed outlier: 4.024A pdb=" N LEU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.668A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.524A pdb=" N CYS A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 362 through 379 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.521A pdb=" N LEU A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 457 Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 51 through 61 removed outlier: 4.141A pdb=" N GLN B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.913A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.830A pdb=" N TYR B 98 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.737A pdb=" N ILE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 140 removed outlier: 4.187A pdb=" N GLU B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 removed outlier: 3.654A pdb=" N ARG B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.742A pdb=" N ILE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.691A pdb=" N MET B 234 " --> pdb=" O HIS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 269 removed outlier: 3.797A pdb=" N THR B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.996A pdb=" N CYS B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 324 through 333 Processing helix chain 'B' and resid 347 through 363 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 418 through 440 removed outlier: 3.520A pdb=" N THR B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 65 Processing helix chain 'C' and resid 73 through 89 removed outlier: 4.708A pdb=" N ASN C 89 " --> pdb=" O ILE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 4.313A pdb=" N ALA C 96 " --> pdb=" O HIS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 130 removed outlier: 4.519A pdb=" N ILE C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 155 through 162 removed outlier: 3.516A pdb=" N ALA C 158 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.091A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 removed outlier: 3.671A pdb=" N ALA C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 235 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.751A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 269 removed outlier: 3.852A pdb=" N HIS C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 293 through 311 removed outlier: 3.696A pdb=" N THR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 329 through 345 removed outlier: 4.453A pdb=" N GLU C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 399 removed outlier: 3.659A pdb=" N ASN C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 397 " --> pdb=" O MET C 393 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 399 " --> pdb=" O GLN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 407 Processing helix chain 'D' and resid 24 through 36 Processing helix chain 'D' and resid 38 through 52 removed outlier: 4.268A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 80 through 93 removed outlier: 3.577A pdb=" N ILE D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 removed outlier: 6.058A pdb=" N ILE D 97 " --> pdb=" O PRO D 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 98 " --> pdb=" O ARG D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 117 removed outlier: 3.646A pdb=" N GLN D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 117 " --> pdb=" O ILE D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 129 Processing helix chain 'D' and resid 140 through 157 removed outlier: 3.760A pdb=" N LYS D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.766A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 removed outlier: 3.587A pdb=" N GLN D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 219 through 236 removed outlier: 3.664A pdb=" N LEU D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 252 Processing helix chain 'D' and resid 253 through 257 removed outlier: 3.929A pdb=" N GLN D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 257' Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.529A pdb=" N LEU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.595A pdb=" N ALA D 283 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.833A pdb=" N ALA D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 331 through 345 removed outlier: 3.708A pdb=" N GLU D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 390 removed outlier: 3.615A pdb=" N THR D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 401 removed outlier: 3.697A pdb=" N GLU D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 43 removed outlier: 3.734A pdb=" N LYS E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 70 Processing helix chain 'E' and resid 110 through 125 removed outlier: 3.778A pdb=" N ALA E 118 " --> pdb=" O TYR E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 removed outlier: 3.620A pdb=" N ASN E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN E 160 " --> pdb=" O MET E 156 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'E' and resid 231 through 241 removed outlier: 3.543A pdb=" N ARG E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 283 removed outlier: 3.792A pdb=" N GLY E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 329 Processing helix chain 'F' and resid 44 through 62 removed outlier: 4.034A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.753A pdb=" N TYR F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 removed outlier: 3.879A pdb=" N ILE F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 204 Processing helix chain 'F' and resid 218 through 248 removed outlier: 3.687A pdb=" N ARG F 234 " --> pdb=" O MET F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.884A pdb=" N LEU F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 312 removed outlier: 3.950A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 19 Processing helix chain 'G' and resid 26 through 36 removed outlier: 4.036A pdb=" N GLU G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 removed outlier: 3.628A pdb=" N GLN G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 61 through 73 removed outlier: 3.870A pdb=" N GLN G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 89 through 108 removed outlier: 4.089A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.677A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 222 removed outlier: 3.792A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 27 Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.538A pdb=" N TYR H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 60 Processing helix chain 'H' and resid 61 through 68 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.520A pdb=" N GLY H 73 " --> pdb=" O SER H 69 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 4.033A pdb=" N ASN H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 Processing helix chain 'H' and resid 130 through 137 Processing helix chain 'H' and resid 140 through 147 Processing helix chain 'H' and resid 148 through 152 Processing helix chain 'H' and resid 196 through 209 removed outlier: 3.504A pdb=" N LEU H 200 " --> pdb=" O GLN H 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 251 removed outlier: 3.606A pdb=" N ALA I 238 " --> pdb=" O SER I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 279 Processing helix chain 'I' and resid 283 through 309 removed outlier: 3.705A pdb=" N LYS I 298 " --> pdb=" O VAL I 294 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU I 301 " --> pdb=" O GLU I 297 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE I 302 " --> pdb=" O LYS I 298 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN I 308 " --> pdb=" O HIS I 304 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 315 removed outlier: 4.017A pdb=" N ALA I 313 " --> pdb=" O ASN I 309 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP I 314 " --> pdb=" O LEU I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 327 removed outlier: 5.660A pdb=" N ASN I 324 " --> pdb=" O GLY I 320 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU I 325 " --> pdb=" O ARG I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 353 removed outlier: 4.211A pdb=" N GLY I 334 " --> pdb=" O GLN I 330 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU I 335 " --> pdb=" O ASP I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 385 removed outlier: 3.772A pdb=" N VAL I 370 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE I 385 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 411 removed outlier: 3.634A pdb=" N LEU I 395 " --> pdb=" O PHE I 391 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP I 396 " --> pdb=" O VAL I 392 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 398 " --> pdb=" O ALA I 394 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS I 399 " --> pdb=" O LEU I 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY I 400 " --> pdb=" O ASP I 396 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG I 401 " --> pdb=" O LYS I 397 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE I 403 " --> pdb=" O CYS I 399 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN I 404 " --> pdb=" O GLY I 400 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN I 406 " --> pdb=" O PHE I 402 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA I 407 " --> pdb=" O ILE I 403 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS I 410 " --> pdb=" O ASN I 406 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET I 411 " --> pdb=" O ALA I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 417 through 429 Processing helix chain 'I' and resid 438 through 454 Processing helix chain 'I' and resid 458 through 476 removed outlier: 4.157A pdb=" N PHE I 462 " --> pdb=" O ASP I 458 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS I 468 " --> pdb=" O LYS I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 496 removed outlier: 3.768A pdb=" N GLU I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA I 486 " --> pdb=" O ASP I 482 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN I 494 " --> pdb=" O SER I 490 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA I 495 " --> pdb=" O LYS I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 502 removed outlier: 3.508A pdb=" N THR I 501 " --> pdb=" O GLY I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 504 through 526 removed outlier: 3.987A pdb=" N LYS I 515 " --> pdb=" O ILE I 511 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR I 526 " --> pdb=" O LYS I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 556 through 558 No H-bonds generated for 'chain 'I' and resid 556 through 558' Processing helix chain 'I' and resid 559 through 574 removed outlier: 4.014A pdb=" N TYR I 563 " --> pdb=" O LEU I 559 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 616 Processing helix chain 'I' and resid 621 through 630 removed outlier: 3.923A pdb=" N LEU I 625 " --> pdb=" O THR I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 632 through 646 removed outlier: 4.933A pdb=" N GLN I 638 " --> pdb=" O ASP I 634 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL I 639 " --> pdb=" O ILE I 635 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER I 646 " --> pdb=" O ILE I 642 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 722 removed outlier: 3.679A pdb=" N GLN I 712 " --> pdb=" O LYS I 708 " (cutoff:3.500A) Processing helix chain 'I' and resid 727 through 736 Processing helix chain 'I' and resid 745 through 759 Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 81 through 88 Processing helix chain 'K' and resid 22 through 35 removed outlier: 4.101A pdb=" N LYS K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 removed outlier: 3.524A pdb=" N TYR K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.159A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 411 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 408 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN H 154 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 54 through 58 removed outlier: 7.129A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER E 58 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N PHE E 96 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU E 82 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER E 95 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU E 80 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA E 97 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N MET E 78 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY E 184 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LEU E 183 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL E 226 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA E 185 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 187 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR E 222 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS E 55 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE E 229 " --> pdb=" O CYS E 55 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE E 57 " --> pdb=" O PHE E 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 185 through 186 removed outlier: 4.269A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE F 151 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP F 124 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LEU F 154 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR F 126 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY F 123 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA F 71 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER F 86 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE F 73 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL F 41 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 110 through 112 removed outlier: 6.741A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 535 through 541 removed outlier: 9.342A pdb=" N VAL J 24 " --> pdb=" O GLY I 588 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N GLY I 588 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N LYS J 26 " --> pdb=" O SER I 586 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N SER I 586 " --> pdb=" O LYS J 26 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N ASN J 28 " --> pdb=" O GLN I 584 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLN I 584 " --> pdb=" O ASN J 28 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL J 30 " --> pdb=" O LEU I 582 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR I 600 " --> pdb=" O LEU I 680 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 619 through 620 removed outlier: 3.865A pdb=" N TYR I 620 " --> pdb=" O ILE I 669 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 725 through 726 Processing sheet with id=AA8, first strand: chain 'J' and resid 70 through 71 Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16 Processing sheet with id=AB1, first strand: chain 'K' and resid 44 through 45 1421 hydrogen bonds defined for protein. 4176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8297 1.34 - 1.46: 5310 1.46 - 1.58: 11989 1.58 - 1.70: 6 1.70 - 1.82: 222 Bond restraints: 25824 Sorted by residual: bond pdb=" C LYS A 343 " pdb=" N MET A 344 " ideal model delta sigma weight residual 1.335 1.447 -0.112 1.36e-02 5.41e+03 6.77e+01 bond pdb=" C THR A 102 " pdb=" N ARG A 103 " ideal model delta sigma weight residual 1.335 1.264 0.071 1.30e-02 5.92e+03 3.02e+01 bond pdb=" CA TYR A 47 " pdb=" C TYR A 47 " ideal model delta sigma weight residual 1.524 1.466 0.057 1.32e-02 5.74e+03 1.89e+01 bond pdb=" C LEU A 353 " pdb=" N LEU A 354 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.49e-02 4.50e+03 1.27e+01 bond pdb=" O12 IHP B 501 " pdb=" P2 IHP B 501 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 25819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 34799 4.37 - 8.73: 66 8.73 - 13.10: 2 13.10 - 17.46: 1 17.46 - 21.83: 2 Bond angle restraints: 34870 Sorted by residual: angle pdb=" CA THR A 102 " pdb=" C THR A 102 " pdb=" N ARG A 103 " ideal model delta sigma weight residual 116.92 95.09 21.83 1.16e+00 7.43e-01 3.54e+02 angle pdb=" O THR A 102 " pdb=" C THR A 102 " pdb=" N ARG A 103 " ideal model delta sigma weight residual 122.03 139.00 -16.97 1.04e+00 9.25e-01 2.66e+02 angle pdb=" C THR A 102 " pdb=" N ARG A 103 " pdb=" CA ARG A 103 " ideal model delta sigma weight residual 120.38 98.82 21.56 1.37e+00 5.33e-01 2.48e+02 angle pdb=" N GLN G 93 " pdb=" CA GLN G 93 " pdb=" C GLN G 93 " ideal model delta sigma weight residual 111.82 104.45 7.37 1.16e+00 7.43e-01 4.04e+01 angle pdb=" N TYR A 47 " pdb=" CA TYR A 47 " pdb=" CB TYR A 47 " ideal model delta sigma weight residual 110.20 102.14 8.06 1.49e+00 4.50e-01 2.93e+01 ... (remaining 34865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13273 17.99 - 35.98: 1777 35.98 - 53.97: 542 53.97 - 71.96: 135 71.96 - 89.95: 47 Dihedral angle restraints: 15774 sinusoidal: 6431 harmonic: 9343 Sorted by residual: dihedral pdb=" N TYR A 47 " pdb=" C TYR A 47 " pdb=" CA TYR A 47 " pdb=" CB TYR A 47 " ideal model delta harmonic sigma weight residual 122.80 108.52 14.28 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" CA MET A 454 " pdb=" C MET A 454 " pdb=" N LEU A 455 " pdb=" CA LEU A 455 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA HIS A 197 " pdb=" C HIS A 197 " pdb=" N VAL A 198 " pdb=" CA VAL A 198 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 15771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3661 0.071 - 0.142: 269 0.142 - 0.213: 13 0.213 - 0.284: 1 0.284 - 0.355: 1 Chirality restraints: 3945 Sorted by residual: chirality pdb=" CA TYR A 47 " pdb=" N TYR A 47 " pdb=" C TYR A 47 " pdb=" CB TYR A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C3 IHP B 501 " pdb=" C2 IHP B 501 " pdb=" C4 IHP B 501 " pdb=" O13 IHP B 501 " both_signs ideal model delta sigma weight residual False -2.34 -2.58 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL I 622 " pdb=" N VAL I 622 " pdb=" C VAL I 622 " pdb=" CB VAL I 622 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3942 not shown) Planarity restraints: 4445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 102 " -0.026 2.00e-02 2.50e+03 7.15e-02 5.11e+01 pdb=" C THR A 102 " 0.123 2.00e-02 2.50e+03 pdb=" O THR A 102 " -0.053 2.00e-02 2.50e+03 pdb=" N ARG A 103 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 250 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO F 251 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO F 251 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 251 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 280 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 281 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.035 5.00e-02 4.00e+02 ... (remaining 4442 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 681 2.70 - 3.25: 25478 3.25 - 3.80: 37903 3.80 - 4.35: 47790 4.35 - 4.90: 80607 Nonbonded interactions: 192459 Sorted by model distance: nonbonded pdb=" O35 IHP B 501 " pdb=" O46 IHP B 501 " model vdw 2.145 3.040 nonbonded pdb=" O12 IHP B 501 " pdb=" O31 IHP B 501 " model vdw 2.191 3.040 nonbonded pdb=" N GLN D 102 " pdb=" OE1 GLN D 102 " model vdw 2.206 3.120 nonbonded pdb=" OE2 GLU B 164 " pdb=" N LYS B 167 " model vdw 2.214 3.120 nonbonded pdb=" O TYR C 227 " pdb=" OG SER C 231 " model vdw 2.219 3.040 ... (remaining 192454 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 22.070 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.004 0.270 25836 Z= 0.258 Angle : 0.653 21.827 34873 Z= 0.380 Chirality : 0.038 0.355 3945 Planarity : 0.004 0.078 4445 Dihedral : 18.691 89.950 9702 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.01 % Allowed : 26.00 % Favored : 71.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3108 helix: 1.49 (0.12), residues: 1904 sheet: -1.27 (0.40), residues: 168 loop : -2.05 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 461 TYR 0.018 0.001 TYR I 228 PHE 0.026 0.001 PHE B 131 TRP 0.022 0.001 TRP J 27 HIS 0.010 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00338 (25824) covalent geometry : angle 0.65270 (34870) hydrogen bonds : bond 0.15989 ( 1421) hydrogen bonds : angle 5.43199 ( 4176) metal coordination : bond 0.00278 ( 10) metal coordination : angle 1.10163 ( 3) Misc. bond : bond 0.20993 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 678 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7155 (t80) REVERT: A 93 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7334 (mm-30) REVERT: A 96 ARG cc_start: 0.6988 (ttp-110) cc_final: 0.6328 (ttp-110) REVERT: A 100 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7713 (mp0) REVERT: B 36 TYR cc_start: 0.7820 (m-10) cc_final: 0.7513 (m-10) REVERT: B 124 GLN cc_start: 0.8033 (tt0) cc_final: 0.7755 (tt0) REVERT: B 201 GLU cc_start: 0.6925 (pp20) cc_final: 0.6597 (pp20) REVERT: B 260 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7787 (mm-30) REVERT: B 344 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7782 (mtt90) REVERT: B 364 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8130 (ttpp) REVERT: B 402 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8206 (mt) REVERT: B 425 ASP cc_start: 0.8010 (m-30) cc_final: 0.7680 (m-30) REVERT: C 192 TYR cc_start: 0.8328 (m-80) cc_final: 0.8109 (m-80) REVERT: C 223 SER cc_start: 0.8394 (t) cc_final: 0.7724 (m) REVERT: C 252 PHE cc_start: 0.8592 (m-80) cc_final: 0.8034 (m-80) REVERT: C 318 SER cc_start: 0.8308 (m) cc_final: 0.8038 (p) REVERT: C 324 SER cc_start: 0.8678 (t) cc_final: 0.8401 (m) REVERT: C 325 ARG cc_start: 0.7593 (mmt-90) cc_final: 0.7309 (mmt180) REVERT: C 378 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: C 396 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 405 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 105 SER cc_start: 0.8249 (m) cc_final: 0.8008 (t) REVERT: D 182 GLN cc_start: 0.8207 (mp10) cc_final: 0.7810 (mp10) REVERT: D 203 GLU cc_start: 0.7588 (mp0) cc_final: 0.7269 (mp0) REVERT: D 245 MET cc_start: 0.8253 (mmm) cc_final: 0.7850 (mmm) REVERT: D 394 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7864 (mt-10) REVERT: D 400 MET cc_start: 0.8079 (mpp) cc_final: 0.7250 (mpp) REVERT: E 51 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7695 (t80) REVERT: E 70 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8242 (ttm-80) REVERT: E 86 ASP cc_start: 0.7272 (t0) cc_final: 0.6954 (t0) REVERT: E 93 MET cc_start: 0.8627 (mtt) cc_final: 0.8199 (mmm) REVERT: E 158 ASN cc_start: 0.8006 (m-40) cc_final: 0.7729 (m-40) REVERT: F 43 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6863 (tp) REVERT: F 102 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7483 (mmtt) REVERT: F 139 HIS cc_start: 0.7427 (t70) cc_final: 0.7119 (t-90) REVERT: F 186 LEU cc_start: 0.8188 (mt) cc_final: 0.7772 (mt) REVERT: F 234 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7140 (mtm-85) REVERT: F 243 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7706 (mtmt) REVERT: F 255 GLU cc_start: 0.7322 (pt0) cc_final: 0.7022 (pt0) REVERT: F 302 MET cc_start: 0.8071 (ttt) cc_final: 0.7734 (ttm) REVERT: G 129 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7271 (mt-10) REVERT: G 182 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7659 (mm-30) REVERT: G 189 GLU cc_start: 0.7901 (tt0) cc_final: 0.7579 (tt0) REVERT: G 194 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7001 (ttt-90) REVERT: H 146 LYS cc_start: 0.8408 (mttt) cc_final: 0.7999 (mttt) REVERT: H 202 ASP cc_start: 0.7805 (t70) cc_final: 0.7460 (m-30) REVERT: I 273 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7893 (mtt-85) REVERT: I 275 VAL cc_start: 0.7356 (m) cc_final: 0.7123 (p) REVERT: I 285 ASP cc_start: 0.7975 (p0) cc_final: 0.6857 (m-30) REVERT: I 312 ASP cc_start: 0.7689 (t0) cc_final: 0.7484 (t0) REVERT: I 337 LYS cc_start: 0.8385 (mppt) cc_final: 0.8107 (mmtm) REVERT: I 385 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: I 424 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7535 (mtt180) REVERT: I 427 ASP cc_start: 0.7563 (t0) cc_final: 0.7200 (t0) REVERT: I 444 ASP cc_start: 0.6600 (p0) cc_final: 0.6356 (p0) REVERT: I 469 MET cc_start: 0.6007 (mmt) cc_final: 0.5458 (mmt) REVERT: I 472 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7935 (mmtm) REVERT: I 483 ASP cc_start: 0.7304 (t0) cc_final: 0.7020 (t0) REVERT: I 494 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: I 624 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5525 (mp10) REVERT: I 750 LYS cc_start: 0.7063 (tppt) cc_final: 0.6416 (tppt) REVERT: I 752 CYS cc_start: 0.8265 (m) cc_final: 0.7911 (m) REVERT: I 754 ASP cc_start: 0.7214 (m-30) cc_final: 0.6787 (m-30) REVERT: J 101 TRP cc_start: 0.8430 (t-100) cc_final: 0.7006 (t-100) REVERT: K 33 LYS cc_start: 0.8213 (mmmm) cc_final: 0.8009 (mmmm) outliers start: 83 outliers final: 54 residues processed: 725 average time/residue: 0.1778 time to fit residues: 197.7239 Evaluate side-chains 714 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 650 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 298 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 194 ARG Chi-restraints excluded: chain G residue 201 ASN Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 494 GLN Chi-restraints excluded: chain I residue 522 LYS Chi-restraints excluded: chain I residue 527 ASN Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 569 PHE Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 602 GLN Chi-restraints excluded: chain I residue 624 GLN Chi-restraints excluded: chain I residue 633 MET Chi-restraints excluded: chain I residue 648 LEU Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain P residue 53 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0070 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 HIS I 574 HIS J 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123590 restraints weight = 41752.287| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.31 r_work: 0.3487 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25836 Z= 0.164 Angle : 0.587 8.178 34873 Z= 0.309 Chirality : 0.041 0.233 3945 Planarity : 0.004 0.067 4445 Dihedral : 7.521 78.818 3570 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 4.92 % Allowed : 23.39 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3108 helix: 1.54 (0.12), residues: 1915 sheet: -1.03 (0.41), residues: 166 loop : -2.01 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 461 TYR 0.031 0.002 TYR A 152 PHE 0.021 0.002 PHE D 48 TRP 0.022 0.002 TRP J 27 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00367 (25824) covalent geometry : angle 0.58634 (34870) hydrogen bonds : bond 0.05517 ( 1421) hydrogen bonds : angle 4.37391 ( 4176) metal coordination : bond 0.00806 ( 10) metal coordination : angle 1.98384 ( 3) Misc. bond : bond 0.00594 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 668 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.6875 (ttm) cc_final: 0.6574 (ttm) REVERT: A 93 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 96 ARG cc_start: 0.6985 (ttp-110) cc_final: 0.6626 (ttp-110) REVERT: A 100 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 201 MET cc_start: 0.7602 (tmm) cc_final: 0.7350 (ppp) REVERT: B 201 GLU cc_start: 0.7172 (pp20) cc_final: 0.6677 (pp20) REVERT: B 252 GLU cc_start: 0.8177 (tp30) cc_final: 0.7939 (tp30) REVERT: B 260 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7853 (mm-30) REVERT: B 344 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7796 (mtt90) REVERT: B 364 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8231 (ttpp) REVERT: B 425 ASP cc_start: 0.7971 (m-30) cc_final: 0.7642 (m-30) REVERT: C 81 VAL cc_start: 0.7745 (t) cc_final: 0.7538 (m) REVERT: C 138 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7848 (tp) REVERT: C 223 SER cc_start: 0.8458 (t) cc_final: 0.7752 (m) REVERT: C 318 SER cc_start: 0.8305 (m) cc_final: 0.8048 (p) REVERT: C 324 SER cc_start: 0.8830 (t) cc_final: 0.8585 (m) REVERT: C 325 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7543 (mmt180) REVERT: C 378 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: C 396 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 405 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7627 (tm-30) REVERT: D 31 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6236 (pp20) REVERT: D 102 GLN cc_start: 0.7770 (mp10) cc_final: 0.7444 (mt0) REVERT: D 105 SER cc_start: 0.8265 (m) cc_final: 0.8033 (t) REVERT: D 182 GLN cc_start: 0.8339 (mp10) cc_final: 0.7979 (mp10) REVERT: D 203 GLU cc_start: 0.7876 (mp0) cc_final: 0.7588 (mp0) REVERT: D 245 MET cc_start: 0.8272 (mmm) cc_final: 0.7929 (mmm) REVERT: D 354 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: D 387 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8052 (tttt) REVERT: D 394 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7998 (mt-10) REVERT: D 400 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7452 (mpp) REVERT: E 51 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7768 (t80) REVERT: E 93 MET cc_start: 0.8716 (mtt) cc_final: 0.8356 (mmm) REVERT: E 158 ASN cc_start: 0.7990 (m-40) cc_final: 0.7700 (m110) REVERT: E 163 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.5337 (tm-30) REVERT: E 275 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: F 102 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7557 (mmtt) REVERT: F 139 HIS cc_start: 0.7326 (t70) cc_final: 0.6987 (t-90) REVERT: F 186 LEU cc_start: 0.8331 (mt) cc_final: 0.7969 (mt) REVERT: F 234 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7941 (mtt-85) REVERT: F 243 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7948 (mtmt) REVERT: F 302 MET cc_start: 0.8032 (ttm) cc_final: 0.7616 (ttm) REVERT: G 129 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7452 (mt-10) REVERT: G 182 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7834 (mm-30) REVERT: G 189 GLU cc_start: 0.8121 (tt0) cc_final: 0.7823 (tt0) REVERT: H 146 LYS cc_start: 0.8525 (mttt) cc_final: 0.8088 (mttt) REVERT: H 202 ASP cc_start: 0.7914 (t70) cc_final: 0.7687 (m-30) REVERT: I 241 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7929 (pp20) REVERT: I 273 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.8073 (mtt-85) REVERT: I 275 VAL cc_start: 0.7457 (m) cc_final: 0.7238 (p) REVERT: I 285 ASP cc_start: 0.7781 (p0) cc_final: 0.7477 (p0) REVERT: I 312 ASP cc_start: 0.7647 (t0) cc_final: 0.7381 (t0) REVERT: I 337 LYS cc_start: 0.8350 (mppt) cc_final: 0.8068 (mptt) REVERT: I 424 ARG cc_start: 0.7964 (mtt180) cc_final: 0.7598 (mtt180) REVERT: I 427 ASP cc_start: 0.7618 (t0) cc_final: 0.7295 (t0) REVERT: I 444 ASP cc_start: 0.6757 (p0) cc_final: 0.6511 (p0) REVERT: I 450 MET cc_start: 0.7742 (tmm) cc_final: 0.7391 (tmm) REVERT: I 469 MET cc_start: 0.6070 (mmt) cc_final: 0.5507 (mmt) REVERT: I 483 ASP cc_start: 0.7395 (t0) cc_final: 0.7173 (t0) REVERT: I 494 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7216 (mp10) REVERT: I 540 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8351 (mt) REVERT: I 573 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7795 (ttm-80) REVERT: I 620 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5925 (t80) REVERT: I 624 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5565 (mp10) REVERT: I 750 LYS cc_start: 0.7254 (tppt) cc_final: 0.6728 (tppt) REVERT: I 752 CYS cc_start: 0.8305 (m) cc_final: 0.7974 (m) REVERT: I 754 ASP cc_start: 0.7203 (m-30) cc_final: 0.6816 (m-30) REVERT: J 101 TRP cc_start: 0.8457 (t-100) cc_final: 0.7121 (t-100) outliers start: 136 outliers final: 82 residues processed: 750 average time/residue: 0.1710 time to fit residues: 197.9694 Evaluate side-chains 735 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 638 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 275 GLN Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 494 GLN Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 569 PHE Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 620 TYR Chi-restraints excluded: chain I residue 624 GLN Chi-restraints excluded: chain I residue 625 LEU Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain J residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 27 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 129 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS C 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.145657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122521 restraints weight = 42087.758| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.32 r_work: 0.3479 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25836 Z= 0.181 Angle : 0.579 8.413 34873 Z= 0.306 Chirality : 0.042 0.247 3945 Planarity : 0.004 0.068 4445 Dihedral : 6.695 65.679 3506 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 5.79 % Allowed : 23.53 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3108 helix: 1.46 (0.12), residues: 1929 sheet: -0.93 (0.42), residues: 166 loop : -2.08 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 461 TYR 0.047 0.002 TYR A 152 PHE 0.035 0.002 PHE A 280 TRP 0.023 0.002 TRP H 82 HIS 0.005 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00414 (25824) covalent geometry : angle 0.57921 (34870) hydrogen bonds : bond 0.05475 ( 1421) hydrogen bonds : angle 4.25230 ( 4176) metal coordination : bond 0.01004 ( 10) metal coordination : angle 1.75817 ( 3) Misc. bond : bond 0.00143 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 656 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.6935 (ttm) cc_final: 0.6641 (ttm) REVERT: A 93 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 