Starting phenix.real_space_refine on Sat Aug 8 23:25:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yk9_73042/08_2026/9yk9_73042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yk9_73042/08_2026/9yk9_73042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yk9_73042/08_2026/9yk9_73042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yk9_73042/08_2026/9yk9_73042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yk9_73042/08_2026/9yk9_73042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yk9_73042/08_2026/9yk9_73042.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.178 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 179 5.16 5 C 19353 2.51 5 N 5226 2.21 5 O 5908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30678 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 285 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "F" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 285 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "G" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1238 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 1, 'TRANS': 153} Chain: "H" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1238 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 1, 'TRANS': 153} Chain: "I" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 408 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 6475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6475 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 30, 'TRANS': 774} Chain: "K" Number of atoms: 6475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6475 Classifications: {'peptide': 805} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 774} Chain: "L" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1217 Classifications: {'peptide': 153} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 146} Chain: "M" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1217 Classifications: {'peptide': 153} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 146} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.25, per 1000 atoms: 0.20 Number of scatterers: 30678 At special positions: 0 Unit cell: (181.704, 126.108, 273.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 179 16.00 P 8 15.00 Mg 4 11.99 O 5908 8.00 N 5226 7.00 C 19353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 37 sheets defined 56.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.850A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 4.405A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.179A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 145 removed outlier: 3.920A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 192 Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.548A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 308 through 321 removed outlier: 4.097A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 348 through 355 removed outlier: 6.081A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 364 through 372 Proline residue: A 367 - end of helix Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.230A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.568A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.800A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.717A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.861A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.553A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.598A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.911A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 364 through 372 Proline residue: B 367 - end of helix Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 79 through 92 removed outlier: 4.245A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.848A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.815A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.508A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.701A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.545A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.532A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 372 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 4.191A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 55 through 60' Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.657A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.352A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.566A pdb=" N LEU D 140 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 183 through 193 removed outlier: 3.886A pdb=" N ASP D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 removed outlier: 3.634A pdb=" N GLY D 197 " --> pdb=" O THR D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.815A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.596A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.606A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 285 through 290 removed outlier: 6.131A pdb=" N ASP D 288 " --> pdb=" O CYS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.884A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.579A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 370 removed outlier: 3.996A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 370' Processing helix chain 'E' and resid 251 through 284 removed outlier: 3.964A pdb=" N ILE E 284 " --> pdb=" O ASP E 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 282 Processing helix chain 'G' and resid 2 through 155 Proline residue: G 64 - end of helix removed outlier: 3.773A pdb=" N LYS G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG G 125 " --> pdb=" O ASP G 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 155 Proline residue: H 64 - end of helix removed outlier: 4.120A pdb=" N LYS H 118 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA H 119 " --> pdb=" O GLU H 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 130 Processing helix chain 'J' and resid 5 through 17 removed outlier: 3.517A pdb=" N PHE J 9 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY J 10 " --> pdb=" O ALA J 7 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLU J 11 " --> pdb=" O ALA J 8 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA J 12 " --> pdb=" O PHE J 9 " (cutoff:3.500A) Proline residue: J 14 - end of helix removed outlier: 4.207A pdb=" N ARG J 17 " --> pdb=" O PRO J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 26 Processing helix chain 'J' and resid 81 through 85 Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.611A pdb=" N MET J 92 " --> pdb=" O ASP J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 111 removed outlier: 3.514A pdb=" N LEU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 142 removed outlier: 3.825A pdb=" N VAL J 139 " --> pdb=" O ASN J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 169 removed outlier: 3.661A pdb=" N ILE J 157 " --> pdb=" O HIS J 153 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU J 166 " --> pdb=" O TYR J 162 