96 ARG cc_start: 0.6957 (ttp-110) cc_final: 0.6558 (ttp-110) REVERT: A 100 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7693 (mt-10) REVERT: A 201 MET cc_start: 0.7506 (tmm) cc_final: 0.7277 (ppp) REVERT: A 401 GLU cc_start: 0.7457 (tt0) cc_final: 0.7232 (tt0) REVERT: B 201 GLU cc_start: 0.7214 (pp20) cc_final: 0.6992 (pp20) REVERT: B 252 GLU cc_start: 0.8177 (tp30) cc_final: 0.7927 (tp30) REVERT: B 260 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7864 (mm-30) REVERT: B 266 ASP cc_start: 0.7954 (t0) cc_final: 0.7680 (t0) REVERT: B 323 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8369 (mt) REVERT: B 344 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7784 (mtt90) REVERT: B 364 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8248 (ttpp) REVERT: B 425 ASP cc_start: 0.7958 (m-30) cc_final: 0.7635 (m-30) REVERT: C 81 VAL cc_start: 0.7741 (t) cc_final: 0.7513 (m) REVERT: C 108 THR cc_start: 0.6865 (OUTLIER) cc_final: 0.6403 (t) REVERT: C 223 SER cc_start: 0.8496 (t) cc_final: 0.7789 (m) REVERT: C 318 SER cc_start: 0.8296 (m) cc_final: 0.7847 (p) REVERT: C 321 ASP cc_start: 0.7430 (m-30) cc_final: 0.7121 (m-30) REVERT: C 324 SER cc_start: 0.8816 (t) cc_final: 0.8581 (m) REVERT: C 325 ARG cc_start: 0.7952 (mmt-90) cc_final: 0.7523 (mmt180) REVERT: C 341 MET cc_start: 0.7949 (mmm) cc_final: 0.7608 (mtt) REVERT: C 377 ASP cc_start: 0.7589 (m-30) cc_final: 0.7346 (m-30) REVERT: C 378 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: C 396 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8074 (tm-30) REVERT: C 405 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 31 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6246 (pp20) REVERT: D 105 SER cc_start: 0.8365 (m) cc_final: 0.8084 (t) REVERT: D 117 GLU cc_start: 0.7514 (tt0) cc_final: 0.7017 (tm-30) REVERT: D 167 TYR cc_start: 0.7753 (m-80) cc_final: 0.7228 (m-80) REVERT: D 182 GLN cc_start: 0.8348 (mp10) cc_final: 0.8001 (mp10) REVERT: D 245 MET cc_start: 0.8250 (mmm) cc_final: 0.7832 (mmm) REVERT: D 387 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8051 (tttt) REVERT: D 394 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7989 (mt-10) REVERT: D 400 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7237 (mpp) REVERT: E 51 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7789 (t80) REVERT: E 93 MET cc_start: 0.8746 (mtt) cc_final: 0.8513 (mtt) REVERT: E 129 ARG cc_start: 0.8545 (mmp80) cc_final: 0.8214 (mmt-90) REVERT: E 158 ASN cc_start: 0.7969 (m-40) cc_final: 0.7705 (m110) REVERT: E 163 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.5390 (tm-30) REVERT: E 212 GLU cc_start: 0.7130 (tp30) cc_final: 0.6818 (tp30) REVERT: E 226 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7911 (p) REVERT: E 237 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8294 (mm) REVERT: E 275 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: F 102 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7602 (mmmt) REVERT: F 139 HIS cc_start: 0.7376 (t70) cc_final: 0.7055 (t-90) REVERT: F 186 LEU cc_start: 0.8298 (mt) cc_final: 0.7939 (mt) REVERT: F 194 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7252 (mm-30) REVERT: F 243 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7971 (mtmt) REVERT: F 302 MET cc_start: 0.8344 (ttm) cc_final: 0.7932 (ttm) REVERT: G 23 SER cc_start: 0.7200 (OUTLIER) cc_final: 0.6877 (t) REVERT: G 182 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7854 (mm-30) REVERT: G 189 GLU cc_start: 0.8112 (tt0) cc_final: 0.7872 (tt0) REVERT: H 146 LYS cc_start: 0.8530 (mttt) cc_final: 0.8165 (mttt) REVERT: H 202 ASP cc_start: 0.7900 (t70) cc_final: 0.7677 (m-30) REVERT: I 273 ARG cc_start: 0.8422 (mtt-85) cc_final: 0.8170 (mtt-85) REVERT: I 275 VAL cc_start: 0.7351 (m) cc_final: 0.7149 (p) REVERT: I 285 ASP cc_start: 0.7846 (p0) cc_final: 0.7531 (p0) REVERT: I 312 ASP cc_start: 0.7628 (t0) cc_final: 0.7383 (t0) REVERT: I 337 LYS cc_start: 0.8367 (mppt) cc_final: 0.7966 (mmtm) REVERT: I 424 ARG cc_start: 0.7964 (mtt180) cc_final: 0.7597 (mtt180) REVERT: I 427 ASP cc_start: 0.7650 (t0) cc_final: 0.7332 (t0) REVERT: I 444 ASP cc_start: 0.6761 (p0) cc_final: 0.6539 (p0) REVERT: I 450 MET cc_start: 0.7714 (tmm) cc_final: 0.7369 (tmm) REVERT: I 469 MET cc_start: 0.6106 (mmt) cc_final: 0.5583 (mmt) REVERT: I 472 LYS cc_start: 0.8351 (mtpt) cc_final: 0.8024 (mmtm) REVERT: I 483 ASP cc_start: 0.7430 (t0) cc_final: 0.7221 (t0) REVERT: I 494 GLN cc_start: 0.7773 (tp40) cc_final: 0.7239 (mp10) REVERT: I 540 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8405 (mt) REVERT: I 624 GLN cc_start: 0.6272 (OUTLIER) cc_final: 0.5229 (mp10) REVERT: I 750 LYS cc_start: 0.7166 (tppt) cc_final: 0.6836 (tptp) REVERT: I 752 CYS cc_start: 0.8301 (m) cc_final: 0.7996 (m) REVERT: I 754 ASP cc_start: 0.7188 (m-30) cc_final: 0.6962 (m-30) REVERT: J 101 TRP cc_start: 0.8438 (t-100) cc_final: 0.6965 (t-100) REVERT: J 102 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7650 (mm-30) outliers start: 160 outliers final: 108 residues processed: 754 average time/residue: 0.1715 time to fit residues: 199.7443 Evaluate side-chains 762 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 640 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 275 GLN Chi-restraints excluded: chain E residue 298 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 569 PHE Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 624 GLN Chi-restraints excluded: chain I residue 625 LEU Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain K residue 36 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 290 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 203 optimal weight: 0.0570 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 HIS ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.147535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124530 restraints weight = 41758.580| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.31 r_work: 0.3504 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25836 Z= 0.131 Angle : 0.560 13.283 34873 Z= 0.290 Chirality : 0.040 0.244 3945 Planarity : 0.004 0.069 4445 Dihedral : 6.342 68.059 3496 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 5.32 % Allowed : 24.40 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3108 helix: 1.57 (0.12), residues: 1936 sheet: -0.73 (0.42), residues: 169 loop : -2.05 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 461 TYR 0.021 0.001 TYR I 228 PHE 0.038 0.002 PHE I 251 TRP 0.020 0.002 TRP A 130 HIS 0.011 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00287 (25824) covalent geometry : angle 0.55940 (34870) hydrogen bonds : bond 0.04720 ( 1421) hydrogen bonds : angle 4.09210 ( 4176) metal coordination : bond 0.00520 ( 10) metal coordination : angle 1.41025 ( 3) Misc. bond : bond 0.00093 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 663 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.6877 (ttm) cc_final: 0.6669 (ttm) REVERT: A 93 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 96 ARG cc_start: 0.6921 (ttp-110) cc_final: 0.6533 (ttp-110) REVERT: A 100 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 201 MET cc_start: 0.7593 (tmm) cc_final: 0.7236 (ppp) REVERT: B 201 GLU cc_start: 0.7214 (pp20) cc_final: 0.6955 (pp20) REVERT: B 252 GLU cc_start: 0.8150 (tp30) cc_final: 0.7890 (tp30) REVERT: B 260 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7852 (mm-30) REVERT: B 323 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 344 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7756 (mtt90) REVERT: B 364 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8233 (ttpp) REVERT: B 439 VAL cc_start: 0.8238 (t) cc_final: 0.7959 (t) REVERT: C 81 VAL cc_start: 0.7747 (t) cc_final: 0.7517 (m) REVERT: C 108 THR cc_start: 0.6871 (OUTLIER) cc_final: 0.6477 (t) REVERT: C 138 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7905 (tp) REVERT: C 223 SER cc_start: 0.8473 (t) cc_final: 0.7761 (m) REVERT: C 271 ASN cc_start: 0.8660 (t0) cc_final: 0.8343 (t0) REVERT: C 318 SER cc_start: 0.8249 (m) cc_final: 0.7637 (p) REVERT: C 321 ASP cc_start: 0.7421 (m-30) cc_final: 0.7099 (m-30) REVERT: C 324 SER cc_start: 0.8823 (t) cc_final: 0.8617 (m) REVERT: C 325 ARG cc_start: 0.7952 (mmt-90) cc_final: 0.7594 (mmt180) REVERT: C 378 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: C 396 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8062 (tm-30) REVERT: D 31 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6290 (pp20) REVERT: D 105 SER cc_start: 0.8381 (m) cc_final: 0.8110 (t) REVERT: D 117 GLU cc_start: 0.7402 (tt0) cc_final: 0.6913 (tm-30) REVERT: D 167 TYR cc_start: 0.7724 (m-80) cc_final: 0.7214 (m-80) REVERT: D 182 GLN cc_start: 0.8315 (mp10) cc_final: 0.7962 (mp10) REVERT: D 203 GLU cc_start: 0.7892 (mp0) cc_final: 0.7604 (mp0) REVERT: D 245 MET cc_start: 0.8278 (mmm) cc_final: 0.7905 (mmm) REVERT: D 354 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: D 387 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8036 (tttt) REVERT: D 394 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7960 (mt-10) REVERT: D 400 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7449 (mpp) REVERT: E 51 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7789 (t80) REVERT: E 93 MET cc_start: 0.8736 (mtt) cc_final: 0.8524 (mtt) REVERT: E 114 TYR cc_start: 0.8619 (m-80) cc_final: 0.8336 (m-80) REVERT: E 158 ASN cc_start: 0.7887 (m-40) cc_final: 0.7596 (m-40) REVERT: E 212 GLU cc_start: 0.7195 (tp30) cc_final: 0.6850 (tp30) REVERT: E 226 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7944 (p) REVERT: E 275 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: F 43 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6867 (tp) REVERT: F 102 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7603 (mmmt) REVERT: F 139 HIS cc_start: 0.7350 (t70) cc_final: 0.7129 (t-170) REVERT: F 144 GLU cc_start: 0.7342 (pt0) cc_final: 0.7077 (pt0) REVERT: F 153 LYS cc_start: 0.8478 (tttt) cc_final: 0.8216 (tttt) REVERT: F 186 LEU cc_start: 0.8240 (mt) cc_final: 0.7911 (mt) REVERT: F 194 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7160 (mm-30) REVERT: F 243 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7957 (mtmt) REVERT: F 302 MET cc_start: 0.8020 (ttm) cc_final: 0.7654 (ttm) REVERT: G 55 LEU cc_start: 0.8285 (mm) cc_final: 0.7748 (mm) REVERT: G 114 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8490 (p) REVERT: G 182 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7855 (mm-30) REVERT: G 189 GLU cc_start: 0.8093 (tt0) cc_final: 0.7860 (tt0) REVERT: I 273 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.8218 (mtt-85) REVERT: I 312 ASP cc_start: 0.7578 (t0) cc_final: 0.7366 (t0) REVERT: I 337 LYS cc_start: 0.8363 (mppt) cc_final: 0.8083 (mptt) REVERT: I 349 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7159 (mm) REVERT: I 424 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7534 (mtt180) REVERT: I 427 ASP cc_start: 0.7558 (t0) cc_final: 0.7239 (t0) REVERT: I 450 MET cc_start: 0.7706 (tmm) cc_final: 0.7382 (tmm) REVERT: I 469 MET cc_start: 0.6046 (mmt) cc_final: 0.5535 (mmt) REVERT: I 472 