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR J 167 " --> pdb=" O GLN J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 199 Processing helix chain 'J' and resid 216 through 231 removed outlier: 4.218A pdb=" N GLN J 222 " --> pdb=" O ASP J 218 " (cutoff:3.500A) Proline residue: J 225 - end of helix removed outlier: 3.873A pdb=" N PHE J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 289 Processing helix chain 'J' and resid 294 through 302 removed outlier: 3.853A pdb=" N LEU J 298 " --> pdb=" O LYS J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 309 removed outlier: 3.554A pdb=" N ASP J 309 " --> pdb=" O ASN J 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 306 through 309' Processing helix chain 'J' and resid 310 through 315 removed outlier: 3.803A pdb=" N GLN J 315 " --> pdb=" O ALA J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 338 removed outlier: 3.916A pdb=" N MET J 330 " --> pdb=" O ALA J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 359 Processing helix chain 'J' and resid 360 through 362 No H-bonds generated for 'chain 'J' and resid 360 through 362' Processing helix chain 'J' and resid 378 through 389 Processing helix chain 'J' and resid 391 through 401 removed outlier: 4.194A pdb=" N LYS J 397 " --> pdb=" O ALA J 393 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU J 399 " --> pdb=" O LEU J 395 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS J 401 " --> pdb=" O LYS J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 447 removed outlier: 3.790A pdb=" N GLY J 425 " --> pdb=" O MET J 421 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR J 446 " --> pdb=" O ARG J 442 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU J 447 " --> pdb=" O ILE J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 505 removed outlier: 3.592A pdb=" N THR J 481 " --> pdb=" O CYS J 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 526 removed outlier: 4.707A pdb=" N CYS J 520 " --> pdb=" O ASP J 516 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU J 523 " --> pdb=" O ALA J 519 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE J 524 " --> pdb=" O CYS J 520 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 537 Processing helix chain 'J' and resid 544 through 555 Processing helix chain 'J' and resid 593 through 598 removed outlier: 3.628A pdb=" N LYS J 598 " --> pdb=" O LEU J 594 " (cutoff:3.500A) Processing helix chain 'J' and resid 602 through 611 removed outlier: 3.852A pdb=" N VAL J 606 " --> pdb=" O ASN J 602 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU J 608 " --> pdb=" O THR J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 621 Processing helix chain 'J' and resid 641 through 645 Processing helix chain 'J' and resid 646 through 663 removed outlier: 3.771A pdb=" N LEU J 650 " --> pdb=" O THR J 646 " (cutoff:3.500A) Processing helix chain 'J' and resid 685 through 696 removed outlier: 3.783A pdb=" N VAL J 689 " --> pdb=" O ASP J 685 " (cutoff:3.500A) Processing helix chain 'J' and resid 697 through 708 removed outlier: 3.734A pdb=" N GLY J 708 " --> pdb=" O ILE J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 715 through 722 removed outlier: 3.541A pdb=" N ARG J 719 " --> pdb=" O TYR J 715 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN J 720 " --> pdb=" O GLY J 716 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG J 721 " --> pdb=" O ASP J 717 " (cutoff:3.500A) Processing helix chain 'J' and resid 723 through 726 removed outlier: 3.595A pdb=" N ASN J 726 " --> pdb=" O ARG J 723 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 723 through 726' Processing helix chain 'J' and resid 737 through 747 Processing helix chain 'J' and resid 752 through 754 No H-bonds generated for 'chain 'J' and resid 752 through 754' Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.634A pdb=" N ARG J 780 " --> pdb=" O MET J 776 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG J 783 " --> pdb=" O GLU J 779 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET J 799 " --> pdb=" O VAL J 795 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU J 800 " --> pdb=" O LEU J 796 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU J 805 " --> pdb=" O PHE J 801 " (cutoff:3.500A) Processing helix chain 'J' and resid 806 through 808 No H-bonds generated for 'chain 'J' and resid 806 through 808' Processing helix chain 'K' and resid 12 through 17 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.581A pdb=" N ALA K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 29 No H-bonds generated for 'chain 'K' and resid 27 through 29' Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 89 through 93 removed outlier: 3.902A pdb=" N MET K 92 " --> pdb=" O ASP K 89 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU K 93 " --> pdb=" O MET K 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 89 through 93' Processing helix chain 'K' and resid 97 through 111 removed outlier: 4.116A pdb=" N ASN K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU K 105 " --> pdb=" O VAL K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 134 removed outlier: 4.205A pdb=" N TYR K 134 " --> pdb=" O LEU K 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 131 through 134' Processing helix chain 'K' and resid 135 through 143 removed outlier: 3.645A pdb=" N ARG K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 168 removed outlier: 4.057A pdb=" N ILE K 157 " --> pdb=" O HIS K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 199 removed outlier: 3.697A pdb=" N ASN K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 231 removed outlier: 3.527A pdb=" N GLN K 219 " --> pdb=" O THR K 215 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN K 222 " --> pdb=" O ASP K 218 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA K 223 " --> pdb=" O GLN K 219 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN K 224 " --> pdb=" O ILE K 220 " (cutoff:3.500A) Proline residue: K 225 - end of helix removed outlier: 4.345A pdb=" N ALA K 229 " --> pdb=" O PRO K 225 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 274 Processing helix chain 'K' and resid 284 through 291 Processing helix chain 'K' and resid 294 through 302 removed outlier: 4.449A pdb=" N LEU K 298 " --> pdb=" O LYS K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 339 removed outlier: 3.505A pdb=" N ASP K 337 " --> pdb=" O ASP K 333 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU K 339 " --> pdb=" O ALA K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 361 removed outlier: 3.539A pdb=" N MET K 357 " --> pdb=" O THR K 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN K 361 " --> pdb=" O MET K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 389 Processing helix chain 'K' and resid 391 through 401 Processing helix chain 'K' and resid 416 through 448 Processing helix chain 'K' and resid 472 through 504 removed outlier: 3.583A pdb=" N THR K 481 " --> pdb=" O CYS K 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 517 through 526 removed outlier: 4.428A pdb=" N ILE K 521 " --> pdb=" O LEU K 517 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE K 524 " --> pdb=" O CYS K 520 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 539 removed outlier: 3.704A pdb=" N MET K 539 " --> pdb=" O GLU K 535 " (cutoff:3.500A) Processing helix chain 'K' and resid 544 through 557 removed outlier: 3.660A pdb=" N TYR K 553 " --> pdb=" O LYS K 549 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP K 554 " --> pdb=" O ALA K 550 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN K 555 " --> pdb=" O LYS K 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS K 556 " --> pdb=" O LEU K 552 " (cutoff:3.500A) Processing helix chain 'K' and resid 593 through 597 removed outlier: 3.539A pdb=" N ASN K 597 " --> pdb=" O LEU K 594 " (cutoff:3.500A) Processing helix chain 'K' and resid 602 through 607 Processing helix chain 'K' and resid 608 through 612 Processing helix chain 'K' and resid 614 through 621 removed outlier: 3.813A pdb=" N PHE K 621 " --> pdb=" O LEU K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 646 through 664 removed outlier: 3.922A pdb=" N SER K 664 " --> pdb=" O THR K 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 685 through 697 Processing helix chain 'K' and resid 697 through 708 Processing helix chain 'K' and resid 715 through 723 removed outlier: 4.062A pdb=" N ARG K 723 " --> pdb=" O ARG K 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 724 through 726 No H-bonds generated for 'chain 'K' and resid 724 through 726' Processing helix chain 'K' and resid 737 through 747 Processing helix chain 'K' and resid 769 through 805 removed outlier: 3.716A pdb=" N LEU K 773 " --> pdb=" O LEU K 769 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG K 787 " --> pdb=" O ARG K 783 " (cutoff:3.500A) Processing helix chain 'K' and resid 806 through 808 No H-bonds generated for 'chain 'K' and resid 806 through 808' Processing helix chain 'L' and resid 48 through 62 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 91 through 98 Processing helix chain 'L' and resid 102 through 107 Processing helix chain 'L' and resid 111 through 124 Proline residue: L 117 - end of helix Processing helix chain 'L' and resid 130 through 139 removed outlier: 3.515A pdb=" N PHE L 134 " --> pdb=" O THR L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 160 Processing helix chain 'L' and resid 166 through 175 removed outlier: 4.011A pdb=" N VAL L 170 " --> pdb=" O THR L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 194 removed outlier: 4.111A pdb=" N LYS L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 60 removed outlier: 3.737A pdb=" N ILE M 52 " --> pdb=" O THR M 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU M 57 " --> pdb=" O GLU M 53 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA M 58 " --> pdb=" O GLU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 75 through 83 removed outlier: 4.138A pdb=" N ASP M 79 " --> pdb=" O GLY M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 107 Processing helix chain 'M' and resid 111 through 120 Proline residue: M 117 - end of helix removed outlier: 3.623A pdb=" N GLN M 120 " --> pdb=" O LEU M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 140 Processing helix chain 'M' and resid 151 through 161 Processing helix chain 'M' and resid 166 through 175 removed outlier: 3.627A pdb=" N VAL M 170 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS M 172 " --> pdb=" O ASP M 168 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU M 173 " --> pdb=" O GLU M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 178 No H-bonds generated for 'chain 'M' and resid 176 through 178' Processing helix chain 'M' and resid 186 through 194 removed outlier: 3.762A pdb=" N LYS M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS M 192 " --> pdb=" O ALA M 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.509A pdb=" N GLY A 20 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.787A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 242 removed outlier: 5.482A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.698A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.551A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 242 removed outlier: 6.625A pdb=" N LYS B 238 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR B 249 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR B 240 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 247 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.607A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.557A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 242 removed outlier: 5.961A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.749A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 357 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.568A pdb=" N VAL D 35 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 removed outlier: 7.608A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'J' and resid 68 through 72 removed outlier: 6.799A pdb=" N LYS J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG J 54 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR J 60 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU J 77 " --> pdb=" O TYR J 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 115 through 118 removed outlier: 6.426A pdb=" N CYS J 122 " --> pdb=" O ARG J 671 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE J 673 " --> pdb=" O CYS J 122 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR J 124 " --> pdb=" O ILE J 673 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASN J 171 " --> pdb=" O HIS J 666 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N HIS J 668 " --> pdb=" O ASN J 171 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER J 173 " --> pdb=" O HIS J 668 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL J 670 " --> pdb=" O SER J 173 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU J 175 " --> pdb=" O VAL J 670 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N CYS J 672 " --> pdb=" O LEU J 175 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR J 177 " --> pdb=" O CYS J 672 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLN J 172 " --> pdb=" O GLY J 458 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU J 460 " --> pdb=" O GLN J 172 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE J 174 " --> pdb=" O LEU J 460 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 232 through 233 Processing sheet with id=AC6, first strand: chain 'J' and resid 363 through 366 removed outlier: 4.067A pdb=" N LYS J 363 " --> pdb=" O ASP J 376 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 403 through 406 Processing sheet with id=AC8, first strand: chain 'J' and resid 577 through 581 removed outlier: 3.635A pdb=" N PHE J 577 " --> pdb=" O TYR J 588 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS J 581 " --> pdb=" O GLY J 584 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 711 through 714 removed outlier: 3.569A pdb=" N ILE J 713 " --> pdb=" O VAL J 763 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 67 through 71 removed outlier: 7.356A pdb=" N THR K 60 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 115 through 118 removed outlier: 5.943A pdb=" N CYS K 122 " --> pdb=" O ARG K 671 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE K 673 " --> pdb=" O CYS K 122 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR K 124 " --> pdb=" O ILE K 673 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER K 173 " --> pdb=" O HIS K 668 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL K 670 " --> pdb=" O SER K 173 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU K 175 " --> pdb=" O VAL K 670 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N CYS K 672 " --> pdb=" O LEU K 175 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR K 177 " --> pdb=" O CYS K 672 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN K 172 " --> pdb=" O GLY K 458 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU K 460 " --> pdb=" O GLN K 172 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE K 174 " --> pdb=" O LEU K 460 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 232 through 233 removed outlier: 3.792A pdb=" N ALA K 233 " --> pdb=" O SER K 241 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER K 241 " --> pdb=" O ALA K 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'K' and resid 364 through 366 Processing sheet with id=AD5, first strand: chain 'K' and resid 403 through 406 removed outlier: 3.725A pdb=" N VAL K 411 " --> pdb=" O VAL K 404 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 406 " --> pdb=" O GLU K 409 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 563 through 564 removed outlier: 3.554A pdb=" N ALA K 578 " --> pdb=" O GLN K 564 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE K 577 " --> pdb=" O TYR K 588 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 711 through 714 removed outlier: 3.592A pdb=" N ASN K 711 " --> pdb=" O PHE K 765 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 148 through 149 Processing sheet with id=AD9, first strand: chain 'M' and resid 72 through 73 removed outlier: 3.964A pdb=" N ILE M 72 " --> pdb=" O MET M 110 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET M 110 " --> pdb=" O ILE M 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'M' and resid 148 through 150 1546 hydrogen bonds defined for protein. 4287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.04 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6250 1.33 - 1.46: 7846 1.46 - 1.58: 16827 1.58 - 1.71: 12 1.71 - 1.84: 316 Bond restraints: 31251 Sorted by residual: bond pdb=" CE1 HIS K 691 " pdb=" NE2 HIS K 691 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.22e+01 bond pdb=" CE1 HIS K 651 " pdb=" NE2 HIS K 651 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.19e+01 bond pdb=" CE1 HIS K 760 " pdb=" NE2 HIS K 760 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.18e+01 bond pdb=" CE1 HIS K 491 " pdb=" NE2 HIS K 491 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.18e+01 bond pdb=" CE1 HIS K 492 " pdb=" NE2 HIS K 492 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.15e+01 ... (remaining 31246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 40823 2.80 - 5.60: 1258 5.60 - 8.40: 55 8.40 - 11.20: 0 11.20 - 14.00: 2 Bond angle restraints: 42138 Sorted by residual: angle pdb=" C GLY M 182 " pdb=" N CYS M 183 " pdb=" CA CYS M 183 " ideal model delta sigma weight residual 121.70 135.70 -14.00 1.80e+00 3.09e-01 6.05e+01 angle pdb=" C GLY L 182 " pdb=" N CYS L 183 " pdb=" CA CYS L 183 " ideal model delta sigma weight residual 121.70 134.82 -13.12 1.80e+00 3.09e-01 5.31e+01 angle pdb=" C HIS K 401 " pdb=" N PRO K 402 " pdb=" CA PRO K 402 " ideal model delta sigma weight residual 120.11 127.04 -6.93 1.12e+00 7.97e-01 3.82e+01 angle pdb=" N GLN K 368 " pdb=" CA GLN K 368 " pdb=" C GLN K 368 " ideal model delta sigma weight residual 111.33 118.08 -6.75 1.21e+00 6.83e-01 3.11e+01 angle pdb=" CA GLU K 374 " pdb=" C GLU K 374 " pdb=" N PRO K 375 " ideal model delta sigma weight residual 117.94 125.42 -7.48 1.37e+00 5.33e-01 2.98e+01 ... (remaining 42133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 17493 17.84 - 35.69: 1226 35.69 - 53.53: 286 53.53 - 71.38: 88 71.38 - 89.22: 33 Dihedral angle restraints: 19126 sinusoidal: 7950 harmonic: 11176 Sorted by residual: dihedral pdb=" CA GLU B 4 " pdb=" C GLU B 4 " pdb=" N THR B 5 " pdb=" CA THR B 5 " ideal model delta harmonic sigma weight residual -180.00 -144.08 -35.92 0 5.00e+00 4.00e-02 5.16e+01 dihedral pdb=" CA GLY K 407 " pdb=" C GLY K 407 " pdb=" N ASN K 408 " pdb=" CA ASN K 408 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLU B 3 " pdb=" C GLU B 3 " pdb=" N GLU B 4 " pdb=" CA GLU B 4 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 19123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4139 0.095 - 0.189: 402 0.189 - 0.284: 55 0.284 - 0.379: 12 0.379 - 0.474: 4 Chirality restraints: 4612 Sorted by residual: chirality pdb=" CA GLU K 535 " pdb=" N GLU K 535 " pdb=" C GLU K 535 " pdb=" CB GLU K 535 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA LEU K 105 " pdb=" N LEU K 105 " pdb=" C LEU K 105 " pdb=" CB LEU K 105 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA THR K 215 " pdb=" N THR K 215 " pdb=" C THR K 215 " pdb=" CB THR K 215 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 4609 not shown) Planarity restraints: 5470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 422 " 0.133 2.00e-02 2.50e+03 7.11e-02 1.01e+02 pdb=" CG TYR K 422 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR K 422 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR K 422 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR K 422 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR K 422 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR K 422 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR K 422 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 310 " -0.117 2.00e-02 2.50e+03 6.39e-02 8.16e+01 pdb=" CG TYR K 310 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR K 310 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR K 310 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR K 310 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR K 310 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR K 310 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR K 310 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 401 " -0.098 2.00e-02 2.50e+03 7.36e-02 8.12e+01 pdb=" CG HIS K 401 " 0.105 2.00e-02 2.50e+03 pdb=" ND1 HIS K 401 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS K 401 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 HIS K 401 " -0.047 2.00e-02 2.50e+03 pdb=" NE2 HIS K 401 " -0.064 2.00e-02 2.50e+03 ... (remaining 5467 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 106 2.46 - 3.07: 19831 3.07 - 3.68: 45689 3.68 - 4.29: 63961 4.29 - 4.90: 106186 Nonbonded interactions: 235773 Sorted by model distance: nonbonded pdb=" OE1 GLN C 137 " pdb="MG MG C 402 " model vdw 1.850 2.170 nonbonded pdb=" OD2 ASP A 11 " pdb="MG MG A 402 " model vdw 1.877 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.940 2.170 nonbonded pdb=" OE1 GLN B 137 " pdb="MG MG B 402 " model vdw 1.962 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 1.976 2.170 ... (remaining 235768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.470 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.007 0.045 31251 Z= 0.406 Angle : 1.012 14.005 42138 Z= 0.659 Chirality : 0.061 0.474 4612 Planarity : 0.008 0.129 5470 Dihedral : 14.061 89.219 11920 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.90 % Favored : 94.97 % Rotamer: Outliers : 3.22 % Allowed : 7.34 % Favored : 89.44 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3817 helix: 1.31 (0.13), residues: 1730 sheet: -0.10 (0.27), residues: 364 loop : -0.89 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG K 723 TYR 0.133 0.006 TYR K 422 PHE 0.062 0.004 PHE K 489 TRP 0.053 0.004 TRP K 438 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.41 (31251) covalent geometry : angle 1.01221 / 0.66 (42138) hydrogen bonds : bond 0.16585 / 11.06 ( 1538) hydrogen bonds : angle 5.69276 / 3.93 ( 4287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1098 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7645 (mmm) cc_final: 0.6487 (mmm) REVERT: A 127 PHE cc_start: 0.7099 (m-80) cc_final: 0.6775 (m-80) REVERT: A 147 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7429 (mmm160) REVERT: A 222 ASP cc_start: 0.8929 (t0) cc_final: 0.8622 (t0) REVERT: A 264 PRO cc_start: 0.8858 (Cg_exo) cc_final: 0.8635 (Cg_endo) REVERT: A 279 TYR cc_start: 0.8169 (t80) cc_final: 0.7808 (t80) REVERT: A 313 MET cc_start: 0.6975 (ttm) cc_final: 0.6749 (ttm) REVERT: B 65 LEU cc_start: 0.8368 (mt) cc_final: 0.8092 (mt) REVERT: B 79 TRP cc_start: 0.8107 (m100) cc_final: 0.7601 (m100) REVERT: B 82 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8239 (tmm) REVERT: B 123 MET cc_start: 0.8145 (mmm) cc_final: 0.7592 (mmm) REVERT: B 130 PRO cc_start: 0.8422 (Cg_endo) cc_final: 0.8197 (Cg_exo) REVERT: B 132 MET cc_start: 0.9085 (ppp) cc_final: 0.8774 (ppp) REVERT: B 162 ASN cc_start: 0.8859 (t0) cc_final: 0.8482 (m-40) REVERT: B 167 GLU cc_start: 0.5971 (tp30) cc_final: 0.4976 (tp30) REVERT: B 235 SER cc_start: 0.8978 (p) cc_final: 0.8677 (t) REVERT: C 82 MET cc_start: 0.7920 (tpt) cc_final: 0.6632 (tpp) REVERT: C 86 TRP cc_start: 0.9013 (m-10) cc_final: 0.8621 (m-90) REVERT: C 132 MET cc_start: 0.9080 (ppp) cc_final: 0.8797 (ppp) REVERT: C 136 ILE cc_start: 0.9035 (mm) cc_final: 0.8608 (mt) REVERT: C 180 LEU cc_start: 0.9236 (tt) cc_final: 0.8817 (tp) REVERT: C 185 LEU cc_start: 0.8787 (mt) cc_final: 0.8572 (mt) REVERT: C 186 THR cc_start: 0.7950 (m) cc_final: 0.7721 (m) REVERT: C 260 THR cc_start: 0.8254 (m) cc_final: 0.7960 (t) REVERT: C 305 MET cc_start: 0.7794 (mmm) cc_final: 0.7506 (tpp) REVERT: C 349 LEU cc_start: 0.8764 (mt) cc_final: 0.8155 (mt) REVERT: D 59 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7091 (tp-100) REVERT: D 79 TRP cc_start: 0.7337 (m100) cc_final: 0.7133 (m100) REVERT: D 330 ILE cc_start: 0.8522 (mp) cc_final: 0.8253 (tp) REVERT: E 281 MET cc_start: 0.3949 (ttt) cc_final: 0.3400 (ttt) REVERT: G 60 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6696 (t80) REVERT: G 79 THR cc_start: 0.2339 (m) cc_final: 0.2038 (m) REVERT: G 113 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7386 (tp) REVERT: I 126 LYS cc_start: 0.7831 (tmmt) cc_final: 0.7116 (tmmt) REVERT: J 38 TYR cc_start: 0.7993 (m-80) cc_final: 0.7564 (m-80) REVERT: J 52 LEU cc_start: 0.7435 (mp) cc_final: 0.7234 (mt) REVERT: J 101 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8554 (p) REVERT: J 102 LEU cc_start: 0.8169 (tp) cc_final: 0.7712 (tp) REVERT: J 194 TYR cc_start: 0.7877 (t80) cc_final: 0.7637 (t80) REVERT: J 232 ASN cc_start: 0.6497 (m110) cc_final: 0.6240 (m-40) REVERT: J 268 LEU cc_start: 0.8919 (tp) cc_final: 0.8627 (tp) REVERT: J 441 THR cc_start: 0.8615 (p) cc_final: 0.8400 (t) REVERT: J 449 THR cc_start: 0.8286 (t) cc_final: 0.7440 (m) REVERT: J 523 LEU cc_start: 0.8514 (tt) cc_final: 0.8278 (tt) REVERT: J 537 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7050 (mm-30) REVERT: J 570 LYS cc_start: 0.8398 (tptt) cc_final: 0.8030 (tptm) REVERT: J 683 VAL cc_start: 0.7401 (t) cc_final: 0.7180 (t) REVERT: J 699 LEU cc_start: 0.7199 (tp) cc_final: 0.6577 (tp) REVERT: K 77 LEU cc_start: 0.8265 (mm) cc_final: 0.7842 (mm) REVERT: K 105 LEU cc_start: 0.8579 (pp) cc_final: 0.8375 (pp) REVERT: K 198 ILE cc_start: 0.8091 (pt) cc_final: 0.7835 (pt) REVERT: K 269 GLU cc_start: 0.6657 (tp30) cc_final: 0.5638 (tp30) REVERT: K 305 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7097 (t0) REVERT: K 357 MET cc_start: 0.8584 (mmp) cc_final: 0.8380 (mmt) REVERT: K 424 THR cc_start: 0.8906 (p) cc_final: 0.8583 (p) REVERT: K 465 PHE cc_start: 0.7282 (t80) cc_final: 0.6690 (t80) REVERT: K 475 GLN cc_start: 0.7821 (mp10) cc_final: 0.7387 (mp10) REVERT: K 479 ASN cc_start: 0.8775 (m-40) cc_final: 0.8216 (m-40) REVERT: K 521 ILE cc_start: 0.8734 (mt) cc_final: 0.8446 (mt) REVERT: K 534 LEU cc_start: 0.8311 (tp) cc_final: 0.7511 (tt) REVERT: K 536 GLU cc_start: 0.6949 (tt0) cc_final: 0.6235 (tt0) REVERT: K 586 VAL cc_start: 0.9050 (t) cc_final: 0.8843 (t) REVERT: K 587 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7452 (p0) REVERT: K 694 ARG cc_start: 0.8095 (mtt-85) cc_final: 0.7419 (mtt90) REVERT: K 724 ILE cc_start: 0.8036 (mp) cc_final: 0.7778 (mt) REVERT: K 756 TYR cc_start: 0.8208 (p90) cc_final: 0.7763 (p90) REVERT: L 118 MET cc_start: 0.5745 (mmp) cc_final: 0.5106 (mmp) REVERT: M 118 MET cc_start: 0.2450 (tmm) cc_final: 0.2140 (tmm) REVERT: M 144 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7298 (mm-30) outliers start: 106 outliers final: 27 residues processed: 1164 average time/residue: 0.2137 time to fit residues: 388.5081 Evaluate side-chains 694 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 659 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS B 12 ASN B 59 GLN B 275 HIS B 353 GLN C 40 HIS ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN E 263 GLN G 93 GLN ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN H 9 GLN H 68 GLN J 97 HIS J 160 ASN J 251 HIS J 358 HIS J 498 GLN J 555 ASN J 581 HIS J 692 GLN J 711 ASN ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 GLN K 219 GLN K 372 GLN K 408 ASN K 482 ASN K 492 HIS K 623 ASN K 654 ASN L 87 ASN L 120 GLN L 146 ASN L 156 HIS ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099160 restraints weight = 87669.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100829 restraints weight = 54228.