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7986 (mmtm) REVERT: I 483 ASP cc_start: 0.7439 (t0) cc_final: 0.7219 (t0) REVERT: I 494 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: I 540 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8375 (mt) REVERT: I 552 THR cc_start: 0.7969 (m) cc_final: 0.7527 (p) REVERT: I 590 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5482 (mt) REVERT: I 750 LYS cc_start: 0.7176 (tppt) cc_final: 0.6856 (tptp) REVERT: I 752 CYS cc_start: 0.8257 (m) cc_final: 0.7948 (m) REVERT: I 754 ASP cc_start: 0.7161 (m-30) cc_final: 0.6926 (m-30) REVERT: J 101 TRP cc_start: 0.8423 (t-100) cc_final: 0.6984 (t-100) outliers start: 147 outliers final: 98 residues processed: 750 average time/residue: 0.1770 time to fit residues: 203.9605 Evaluate side-chains 741 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 626 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 275 GLN Chi-restraints excluded: chain E residue 298 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 201 ASN Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 365 MET Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 494 GLN Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 590 LEU Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 602 GLN Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 685 ASN Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain I residue 738 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain K residue 36 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 181 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.146933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123868 restraints weight = 41740.686| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.32 r_work: 0.3498 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25836 Z= 0.150 Angle : 0.573 14.082 34873 Z= 0.296 Chirality : 0.041 0.255 3945 Planarity : 0.004 0.068 4445 Dihedral : 6.083 59.670 3490 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 6.05 % Allowed : 24.37 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 3108 helix: 1.58 (0.12), residues: 1928 sheet: -0.66 (0.43), residues: 161 loop : -2.03 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 242 TYR 0.024 0.001 TYR I 620 PHE 0.048 0.002 PHE I 251 TRP 0.018 0.002 TRP H 82 HIS 0.011 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00341 (25824) covalent geometry : angle 0.57330 (34870) hydrogen bonds : bond 0.04837 ( 1421) hydrogen bonds : angle 4.08313 ( 4176) metal coordination : bond 0.00730 ( 10) metal coordination : angle 1.45286 ( 3) Misc. bond : bond 0.00190 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 647 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7042 (ttp-110) cc_final: 0.6652 (ttp-110) REVERT: A 100 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 201 MET cc_start: 0.7551 (tmm) cc_final: 0.7329 (ppp) REVERT: B 201 GLU cc_start: 0.7285 (pp20) cc_final: 0.7040 (pp20) REVERT: B 252 GLU cc_start: 0.8173 (tp30) cc_final: 0.7915 (tp30) REVERT: B 260 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7850 (mm-30) REVERT: B 323 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 344 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7723 (mtt90) REVERT: B 364 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8222 (ttpp) REVERT: B 425 ASP cc_start: 0.7949 (m-30) cc_final: 0.7621 (m-30) REVERT: B 439 VAL cc_start: 0.8251 (t) cc_final: 0.7980 (t) REVERT: C 81 VAL cc_start: 0.7734 (t) cc_final: 0.7491 (m) REVERT: C 108 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6442 (t) REVERT: C 137 GLN cc_start: 0.8004 (tt0) cc_final: 0.7744 (tt0) REVERT: C 166 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7558 (tpp) REVERT: C 223 SER cc_start: 0.8479 (t) cc_final: 0.7777 (m) REVERT: C 263 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8218 (tt) REVERT: C 271 ASN cc_start: 0.8674 (t0) cc_final: 0.8306 (t0) REVERT: C 318 SER cc_start: 0.8275 (m) cc_final: 0.7658 (p) REVERT: C 321 ASP cc_start: 0.7419 (m-30) cc_final: 0.7095 (m-30) REVERT: C 324 SER cc_start: 0.8809 (t) cc_final: 0.8607 (m) REVERT: C 325 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7594 (mmt180) REVERT: C 377 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: C 378 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: C 396 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 31 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6253 (pp20) REVERT: D 105 SER cc_start: 0.8369 (m) cc_final: 0.8094 (t) REVERT: D 117 GLU cc_start: 0.7502 (tt0) cc_final: 0.6995 (tm-30) REVERT: D 167 TYR cc_start: 0.7746 (m-80) cc_final: 0.7218 (m-80) REVERT: D 182 GLN cc_start: 0.8342 (mp10) cc_final: 0.8002 (mp10) REVERT: D 203 GLU cc_start: 0.7875 (mp0) cc_final: 0.7568 (mp0) REVERT: D 245 MET cc_start: 0.8263 (mmm) cc_final: 0.7884 (mmm) REVERT: D 354 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: D 387 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8047 (tttt) REVERT: D 394 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 400 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7448 (mpp) REVERT: E 51 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7785 (t80) REVERT: E 93 MET cc_start: 0.8743 (mtt) cc_final: 0.8512 (mtt) REVERT: E 114 TYR cc_start: 0.8664 (m-80) cc_final: 0.8453 (m-80) REVERT: E 158 ASN cc_start: 0.7890 (m-40) cc_final: 0.7612 (m-40) REVERT: E 163 GLU cc_start: 0.5336 (OUTLIER) cc_final: 0.5100 (tm-30) REVERT: E 183 LEU cc_start: 0.8666 (mm) cc_final: 0.8247 (mt) REVERT: E 226 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7939 (p) REVERT: E 275 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: F 43 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6852 (tp) REVERT: F 139 HIS cc_start: 0.7369 (t70) cc_final: 0.7136 (t-170) REVERT: F 153 LYS cc_start: 0.8496 (tttt) cc_final: 0.8276 (tttt) REVERT: F 186 LEU cc_start: 0.8223 (mt) cc_final: 0.7915 (mt) REVERT: F 194 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7199 (mm-30) REVERT: F 243 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7995 (mtmt) REVERT: G 114 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8482 (p) REVERT: G 147 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7965 (pt0) REVERT: G 182 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7873 (mm-30) REVERT: G 189 GLU cc_start: 0.8118 (tt0) cc_final: 0.7887 (tt0) REVERT: G 194 ARG cc_start: 0.8465 (ttt-90) cc_final: 0.8211 (ttt-90) REVERT: I 312 ASP cc_start: 0.7627 (t0) cc_final: 0.7408 (t0) REVERT: I 337 LYS cc_start: 0.8349 (mppt) cc_final: 0.8110 (mptt) REVERT: I 349 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7140 (mm) REVERT: I 424 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7519 (mtt180) REVERT: I 427 ASP cc_start: 0.7582 (t0) cc_final: 0.7255 (t0) REVERT: I 450 MET cc_start: 0.7717 (tmm) cc_final: 0.7392 (tmm) REVERT: I 469 MET cc_start: 0.6078 (mmt) cc_final: 0.5561 (mmt) REVERT: I 472 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8044 (mmtm) REVERT: I 483 ASP cc_start: 0.7453 (t0) cc_final: 0.7232 (t0) REVERT: I 494 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: I 540 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8362 (mt) REVERT: I 552 THR cc_start: 0.7962 (m) cc_final: 0.7517 (p) REVERT: I 590 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5528 (mt) REVERT: I 750 LYS cc_start: 0.7185 (tppt) cc_final: 0.6849 (tptp) REVERT: I 752 CYS cc_start: 0.8294 (m) cc_final: 0.7983 (m) REVERT: I 754 ASP cc_start: 0.7191 (m-30) cc_final: 0.6956 (m-30) REVERT: J 101 TRP cc_start: 0.8426 (t-100) cc_final: 0.7022 (t-100) outliers start: 167 outliers final: 119 residues processed: 747 average time/residue: 0.1748 time to fit residues: 202.2893 Evaluate side-chains 768 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 627 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 275 GLN Chi-restraints excluded: chain E residue 298 ASP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 365 MET Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 494 GLN Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 589 GLU Chi-restraints excluded: chain I residue 590 LEU Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 602 GLN Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 685 ASN Chi-restraints excluded: chain I residue 738 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain K residue 36 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 9 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 213 optimal weight: 0.3980 chunk 302 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 GLN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.145450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122379 restraints weight = 41811.524| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.31 r_work: 0.3473 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25836 Z= 0.212 Angle : 0.614 11.872 34873 Z= 0.320 Chirality : 0.043 0.253 3945 Planarity : 0.004 0.068 4445 Dihedral : 6.190 59.817 3490 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 6.44 % Allowed : 24.33 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3108 helix: 1.37 (0.12), residues: 1932 sheet: -0.64 (0.43), residues: 161 loop : -2.10 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 273 TYR 0.024 0.002 TYR I 620 PHE 0.042 0.002 PHE I 251 TRP 0.021 0.002 TRP H 82 HIS 0.011 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00494 (25824) covalent geometry : angle 0.61345 (34870) hydrogen bonds : bond 0.05534 ( 1421) hydrogen bonds : angle 4.20599 ( 4176) metal coordination : bond 0.01314 ( 10) metal coordination : angle 1.83750 ( 3) Misc. bond : bond 0.00148 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 650 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7051 (ttp-110) cc_final: 0.6745 (ttp-110) REVERT: A 100 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 201 MET cc_start: 0.7590 (tmm) cc_final: 0.7381 (ppp) REVERT: B 75 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7136 (tmm) REVERT: B 201 GLU cc_start: 0.7282 (pp20) cc_final: 0.7045 (pp20) REVERT: B 252 GLU cc_start: 0.8160 (tp30) cc_final: 0.7889 (tp30) REVERT: B 260 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 344 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7755 (mtt90) REVERT: B 364 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8223 (ttpp) REVERT: B 425 ASP cc_start: 0.7966 (m-30) cc_final: 0.7637 (m-30) REVERT: C 81 VAL cc_start: 0.7771 (t) cc_final: 0.7522 (m) REVERT: C 108 THR cc_start: 0.6952 (OUTLIER) cc_final: 0.6393 (t) REVERT: C 166 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6994 (tpp) REVERT: C 223 SER cc_start: 0.8496 (t) cc_final: 0.7763 (m) REVERT: C 263 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8474 (tp) REVERT: C 271 ASN cc_start: 0.8695 (t0) cc_final: 0.8288 (t0) REVERT: C 318 SER cc_start: 0.8325 (m) cc_final: 0.8004 (p) REVERT: C 324 SER cc_start: 0.8803 (t) cc_final: 0.8597 (m) REVERT: C 325 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7568 (mmt180) REVERT: C 378 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: C 396 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8107 (tm-30) REVERT: D 31 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6307 (pp20) REVERT: D 105 SER cc_start: 0.8363 (m) cc_final: 0.8082 (t) REVERT: D 117 GLU cc_start: 0.7554 (tt0) cc_final: 0.7037 (tm-30) REVERT: D 158 ASP cc_start: 0.8120 (t70) cc_final: 0.7629 (t70) REVERT: D 182 GLN cc_start: 0.8382 (mp10) cc_final: 0.8017 (mp10) REVERT: D 203 GLU cc_start: 0.7900 (mp0) cc_final: 0.7595 (mp0) REVERT: D 245 MET cc_start: 0.8247 (mmm) cc_final: 0.7899 (mmm) REVERT: D 354 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: D 394 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 400 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7338 (mpp) REVERT: E 30 LYS cc_start: 0.8520 (tptt) cc_final: 0.8218 (tppt) REVERT: E 51 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7787 (t80) REVERT: E 114 TYR cc_start: 0.8715 (m-80) cc_final: 0.8469 (m-80) REVERT: E 158 ASN cc_start: 0.7952 (m-40) cc_final: 0.7691 (m110) REVERT: E 163 GLU cc_start: 0.5447 (OUTLIER) cc_final: 0.5189 (tm-30) REVERT: E 170 ILE cc_start: 0.8655 (mm) cc_final: 0.8453 (mt) REVERT: E 183 LEU cc_start: 0.8719 (mm) cc_final: 0.8347 (mt) REVERT: E 226 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7951 (p) REVERT: E 237 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8344 (mm) REVERT: E 275 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: F 43 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6904 (tp) REVERT: F 139 HIS cc_start: 0.7447 (t70) cc_final: 0.7157 (t-90) REVERT: F 186 LEU cc_start: 0.8234 (mt) cc_final: 0.7931 (mt) REVERT: F 243 LYS cc_start: 0.8272 (mtmt) cc_final: 0.8017 (mtmt) REVERT: F 255 GLU cc_start: 0.7252 (pt0) cc_final: 0.6966 (pt0) REVERT: F 259 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7879 (mm-30) REVERT: G 23 SER cc_start: 0.7285 (OUTLIER) cc_final: 0.7002 (t) REVERT: G 147 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: G 150 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7503 (mm110) REVERT: G 182 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7896 (mm-30) REVERT: G 189 GLU cc_start: 0.8121 (tt0) cc_final: 0.7888 (tt0) REVERT: I 241 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7908 (pp20) REVERT: I 242 ARG cc_start: 0.7655 (tmm160) cc_final: 0.7380 (ttp80) REVERT: I 269 LEU cc_start: 0.8125 (pp) cc_final: 0.7737 (pp) REVERT: I 273 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7775 (mtt-85) REVERT: I 312 ASP cc_start: 0.7622 (t0) cc_final: 0.7403 (t0) REVERT: I 337 LYS cc_start: 0.8308 (mppt) cc_final: 0.7939 (mmtm) REVERT: I 385 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: I 424 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7588 (mtt180) REVERT: I 427 ASP cc_start: 0.7640 (t0) cc_final: 0.7269 (t0) REVERT: I 450 MET cc_start: 0.7701 (tmm) cc_final: 0.7358 (tmm) REVERT: I 469 MET cc_start: 0.6143 (mmt) cc_final: 0.5624 (mmt) REVERT: I 472 LYS cc_start: 0.8329 (mtpt) cc_final: 0.8030 (mmtm) REVERT: I 483 ASP cc_start: 0.7461 (t0) cc_final: 0.7202 (t0) REVERT: I 494 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: I 540 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8413 (mt) REVERT: I 552 THR cc_start: 0.7949 (m) cc_final: 0.7490 (p) REVERT: I 590 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5574 (mt) REVERT: I 750 LYS cc_start: 0.7052 (tppt) cc_final: 0.6716 (tptp) REVERT: I 752 CYS cc_start: 0.8327 (m) cc_final: 0.8046 (m) REVERT: I 754 ASP cc_start: 0.7212 (m-30) cc_final: 0.6977 (m-30) REVERT: J 101 TRP cc_start: 0.8429 (t-100) cc_final: 0.6952 (t-100) REVERT: J 102 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7723 (mm-30) outliers start: 178 outliers final: 130 residues processed: 758 average time/residue: 0.1721 time to fit residues: 201.3531 Evaluate side-chains 783 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 630 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 275 GLN Chi-restraints excluded: chain E residue 298 ASP Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 201 ASN Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 494 GLN Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 569 PHE Chi-restraints excluded: chain I residue 589 GLU Chi-restraints excluded: chain I residue 590 LEU Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 602 GLN Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 685 ASN Chi-restraints excluded: chain I residue 722 ARG Chi-restraints excluded: chain I residue 738 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain K residue 36 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 208 optimal weight: 2.9990 chunk 155 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.146447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123346 restraints weight = 41856.709| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.33 r_work: 0.3486 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25836 Z= 0.161 Angle : 0.597 12.718 34873 Z= 0.309 Chirality : 0.042 0.350 3945 Planarity : 0.004 0.080 4445 Dihedral : 6.114 59.359 3489 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.17 % Rotamer: Outliers : 5.76 % Allowed : 25.16 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3108 helix: 1.46 (0.12), residues: 1933 sheet: -0.61 (0.42), residues: 169 loop : -2.07 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 461 TYR 0.024 0.001 TYR I 228 PHE 0.045 0.002 PHE I 251 TRP 0.018 0.002 TRP H 82 HIS 0.011 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00368 (25824) covalent geometry : angle 0.59720 (34870) hydrogen bonds : bond 0.05008 ( 1421) hydrogen bonds : angle 4.11724 ( 4176) metal coordination : bond 0.00801 ( 10) metal coordination : angle 1.77235 ( 3) Misc. bond : bond 0.00135 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 653 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7065 (ttp-110) cc_final: 0.6820 (ttp-110) REVERT: A 100 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 201 MET cc_start: 0.7563 (tmm) cc_final: 0.7331 (ppp) REVERT: B 167 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8104 (mttp) REVERT: B 201 GLU cc_start: 0.7307 (pp20) cc_final: 0.7061 (pp20) REVERT: B 252 GLU cc_start: 0.8121 (tp30) cc_final: 0.7850 (tp30) REVERT: B 260 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7824 (mm-30) REVERT: B 344 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7735 (mtt90) REVERT: B 364 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8210 (ttpp) REVERT: C 81 VAL cc_start: 0.7766 (t) cc_final: 0.7532 (m) REVERT: C 108 THR cc_start: 0.6829 (OUTLIER) cc_final: 0.6356 (t) REVERT: C 166 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6989 (tpp) REVERT: C 223 SER cc_start: 0.8442 (t) cc_final: 0.7732 (m) REVERT: C 263 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8377 (tp) REVERT: C 271 ASN cc_start: 0.8688 (t0) cc_final: 0.8257 (t0) REVERT: C 318 SER cc_start: 0.8285 (m) cc_final: 0.7949 (p) REVERT: C 324 SER cc_start: 0.8805 (t) cc_final: 0.8600 (m) REVERT: C 325 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7543 (mmt180) REVERT: C 378 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: C 396 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8094 (tm-30) REVERT: D 31 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6291 (pp20) REVERT: D 105 SER cc_start: 0.8371 (m) cc_final: 0.8087 (t) REVERT: D 117 GLU cc_start: 0.7532 (tt0) cc_final: 0.7009 (tm-30) REVERT: D 158 ASP cc_start: 0.8179 (t70) cc_final: 0.7744 (t70) REVERT: D 182 GLN cc_start: 0.8354 (mp10) cc_final: 0.7972 (mp10) REVERT: D 245 MET cc_start: 0.8238 (mmm) cc_final: 0.7877 (mmm) REVERT: D 273 ILE cc_start: 0.8508 (mm) cc_final: 0.8274 (mt) REVERT: D 314 LYS cc_start: 0.8468 (ptpt) cc_final: 0.8230 (ptpt) REVERT: D 354 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: D 394 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 400 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7318 (mpp) REVERT: E 30 LYS cc_start: 0.8513 (tptt) cc_final: 0.8208 (tppt) REVERT: E 51 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7771 (t80) REVERT: E 114 TYR cc_start: 0.8696 (m-80) cc_final: 0.8441 (m-80) REVERT: E 158 ASN cc_start: 0.7908 (m-40) cc_final: 0.7634 (m110) REVERT: E 183 LEU cc_start: 0.8656 (mm) cc_final: 0.8230 (mt) REVERT: E 226 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7960 (p) REVERT: E 237 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8317 (mm) REVERT: E 275 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: F 43 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6870 (tp) REVERT: F 139 HIS cc_start: 0.7437 (t70) cc_final: 0.7215 (t-170) REVERT: F 153 LYS cc_start: 0.8515 (tttt) cc_final: 0.8210 (tttt) REVERT: F 186 LEU cc_start: 0.8210 (mt) cc_final: 0.7913 (mt) REVERT: F 243 LYS cc_start: 0.8258 (mtmt) cc_final: 0.8002 (mtmt) REVERT: G 114 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8484 (p) REVERT: G 147 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: G 150 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: G 182 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7913 (mm-30) REVERT: G 189 GLU cc_start: 0.8117 (tt0) cc_final: 0.7882 (tt0) REVERT: G 194 ARG cc_start: 0.8451 (ttt-90) cc_final: 0.8226 (ttt-90) REVERT: I 312 ASP cc_start: 0.7588 (t0) cc_final: 0.7370 (t0) REVERT: I 337 LYS cc_start: 0.8303 (mppt) cc_final: 0.7974 (mmtp) REVERT: I 349 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7184 (mm) REVERT: I 424 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7561 (mtt180) REVERT: I 427 ASP cc_start: 0.7600 (t0) cc_final: 0.7237 (t0) REVERT: I 450 MET cc_start: 0.7692 (tmm) cc_final: 0.7348 (tmm) REVERT: I 469 MET cc_start: 0.6127 (mmt) cc_final: 0.5600 (mmt) REVERT: I 472 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8023 (mmtm) REVERT: I 483 ASP cc_start: 0.7450 (t0) cc_final: 0.7191 (t0) REVERT: I 494 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: I 540 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8354 (mt) REVERT: I 552 THR cc_start: 0.7942 (m) cc_final: 0.7477 (p) REVERT: I 590 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5572 (mt) REVERT: I 750 LYS cc_start: 0.7200 (tppt) cc_final: 0.6852 (tptp) REVERT: I 752 CYS cc_start: 0.8306 (m) cc_final: 0.8005 (m) REVERT: I 754 ASP cc_start: 0.7201 (m-30) cc_final: 0.6949 (m-30) REVERT: J 101 TRP cc_start: 0.8426 (t-100) cc_final: 0.7075 (t-100) outliers start: 159 outliers final: 125 residues processed: 748 average time/residue: 0.1727 time to fit residues: 197.9647 Evaluate side-chains 778 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 634 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 275 GLN Chi-restraints excluded: chain E residue 298 ASP Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 201 ASN Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 365 MET Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 494 GLN Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 590 LEU Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 685 ASN Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain I residue 738 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain K residue 36 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 307 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 