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103093 restraints weight = 33763.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103220 restraints weight = 21786.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103193 restraints weight = 18426.858| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31251 Z= 0.165 Angle : 0.680 9.224 42138 Z= 0.354 Chirality : 0.044 0.167 4612 Planarity : 0.005 0.059 5470 Dihedral : 5.747 51.617 4208 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 0.15 % Allowed : 3.40 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.43 (0.14), residues: 3817 helix: 1.23 (0.12), residues: 1802 sheet: -0.10 (0.27), residues: 355 loop : -0.63 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 21 TYR 0.021 0.002 TYR J 350 PHE 0.024 0.002 PHE L 59 TRP 0.061 0.002 TRP D 86 HIS 0.019 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (31251) covalent geometry : angle 0.68039 / 0.35 (42138) hydrogen bonds : bond 0.05136 / 3.47 ( 1538) hydrogen bonds : angle 4.71093 / 3.25 ( 4287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 828 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8497 (mmm) cc_final: 0.7324 (mmm) REVERT: A 176 MET cc_start: 0.8999 (mmm) cc_final: 0.7681 (mmm) REVERT: A 279 TYR cc_start: 0.8555 (t80) cc_final: 0.8107 (t80) REVERT: B 79 TRP cc_start: 0.8382 (m100) cc_final: 0.7728 (m100) REVERT: B 84 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7426 (mtmt) REVERT: B 149 THR cc_start: 0.8557 (p) cc_final: 0.8305 (p) REVERT: B 153 LEU cc_start: 0.8914 (tp) cc_final: 0.8187 (tp) REVERT: B 162 ASN cc_start: 0.8980 (t0) cc_final: 0.8199 (m-40) REVERT: B 167 GLU cc_start: 0.7124 (tp30) cc_final: 0.5914 (tp30) REVERT: B 189 LEU cc_start: 0.8203 (tp) cc_final: 0.7951 (tp) REVERT: B 205 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6986 (mt-10) REVERT: B 312 ARG cc_start: 0.8296 (tpt-90) cc_final: 0.7898 (tpt-90) REVERT: C 64 ILE cc_start: 0.9356 (pt) cc_final: 0.8957 (mm) REVERT: C 82 MET cc_start: 0.8424 (tpt) cc_final: 0.7307 (tpp) REVERT: C 86 TRP cc_start: 0.9317 (m-10) cc_final: 0.8648 (m-90) REVERT: C 94 LEU cc_start: 0.9358 (mm) cc_final: 0.9147 (mm) REVERT: C 180 LEU cc_start: 0.9023 (tt) cc_final: 0.8816 (tp) REVERT: C 185 LEU cc_start: 0.9102 (mt) cc_final: 0.8797 (mt) REVERT: C 289 ILE cc_start: 0.8457 (pt) cc_final: 0.8245 (pt) REVERT: C 305 MET cc_start: 0.8297 (mmm) cc_final: 0.7386 (tpp) REVERT: C 330 ILE cc_start: 0.9429 (mp) cc_final: 0.8787 (mt) REVERT: C 339 VAL cc_start: 0.9348 (m) cc_final: 0.9068 (p) REVERT: C 340 TRP cc_start: 0.9108 (t60) cc_final: 0.8670 (t60) REVERT: C 345 ILE cc_start: 0.9412 (tp) cc_final: 0.9194 (mm) REVERT: C 349 LEU cc_start: 0.9155 (mt) cc_final: 0.8404 (tp) REVERT: C 364 GLU cc_start: 0.8084 (tp30) cc_final: 0.7684 (tp30) REVERT: D 10 CYS cc_start: 0.8198 (t) cc_final: 0.7553 (t) REVERT: D 12 ASN cc_start: 0.8195 (m-40) cc_final: 0.7776 (m-40) REVERT: D 44 MET cc_start: 0.7016 (ptt) cc_final: 0.6680 (ppp) REVERT: D 51 ASP cc_start: 0.8769 (t0) cc_final: 0.8417 (t0) REVERT: D 71 ILE cc_start: 0.8486 (mt) cc_final: 0.8235 (mt) REVERT: D 82 MET cc_start: 0.8325 (tpt) cc_final: 0.7077 (tpt) REVERT: D 133 TYR cc_start: 0.8464 (t80) cc_final: 0.7991 (t80) REVERT: D 192 ILE cc_start: 0.8886 (pt) cc_final: 0.8675 (tp) REVERT: D 240 TYR cc_start: 0.7958 (t80) cc_final: 0.7377 (t80) REVERT: E 276 HIS cc_start: 0.7061 (p-80) cc_final: 0.5890 (t70) REVERT: G 80 ASP cc_start: 0.7221 (m-30) cc_final: 0.6973 (m-30) REVERT: G 101 ARG cc_start: 0.7851 (ptm-80) cc_final: 0.7476 (ptm160) REVERT: G 121 ASP cc_start: 0.7534 (m-30) cc_final: 0.7258 (m-30) REVERT: J 38 TYR cc_start: 0.8583 (m-80) cc_final: 0.8232 (m-80) REVERT: J 90 MET cc_start: 0.7788 (mtt) cc_final: 0.7489 (mtp) REVERT: J 131 LEU cc_start: 0.6527 (mt) cc_final: 0.5820 (mp) REVERT: J 160 ASN cc_start: 0.6925 (OUTLIER) cc_final: 0.6658 (t0) REVERT: J 194 TYR cc_start: 0.8467 (t80) cc_final: 0.7896 (t80) REVERT: J 235 THR cc_start: 0.8900 (p) cc_final: 0.8638 (t) REVERT: J 268 LEU cc_start: 0.9142 (tp) cc_final: 0.8854 (tp) REVERT: J 325 ASP cc_start: 0.7978 (p0) cc_final: 0.7764 (p0) REVERT: J 350 TYR cc_start: 0.8918 (m-80) cc_final: 0.8697 (m-80) REVERT: J 441 THR cc_start: 0.9379 (p) cc_final: 0.9169 (t) REVERT: J 593 TRP cc_start: 0.9325 (m-10) cc_final: 0.9124 (m-10) REVERT: K 313 ILE cc_start: 0.8732 (pt) cc_final: 0.8491 (mm) REVERT: K 357 MET cc_start: 0.8874 (mmp) cc_final: 0.8561 (mmm) REVERT: K 378 THR cc_start: 0.8670 (p) cc_final: 0.8395 (p) REVERT: K 380 GLU cc_start: 0.8990 (mp0) cc_final: 0.8678 (mp0) REVERT: K 465 PHE cc_start: 0.7537 (t80) cc_final: 0.7320 (t80) REVERT: K 466 GLU cc_start: 0.8209 (tt0) cc_final: 0.7966 (tt0) REVERT: K 479 ASN cc_start: 0.9054 (m-40) cc_final: 0.8554 (m-40) REVERT: K 534 LEU cc_start: 0.8340 (tp) cc_final: 0.7558 (tt) REVERT: K 535 GLU cc_start: 0.7631 (pt0) cc_final: 0.7217 (pt0) REVERT: K 536 GLU cc_start: 0.7934 (tt0) cc_final: 0.7039 (tt0) REVERT: K 635 LYS cc_start: 0.8622 (mmtm) cc_final: 0.7912 (tttt) REVERT: K 655 LEU cc_start: 0.9499 (tp) cc_final: 0.9249 (tp) REVERT: K 694 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7693 (mtt90) REVERT: L 118 MET cc_start: 0.5865 (mmp) cc_final: 0.5099 (mmm) REVERT: M 118 MET cc_start: 0.3746 (tmm) cc_final: 0.3356 (tmm) REVERT: M 144 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8228 (mm-30) outliers start: 5 outliers final: 1 residues processed: 831 average time/residue: 0.2013 time to fit residues: 267.2485 Evaluate side-chains 595 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 593 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 68 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 137 optimal weight: 0.0070 chunk 236 optimal weight: 1.9990 chunk 370 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 162 ASN A 371 HIS B 92 ASN B 162 ASN B 296 ASN C 275 HIS D 137 GLN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 GLN ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 518 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 GLN K 654 ASN K 666 HIS L 90 GLN ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098815 restraints weight = 85590.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100340 restraints weight = 52881.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.101354 restraints weight = 35884.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102102 restraints weight = 26739.