239 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN G 33 GLN I 386 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124019 restraints weight = 41811.095| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.32 r_work: 0.3502 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25836 Z= 0.140 Angle : 0.597 16.666 34873 Z= 0.307 Chirality : 0.041 0.472 3945 Planarity : 0.004 0.070 4445 Dihedral : 6.022 58.909 3489 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 5.54 % Allowed : 25.67 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 3108 helix: 1.56 (0.12), residues: 1932 sheet: -0.56 (0.42), residues: 169 loop : -2.00 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 242 TYR 0.021 0.001 TYR I 228 PHE 0.041 0.002 PHE I 251 TRP 0.027 0.001 TRP H 82 HIS 0.011 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00315 (25824) covalent geometry : angle 0.59726 (34870) hydrogen bonds : bond 0.04668 ( 1421) hydrogen bonds : angle 4.04988 ( 4176) metal coordination : bond 0.00603 ( 10) metal coordination : angle 1.74201 ( 3) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 647 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7094 (ttp-110) cc_final: 0.6872 (ttp-110) REVERT: A 100 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 201 MET cc_start: 0.7586 (tmm) cc_final: 0.7329 (ppp) REVERT: A 214 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7297 (p0) REVERT: B 75 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7118 (tmm) REVERT: B 201 GLU cc_start: 0.7315 (pp20) cc_final: 0.7082 (pp20) REVERT: B 252 GLU cc_start: 0.8125 (tp30) cc_final: 0.7850 (tp30) REVERT: B 260 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7819 (mm-30) REVERT: B 344 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7721 (mtt90) REVERT: B 364 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8215 (ttpp) REVERT: C 81 VAL cc_start: 0.7773 (t) cc_final: 0.7520 (m) REVERT: C 108 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6390 (t) REVERT: C 166 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7086 (tpp) REVERT: C 223 SER cc_start: 0.8435 (t) cc_final: 0.7708 (m) REVERT: C 271 ASN cc_start: 0.8660 (t0) cc_final: 0.8254 (t0) REVERT: C 318 SER cc_start: 0.8260 (m) cc_final: 0.7941 (p) REVERT: C 324 SER cc_start: 0.8818 (t) cc_final: 0.8611 (m) REVERT: C 325 ARG cc_start: 0.7932 (mmt-90) cc_final: 0.7566 (mmt180) REVERT: C 378 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: C 396 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8134 (tm-30) REVERT: D 31 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6277 (pp20) REVERT: D 105 SER cc_start: 0.8347 (m) cc_final: 0.8063 (t) REVERT: D 117 GLU cc_start: 0.7521 (tt0) cc_final: 0.6988 (tm-30) REVERT: D 158 ASP cc_start: 0.8239 (t70) cc_final: 0.7671 (t70) REVERT: D 182 GLN cc_start: 0.8341 (mp10) cc_final: 0.7933 (mp10) REVERT: D 245 MET cc_start: 0.8233 (mmm) cc_final: 0.7902 (mmm) REVERT: D 314 LYS cc_start: 0.8446 (ptpt) cc_final: 0.8218 (ptpt) REVERT: D 354 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: D 386 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: D 394 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 400 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7286 (mpp) REVERT: E 30 LYS cc_start: 0.8504 (tptt) cc_final: 0.8279 (tppt) REVERT: E 51 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7786 (t80) REVERT: E 114 TYR cc_start: 0.8683 (m-80) cc_final: 0.8421 (m-80) REVERT: E 158 ASN cc_start: 0.7876 (m-40) cc_final: 0.7599 (m110) REVERT: E 226 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7973 (p) REVERT: E 237 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8318 (mm) REVERT: E 275 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: F 43 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6843 (tp) REVERT: F 62 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.5594 (mt-10) REVERT: F 139 HIS cc_start: 0.7457 (t70) cc_final: 0.7212 (t-170) REVERT: F 153 LYS cc_start: 0.8491 (tttt) cc_final: 0.8269 (tttt) REVERT: F 186 LEU cc_start: 0.8233 (mt) cc_final: 0.7958 (mt) REVERT: F 243 LYS cc_start: 0.8273 (mtmt) cc_final: 0.8024 (mtmt) REVERT: G 147 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: G 150 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: G 182 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7901 (mm-30) REVERT: G 189 GLU cc_start: 0.8127 (tt0) cc_final: 0.7893 (tt0) REVERT: H 106 MET cc_start: 0.6488 (mmm) cc_final: 0.6199 (mtp) REVERT: I 273 ARG cc_start: 0.8020 (mtt-85) cc_final: 0.7808 (mtt-85) REVERT: I 337 LYS cc_start: 0.8299 (mppt) cc_final: 0.8075 (mptt) REVERT: I 349 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7145 (mm) REVERT: I 424 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7528 (mtt180) REVERT: I 427 ASP cc_start: 0.7570 (t0) cc_final: 0.7215 (t0) REVERT: I 450 MET cc_start: 0.7673 (tmm) cc_final: 0.7324 (tmm) REVERT: I 469 MET cc_start: 0.6074 (mmt) cc_final: 0.5551 (mmt) REVERT: I 472 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8045 (mmtm) REVERT: I 483 ASP cc_start: 0.7256 (t0) cc_final: 0.7017 (t0) REVERT: I 494 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7222 (mp10) REVERT: I 540 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8327 (mt) REVERT: I 552 THR cc_start: 0.7949 (m) cc_final: 0.7488 (p) REVERT: I 590 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5469 (mt) REVERT: I 708 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7780 (mtpp) REVERT: I 750 LYS cc_start: 0.7161 (tppt) cc_final: 0.6791 (tptp) REVERT: I 754 ASP cc_start: 0.7191 (m-30) cc_final: 0.6970 (m-30) REVERT: J 56 CYS cc_start: 0.5880 (OUTLIER) cc_final: 0.5622 (m) REVERT: J 101 TRP cc_start: 0.8433 (t-100) cc_final: 0.7006 (t-100) REVERT: K 1 MET cc_start: 0.6829 (tpt) cc_final: 0.6268 (tpt) outliers start: 153 outliers final: 116 residues processed: 743 average time/residue: 0.1799 time to fit residues: 205.5097 Evaluate side-chains 762 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 624 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 275 GLN Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 201 ASN Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 365 MET Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 494 GLN Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 590 LEU Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 602 GLN Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 685 ASN Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain K residue 36 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 238 optimal weight: 0.5980 chunk 186 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 247 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.147176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124080 restraints weight = 41945.890| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.32 r_work: 0.3502 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25836 Z= 0.144 Angle : 0.608 14.993 34873 Z= 0.312 Chirality : 0.041 0.429 3945 Planarity : 0.004 0.069 4445 Dihedral : 5.958 58.639 3487 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.54 % Allowed : 25.74 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 3108 helix: 1.54 (0.12), residues: 1938 sheet: -0.54 (0.42), residues: 169 loop : -2.01 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 242 TYR 0.020 0.001 TYR I 228 PHE 0.040 0.002 PHE I 251 TRP 0.022 0.002 TRP H 82 HIS 0.022 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00326 (25824) covalent geometry : angle 0.60808 (34870) hydrogen bonds : bond 0.04664 ( 1421) hydrogen bonds : angle 4.03472 ( 4176) metal coordination : bond 0.00660 ( 10) metal coordination : angle 1.73010 ( 3) Misc. bond : bond 0.00120 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 636 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7056 (ttp-110) cc_final: 0.6812 (ttp-110) REVERT: A 100 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7776 (mt-10) REVERT: A 201 MET cc_start: 0.7582 (tmm) cc_final: 0.7097 (ppp) REVERT: A 214 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7312 (p0) REVERT: B 75 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7115 (tmm) REVERT: B 201 GLU cc_start: 0.7313 (pp20) cc_final: 0.7097 (pp20) REVERT: B 252 GLU cc_start: 0.8147 (tp30) cc_final: 0.7867 (tp30) REVERT: B 260 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7834 (mm-30) REVERT: B 344 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7703 (mtt90) REVERT: B 364 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8209 (ttpp) REVERT: C 81 VAL cc_start: 0.7781 (t) cc_final: 0.7519 (m) REVERT: C 108 THR cc_start: 0.6857 (OUTLIER) cc_final: 0.6430 (t) REVERT: C 137 GLN cc_start: 0.8015 (tt0) cc_final: 0.7811 (tt0) REVERT: C 166 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7469 (ttm) REVERT: C 223 SER cc_start: 0.8426 (t) cc_final: 0.7713 (m) REVERT: C 263 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8241 (tt) REVERT: C 271 ASN cc_start: 0.8645 (t0) cc_final: 0.8237 (t0) REVERT: C 318 SER cc_start: 0.8249 (m) cc_final: 0.7935 (p) REVERT: C 324 SER cc_start: 0.8819 (t) cc_final: 0.8612 (m) REVERT: C 325 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7556 (mmt180) REVERT: C 378 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: C 396 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8126 (tm-30) REVERT: D 31 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6222 (pp20) REVERT: D 45 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7347 (mp) REVERT: D 105 SER cc_start: 0.8337 (m) cc_final: 0.8086 (t) REVERT: D 117 GLU cc_start: 0.7456 (tt0) cc_final: 0.6913 (tm-30) REVERT: D 158 ASP cc_start: 0.8234 (t70) cc_final: 0.7684 (t70) REVERT: D 182 GLN cc_start: 0.8347 (mp10) cc_final: 0.7932 (mp10) REVERT: D 245 MET cc_start: 0.8233 (mmm) cc_final: 0.7898 (mmm) REVERT: D 314 LYS cc_start: 0.8450 (ptpt) cc_final: 0.8226 (ptpt) REVERT: D 354 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: D 386 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: D 394 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7917 (mt-10) REVERT: D 400 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7279 (mpp) REVERT: E 30 LYS cc_start: 0.8506 (tptt) cc_final: 0.8268 (tppt) REVERT: E 51 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7787 (t80) REVERT: E 114 TYR cc_start: 0.8690 (m-80) cc_final: 0.8460 (m-80) REVERT: E 158 ASN cc_start: 0.7876 (m-40) cc_final: 0.7616 (m110) REVERT: E 183 LEU cc_start: 0.8605 (mm) cc_final: 0.8296 (mt) REVERT: E 226 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7966 (p) REVERT: E 237 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8309 (mm) REVERT: E 275 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: F 43 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6785 (tp) REVERT: F 44 HIS cc_start: 0.7683 (m-70) cc_final: 0.7411 (m90) REVERT: F 62 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5603 (mt-10) REVERT: F 139 HIS cc_start: 0.7464 (t70) cc_final: 0.7210 (t-170) REVERT: F 153 LYS cc_start: 0.8492 (tttt) cc_final: 0.8270 (tttt) REVERT: F 186 LEU cc_start: 0.8236 (mt) cc_final: 0.7986 (mt) REVERT: F 194 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7155 (mm-30) REVERT: F 243 LYS cc_start: 0.8274 (mtmt) cc_final: 0.8027 (mtmt) REVERT: G 147 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: G 150 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: G 182 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7900 (mm-30) REVERT: G 189 GLU cc_start: 0.8108 (tt0) cc_final: 0.7872 (tt0) REVERT: G 194 ARG cc_start: 0.8482 (ttt-90) cc_final: 0.8241 (ttt-90) REVERT: H 79 GLN cc_start: 0.7200 (tt0) cc_final: 0.6986 (tt0) REVERT: I 273 ARG cc_start: 0.8020 (mtt-85) cc_final: 0.7791 (mtt-85) REVERT: I 337 LYS cc_start: 0.8295 (mppt) cc_final: 0.8069 (mptt) REVERT: I 349 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7160 (mm) REVERT: I 424 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7521 (mtt180) REVERT: I 427 ASP cc_start: 0.7561 (t0) cc_final: 0.7213 (t0) REVERT: I 450 MET cc_start: 0.7683 (tmm) cc_final: 0.7331 (tmm) REVERT: I 469 MET cc_start: 0.6085 (mmt) cc_final: 0.5563 (mmt) REVERT: I 472 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8045 (mmtm) REVERT: I 483 ASP cc_start: 0.7242 (t0) cc_final: 0.6999 (t0) REVERT: I 494 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: I 540 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8298 (mt) REVERT: I 552 THR cc_start: 0.7952 (m) cc_final: 0.7486 (p) REVERT: I 590 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.5445 (mt) REVERT: I 708 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7766 (mtpp) REVERT: I 750 LYS cc_start: 0.6996 (tppt) cc_final: 0.6658 (tptp) REVERT: I 754 ASP cc_start: 0.7183 (m-30) cc_final: 0.6968 (m-30) REVERT: J 56 CYS cc_start: 0.5869 (OUTLIER) cc_final: 0.5605 (m) REVERT: J 101 TRP cc_start: 0.8425 (t-100) cc_final: 0.6991 (t-100) REVERT: K 1 MET cc_start: 0.6831 (tpt) cc_final: 0.6310 (tpt) outliers start: 153 outliers final: 120 residues processed: 736 average time/residue: 0.1728 time to fit residues: 195.3116 Evaluate side-chains 769 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 625 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 275 GLN Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 201 ASN Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 494 GLN Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 590 LEU Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 602 GLN Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 685 ASN Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain K residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 192 optimal weight: 1.9990 chunk 122 optimal weight: 0.0570 chunk 180 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 234 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 269 optimal weight: 0.0470 chunk 220 optimal weight: 0.8980 chunk 218 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 386 ASN ** I 463 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 = 0.3996 r_free = 0.3996 target = 0.148869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125847 restraints weight = 41988.974| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.33 r_work: 0.3522 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25836 Z= 0.123 Angle : 0.610 15.400 34873 Z= 0.312 Chirality : 0.041 0.410 3945 Planarity : 0.004 0.069 4445 Dihedral : 5.862 58.216 3487 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.60 % Allowed : 26.86 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.16), residues: 3108 helix: 1.65 (0.12), residues: 1934 sheet: -0.52 (0.42), residues: 171 loop : -1.94 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 242 TYR 0.022 0.001 TYR A 91 PHE 0.041 0.001 PHE I 251 TRP 0.022 0.001 TRP H 82 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00271 (25824) covalent geometry : angle 0.60992 (34870) hydrogen bonds : bond 0.04255 ( 1421) hydrogen bonds : angle 3.96234 ( 4176) metal coordination : bond 0.00391 ( 10) metal coordination : angle 1.64566 ( 3) Misc. bond : bond 0.00099 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 630 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 159 GLU cc_start: 0.7232 (mp0) cc_final: 0.6913 (mp0) REVERT: A 201 MET cc_start: 0.7461 (tmm) cc_final: 0.7025 (ppp) REVERT: A 214 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7314 (p0) REVERT: A 427 ARG cc_start: 0.7772 (ttt90) cc_final: 0.7521 (ttt180) REVERT: A 455 LEU cc_start: 0.8115 (tp) cc_final: 0.7847 (tt) REVERT: B 75 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7115 (tmm) REVERT: B 126 ASP cc_start: 0.8049 (t0) cc_final: 0.7707 (t0) REVERT: B 201 GLU cc_start: 0.7326 (pp20) cc_final: 0.7115 (pp20) REVERT: B 260 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 344 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7684 (mtt90) REVERT: B 364 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8209 (ttpp) REVERT: B 439 VAL cc_start: 0.8233 (t) cc_final: 0.7962 (t) REVERT: C 81 VAL cc_start: 0.7798 (t) cc_final: 0.7541 (m) REVERT: C 166 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7530 (ttm) REVERT: C 223 SER cc_start: 0.8436 (t) cc_final: 0.7731 (m) REVERT: C 263 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8228 (tt) REVERT: C 271 ASN cc_start: 0.8617 (t0) cc_final: 0.8222 (t0) REVERT: C 318 SER cc_start: 0.8169 (m) cc_final: 0.7528 (p) REVERT: C 321 ASP cc_start: 0.7405 (m-30) cc_final: 0.7042 (m-30) REVERT: C 324 SER cc_start: 0.8813 (t) cc_final: 0.8609 (m) REVERT: C 325 ARG cc_start: 0.7894 (mmt-90) cc_final: 0.7551 (mmt180) REVERT: C 378 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: C 396 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 31 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6215 (pp20) REVERT: D 45 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7316 (mp) REVERT: D 105 SER cc_start: 0.8336 (m) cc_final: 0.8097 (t) REVERT: D 117 GLU cc_start: 0.7433 (tt0) cc_final: 0.6883 (tm-30) REVERT: D 158 ASP cc_start: 0.8224 (t70) cc_final: 0.7682 (t70) REVERT: D 182 GLN cc_start: 0.8326 (mp10) cc_final: 0.7904 (mp10) REVERT: D 245 MET cc_start: 0.8202 (mmm) cc_final: 0.7866 (mmm) REVERT: D 314 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8084 (ptpt) REVERT: D 354 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: D 386 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: D 394 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7900 (mt-10) REVERT: D 400 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7450 (mpp) REVERT: E 51 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7771 (t80) REVERT: E 114 TYR cc_start: 0.8658 (m-80) cc_final: 0.8403 (m-80) REVERT: E 158 ASN cc_start: 0.7842 (m-40) cc_final: 0.7569 (m110) REVERT: E 183 LEU cc_start: 0.8529 (mm) cc_final: 0.8181 (mt) REVERT: E 226 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7975 (p) REVERT: E 237 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8207 (mm) REVERT: E 275 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: F 43 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6751 (tp) REVERT: F 44 HIS cc_start: 0.7636 (m-70) cc_final: 0.7385 (m90) REVERT: F 139 HIS cc_start: 0.7420 (t70) cc_final: 0.7207 (t-170) REVERT: F 153 LYS cc_start: 0.8503 (tttt) cc_final: 0.8247 (tttt) REVERT: F 186 LEU cc_start: 0.8225 (mt) cc_final: 0.7995 (mt) REVERT: F 194 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6965 (mm-30) REVERT: F 198 ILE cc_start: 0.8403 (mt) cc_final: 0.8169 (mt) REVERT: F 243 LYS cc_start: 0.8262 (mtmt) cc_final: 0.8011 (mtmt) REVERT: G 147 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8071 (pt0) REVERT: G 182 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7880 (mm-30) REVERT: G 189 GLU cc_start: 0.8057 (tt0) cc_final: 0.7819 (tt0) REVERT: G 194 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.8279 (ttt-90) REVERT: H 106 MET cc_start: 0.6463 (mmm) cc_final: 0.6180 (mtp) REVERT: I 337 LYS cc_start: 0.8289 (mppt) cc_final: 0.8069 (mptt) REVERT: I 424 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7578 (mtt180) REVERT: I 427 ASP cc_start: 0.7516 (t0) cc_final: 0.7180 (t0) REVERT: I 450 MET cc_start: 0.7680 (tmm) cc_final: 0.7333 (tmm) REVERT: I 469 MET cc_start: 0.6059 (mmt) cc_final: 0.5526 (mmt) REVERT: I 472 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8022 (mmtm) REVERT: I 483 ASP cc_start: 0.7214 (t0) cc_final: 0.6976 (t0) REVERT: I 494 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: I 552 THR cc_start: 0.7960 (m) cc_final: 0.7497 (p) REVERT: I 590 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5422 (mt) REVERT: I 708 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7771 (mtpp) REVERT: I 750 LYS cc_start: 0.6960 (tppt) cc_final: 0.6591 (tptp) REVERT: I 754 ASP cc_start: 0.7144 (m-30) cc_final: 0.6923 (m-30) REVERT: J 101 TRP cc_start: 0.8412 (t-100) cc_final: 0.6922 (t-100) REVERT: K 1 MET cc_start: 0.6801 (tpt) cc_final: 0.6287 (tpt) outliers start: 127 outliers final: 97 residues processed: 708 average time/residue: 0.1742 time to fit residues: 188.3405 Evaluate side-chains 738 residues out of total 2791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 623 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 275 GLN Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 196 ASN Chi-restraints excluded: chain G residue 201 ASN Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 136 PHE Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 494 GLN Chi-restraints excluded: chain I residue 531 LEU Chi-restraints excluded: chain I residue 590 LEU Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 602 GLN Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 685 ASN Chi-restraints excluded: chain I residue 721 MET Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 GLN Chi-restraints excluded: chain K residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 236 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 305 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** I 463 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 = 0.3990 r_free = 0.3990 target = 0.148571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125473 restraints weight = 41707.418| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.33 r_work: 0.3518 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25836 Z= 0.128 Angle : 0.612 14.521 34873 Z= 0.311 Chirality : 0.041 0.392 3945 Planarity : 0.004 0.068 4445 Dihedral : 5.665 59.090 3482 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.71 % Allowed : 27.08 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 3108 helix: 1.65 (0.12), residues: 1938 sheet: -0.51 (0.42), residues: 171 loop : -1.94 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 96 TYR 0.017 0.001 TYR I 620 PHE 0.038 0.001 PHE I 251 TRP 0.017 0.001 TRP H 82 HIS 0.004 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00286 (25824) covalent geometry : angle 0.61138 (34870) hydrogen bonds : bond 0.04273 ( 1421) hydrogen bonds : angle 3.94552 ( 4176) metal coordination : bond 0.00489 ( 10) metal coordination : angle 1.69239 ( 3) Misc. bond : bond 0.00108 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8800.08 seconds wall clock time: 150 minutes 13.84 seconds (9013.84 seconds total)