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102605 restraints weight = 21343.856| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 31251 Z= 0.216 Angle : 0.710 8.863 42138 Z= 0.370 Chirality : 0.046 0.221 4612 Planarity : 0.005 0.050 5470 Dihedral : 5.704 43.729 4208 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % 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: 0.20 (0.14), residues: 3817 helix: 1.00 (0.12), residues: 1801 sheet: 0.01 (0.27), residues: 359 loop : -0.76 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 21 TYR 0.020 0.002 TYR K 422 PHE 0.017 0.002 PHE K 709 TRP 0.087 0.003 TRP B 86 HIS 0.021 0.002 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (31251) covalent geometry : angle 0.70984 / 0.37 (42138) hydrogen bonds : bond 0.05000 / 3.37 ( 1538) hydrogen bonds : angle 4.75614 / 3.28 ( 4287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 733 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8608 (mt) cc_final: 0.8246 (pp) REVERT: A 119 MET cc_start: 0.8677 (ttm) cc_final: 0.8357 (ttp) REVERT: A 123 MET cc_start: 0.8273 (mmm) cc_final: 0.6974 (mmm) REVERT: A 148 THR cc_start: 0.8154 (p) cc_final: 0.7935 (m) REVERT: A 227 MET cc_start: 0.8063 (tpp) cc_final: 0.7804 (tpp) REVERT: A 330 ILE cc_start: 0.8660 (mm) cc_final: 0.8233 (mm) REVERT: B 79 TRP cc_start: 0.8313 (m100) cc_final: 0.7443 (m100) REVERT: B 153 LEU cc_start: 0.9033 (tp) cc_final: 0.8287 (tp) REVERT: B 162 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8322 (m-40) REVERT: B 167 GLU cc_start: 0.7190 (tp30) cc_final: 0.6847 (mm-30) REVERT: C 64 ILE cc_start: 0.9455 (pt) cc_final: 0.9003 (mm) REVERT: C 82 MET cc_start: 0.8357 (tpt) cc_final: 0.7261 (tpt) REVERT: C 86 TRP cc_start: 0.9377 (m-10) cc_final: 0.8991 (m-90) REVERT: C 99 GLU cc_start: 0.7814 (mm-30) cc_final: 0.6883 (mm-30) REVERT: C 123 MET cc_start: 0.8873 (mmm) cc_final: 0.8602 (mmm) REVERT: C 289 ILE cc_start: 0.8471 (pt) cc_final: 0.8244 (pt) REVERT: C 292 ASP cc_start: 0.7527 (m-30) cc_final: 0.7133 (m-30) REVERT: C 305 MET cc_start: 0.8217 (mmm) cc_final: 0.7960 (tpt) REVERT: C 330 ILE cc_start: 0.9526 (mp) cc_final: 0.8770 (mt) REVERT: C 340 TRP cc_start: 0.9189 (t60) cc_final: 0.8780 (t60) REVERT: C 349 LEU cc_start: 0.9011 (mt) cc_final: 0.8405 (mp) REVERT: C 364 GLU cc_start: 0.7956 (tp30) cc_final: 0.7595 (tp30) REVERT: D 10 CYS cc_start: 0.8095 (t) cc_final: 0.7315 (t) REVERT: D 12 ASN cc_start: 0.8358 (m-40) cc_final: 0.7758 (m110) REVERT: D 71 ILE cc_start: 0.8680 (mt) cc_final: 0.8406 (mt) REVERT: D 79 TRP cc_start: 0.7526 (m100) cc_final: 0.7090 (m100) REVERT: D 82 MET cc_start: 0.8099 (tpt) cc_final: 0.7244 (tpt) REVERT: D 133 TYR cc_start: 0.8566 (t80) cc_final: 0.8160 (t80) REVERT: D 176 MET cc_start: 0.7838 (tpt) cc_final: 0.7314 (tpt) REVERT: D 211 ASP cc_start: 0.7312 (t0) cc_final: 0.7071 (t0) REVERT: E 276 HIS cc_start: 0.6956 (p-80) cc_final: 0.5814 (t70) REVERT: E 281 MET cc_start: 0.7136 (tpp) cc_final: 0.6573 (mmm) REVERT: F 281 MET cc_start: 0.4436 (ppp) cc_final: 0.3802 (ppp) REVERT: G 115 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: H 72 GLU cc_start: 0.6382 (tt0) cc_final: 0.5812 (tt0) REVERT: I 117 LEU cc_start: 0.8549 (mm) cc_final: 0.8328 (mm) REVERT: J 25 GLU cc_start: 0.7447 (mp0) cc_final: 0.7204 (mp0) REVERT: J 38 TYR cc_start: 0.8416 (m-80) cc_final: 0.7536 (m-80) REVERT: J 131 LEU cc_start: 0.6561 (mt) cc_final: 0.6023 (mp) REVERT: J 194 TYR cc_start: 0.8605 (t80) cc_final: 0.7965 (t80) REVERT: J 198 ILE cc_start: 0.7610 (pt) cc_final: 0.7384 (pt) REVERT: J 268 LEU cc_start: 0.9149 (tp) cc_final: 0.8852 (tp) REVERT: J 300 MET cc_start: 0.8295 (tpp) cc_final: 0.8011 (tpp) REVERT: J 593 TRP cc_start: 0.9461 (m-10) cc_final: 0.8565 (m100) REVERT: J 659 MET cc_start: 0.8607 (mmm) cc_final: 0.8274 (mmt) REVERT: J 735 PHE cc_start: 0.6357 (m-80) cc_final: 0.6126 (m-80) REVERT: K 113 MET cc_start: 0.7850 (mmm) cc_final: 0.7491 (mmm) REVERT: K 122 CYS cc_start: 0.8799 (p) cc_final: 0.8224 (p) REVERT: K 172 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7814 (mm110) REVERT: K 313 ILE cc_start: 0.8919 (pt) cc_final: 0.8472 (mm) REVERT: K 357 MET cc_start: 0.8875 (mmp) cc_final: 0.8478 (mmm) REVERT: K 378 THR cc_start: 0.8642 (p) cc_final: 0.8185 (m) REVERT: K 380 GLU cc_start: 0.9048 (mp0) cc_final: 0.8747 (mp0) REVERT: K 465 PHE cc_start: 0.7743 (t80) cc_final: 0.7143 (t80) REVERT: K 466 GLU cc_start: 0.8326 (tt0) cc_final: 0.7896 (tt0) REVERT: K 479 ASN cc_start: 0.9143 (m-40) cc_final: 0.8431 (m-40) REVERT: K 522 ASP cc_start: 0.8804 (m-30) cc_final: 0.8384 (m-30) REVERT: K 526 LYS cc_start: 0.8370 (mmtp) cc_final: 0.7894 (mmtp) REVERT: K 534 LEU cc_start: 0.8471 (tp) cc_final: 0.7796 (tt) REVERT: K 535 GLU cc_start: 0.7584 (pt0) cc_final: 0.7272 (pt0) REVERT: K 536 GLU cc_start: 0.7806 (tt0) cc_final: 0.7322 (tt0) REVERT: K 655 LEU cc_start: 0.9497 (tp) cc_final: 0.9164 (tp) REVERT: K 694 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.7721 (mtt90) REVERT: L 118 MET cc_start: 0.6294 (mmp) cc_final: 0.5042 (mmm) REVERT: M 110 MET cc_start: 0.6644 (ttp) cc_final: 0.6300 (ttp) REVERT: M 118 MET cc_start: 0.3951 (tmm) cc_final: 0.3562 (tmm) REVERT: M 144 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8291 (mm-30) outliers start: 3 outliers final: 0 residues processed: 736 average time/residue: 0.1873 time to fit residues: 220.3665 Evaluate side-chains 550 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 548 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 39 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 260 optimal weight: 0.0970 chunk 307 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 330 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN B 87 HIS B 137 GLN B 296 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 137 GLN D 161 HIS D 225 ASN ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN J 163 GLN J 401 HIS J 475 GLN J 482 ASN K 276 GLN K 372 GLN K 401 HIS K 482 ASN K 654 ASN K 666 HIS K 760 HIS ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090135 restraints weight = 88297.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091826 restraints weight = 53744.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092981 restraints weight = 36425.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093751 restraints weight = 26980.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094300 restraints weight = 21707.500| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 31251 Z= 0.264 Angle : 0.768 9.960 42138 Z= 0.400 Chirality : 0.048 0.222 4612 Planarity : 0.005 0.056 5470 Dihedral : 6.018 58.484 4208 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.29 % Rotamer: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.13), residues: 3817 helix: 0.65 (0.12), residues: 1794 sheet: -0.30 (0.26), residues: 387 loop : -1.04 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 21 TYR 0.023 0.002 TYR J 455 PHE 0.026 0.003 PHE J 510 TRP 0.034 0.003 TRP J 508 HIS 0.012 0.002 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 (31251) covalent geometry : angle 0.76814 / 0.40 (42138) hydrogen bonds : bond 0.05224 / 3.50 ( 1538) hydrogen bonds : angle 4.97048 / 3.42 ( 4287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 681 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8655 (ttm) cc_final: 0.8303 (ttp) REVERT: A 123 MET cc_start: 0.8345 (mmm) cc_final: 0.7526 (mmm) REVERT: A 148 THR cc_start: 0.8481 (p) cc_final: 0.8279 (m) REVERT: A 176 MET cc_start: 0.9080 (mmm) cc_final: 0.7908 (mmm) REVERT: A 279 TYR cc_start: 0.8623 (t80) cc_final: 0.8296 (t80) REVERT: A 330 ILE cc_start: 0.8932 (mm) cc_final: 0.8634 (mm) REVERT: B 79 TRP cc_start: 0.8613 (m100) cc_final: 0.8176 (m100) REVERT: B 149 THR cc_start: 0.9224 (p) cc_final: 0.8996 (p) REVERT: B 167 GLU cc_start: 0.7390 (tp30) cc_final: 0.7044 (mm-30) REVERT: B 176 MET cc_start: 0.8526 (mtm) cc_final: 0.8274 (ttm) REVERT: B 222 ASP cc_start: 0.8525 (t0) cc_final: 0.8109 (m-30) REVERT: B 290 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8168 (mtt-85) REVERT: B 305 MET cc_start: 0.6962 (mtt) cc_final: 0.6686 (mtp) REVERT: B 352 PHE cc_start: 0.8725 (t80) cc_final: 0.8271 (t80) REVERT: C 86 TRP cc_start: 0.9389 (m-10) cc_final: 0.9133 (m-90) REVERT: C 123 MET cc_start: 0.8786 (mmm) cc_final: 0.8372 (mmm) REVERT: C 129 VAL cc_start: 0.8873 (m) cc_final: 0.8618 (t) REVERT: C 140 LEU cc_start: 0.9599 (mm) cc_final: 0.9182 (mt) REVERT: C 149 THR cc_start: 0.9131 (t) cc_final: 0.8876 (p) REVERT: C 227 MET cc_start: 0.8395 (tpp) cc_final: 0.8191 (tpp) REVERT: C 269 MET cc_start: 0.7821 (mmt) cc_final: 0.7551 (mmt) REVERT: C 289 ILE cc_start: 0.8647 (pt) cc_final: 0.8265 (pt) REVERT: C 305 MET cc_start: 0.8202 (mmm) cc_final: 0.7632 (tpt) REVERT: C 330 ILE cc_start: 0.9417 (mp) cc_final: 0.9095 (mm) REVERT: C 339 VAL cc_start: 0.9569 (m) cc_final: 0.9289 (m) REVERT: C 349 LEU cc_start: 0.9034 (mt) cc_final: 0.8205 (mp) REVERT: C 364 GLU cc_start: 0.8123 (tp30) cc_final: 0.7622 (tp30) REVERT: D 10 CYS cc_start: 0.8045 (t) cc_final: 0.7436 (t) REVERT: D 12 ASN cc_start: 0.8364 (m-40) cc_final: 0.7773 (m-40) REVERT: D 79 TRP cc_start: 0.7703 (m100) cc_final: 0.7366 (m100) REVERT: D 82 MET cc_start: 0.8604 (tpt) cc_final: 0.7458 (tpt) REVERT: D 133 TYR cc_start: 0.8636 (t80) cc_final: 0.8110 (t80) REVERT: D 176 MET cc_start: 0.7819 (tpt) cc_final: 0.7379 (tpt) REVERT: D 211 ASP cc_start: 0.7860 (t0) cc_final: 0.7658 (t0) REVERT: D 240 TYR cc_start: 0.8131 (t80) cc_final: 0.7679 (t80) REVERT: D 330 ILE cc_start: 0.9217 (tp) cc_final: 0.8568 (tt) REVERT: G 115 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: H 72 GLU cc_start: 0.6390 (tt0) cc_final: 0.6042 (tt0) REVERT: H 75 GLU cc_start: 0.7425 (mp0) cc_final: 0.6752 (mp0) REVERT: H 105 ARG cc_start: 0.7230 (ttm110) cc_final: 0.6698 (ttm110) REVERT: H 149 LYS cc_start: 0.5826 (mtmm) cc_final: 0.5591 (ptpt) REVERT: I 117 LEU cc_start: 0.8502 (mm) cc_final: 0.8255 (mm) REVERT: J 25 GLU cc_start: 0.7477 (mp0) cc_final: 0.7203 (mp0) REVERT: J 194 TYR cc_start: 0.8645 (t80) cc_final: 0.8366 (t80) REVERT: J 268 LEU cc_start: 0.9167 (tp) cc_final: 0.8812 (tp) REVERT: J 490 ASN cc_start: 0.8865 (t0) cc_final: 0.8448 (t0) REVERT: J 537 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7957 (mm-30) REVERT: J 568 ASN cc_start: 0.9095 (p0) cc_final: 0.8619 (p0) REVERT: J 659 MET cc_start: 0.8565 (mmm) cc_final: 0.7921 (mmt) REVERT: J 699 LEU cc_start: 0.8421 (tp) cc_final: 0.8204 (tp) REVERT: K 154 ILE cc_start: 0.9181 (mm) cc_final: 0.8896 (mm) REVERT: K 349 MET cc_start: 0.8132 (mpp) cc_final: 0.7543 (mpp) REVERT: K 378 THR cc_start: 0.8823 (p) cc_final: 0.8348 (m) REVERT: K 380 GLU cc_start: 0.9214 (mp0) cc_final: 0.8879 (mp0) REVERT: K 465 PHE cc_start: 0.7953 (t80) cc_final: 0.7060 (t80) REVERT: K 479 ASN cc_start: 0.9229 (m-40) cc_final: 0.8452 (m-40) REVERT: K 522 ASP cc_start: 0.8723 (m-30) cc_final: 0.8155 (m-30) REVERT: K 526 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7470 (mmtp) REVERT: K 534 LEU cc_start: 0.8479 (tp) cc_final: 0.8082 (tp) REVERT: K 535 GLU cc_start: 0.8081 (pt0) cc_final: 0.7804 (pt0) REVERT: K 536 GLU cc_start: 0.8084 (tt0) cc_final: 0.7410 (tt0) REVERT: K 538 CYS cc_start: 0.8809 (m) cc_final: 0.8588 (m) REVERT: K 655 LEU cc_start: 0.9459 (tp) cc_final: 0.9250 (tp) REVERT: K 694 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7742 (mtt90) REVERT: L 72 ILE cc_start: 0.7664 (tt) cc_final: 0.7460 (tt) REVERT: M 84 LEU cc_start: 0.8599 (mt) cc_final: 0.8271 (mp) REVERT: M 110 MET cc_start: 0.6758 (ttp) cc_final: 0.6432 (ttp) REVERT: M 118 MET cc_start: 0.4010 (tmm) cc_final: 0.3636 (tmm) REVERT: M 144 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8218 (mm-30) outliers start: 4 outliers final: 1 residues processed: 685 average time/residue: 0.1857 time to fit residues: 205.0154 Evaluate side-chains 515 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 513 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 104 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 376 optimal weight: 0.0670 chunk 231 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 296 ASN D 40 HIS D 225 ASN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN J 482 ASN ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 564 GLN K 654 ASN ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.092831 restraints weight = 88080.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094667 restraints weight = 50742.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096226 restraints weight = 33260.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096647 restraints weight = 21535.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.096837 restraints weight = 17731.944| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31251 Z= 0.149 Angle : 0.651 9.095 42138 Z= 0.336 Chirality : 0.044 0.253 4612 Planarity : 0.005 0.057 5470 Dihedral : 5.664 56.694 4208 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.26 % Rotamer: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % 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: 0.09 (0.14), residues: 3817 helix: 0.94 (0.12), residues: 1813 sheet: -0.16 (0.26), residues: 389 loop : -0.83 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 21 TYR 0.017 0.002 TYR C 143 PHE 0.029 0.001 PHE K 359 TRP 0.060 0.002 TRP B 86 HIS 0.014 0.001 HIS M 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (31251) covalent geometry : angle 0.65123 / 0.34 (42138) hydrogen bonds : bond 0.04623 / 3.12 ( 1538) hydrogen bonds : angle 4.64244 / 3.21 ( 4287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 693 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8629 (ttm) cc_final: 0.8223 (ttp) REVERT: A 123 MET cc_start: 0.8269 (mmm) cc_final: 0.7468 (mmm) REVERT: A 132 MET cc_start: 0.7805 (ppp) cc_final: 0.7385 (ppp) REVERT: A 176 MET cc_start: 0.9061 (mmm) cc_final: 0.8669 (mmm) REVERT: A 279 TYR cc_start: 0.8657 (t80) cc_final: 0.8418 (t80) REVERT: A 330 ILE cc_start: 0.8791 (mm) cc_final: 0.8579 (mm) REVERT: B 79 TRP cc_start: 0.8531 (m100) cc_final: 0.8111 (m100) REVERT: B 82 MET cc_start: 0.8631 (tpp) cc_final: 0.7968 (ttm) REVERT: B 84 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7848 (mtmt) REVERT: B 149 THR cc_start: 0.9142 (p) cc_final: 0.8708 (p) REVERT: B 167 GLU cc_start: 0.7121 (tp30) cc_final: 0.6519 (tp30) REVERT: B 222 ASP cc_start: 0.8435 (t0) cc_final: 0.8027 (m-30) REVERT: B 290 ARG cc_start: 0.8352 (mtt180) cc_final: 0.8018 (mtt-85) REVERT: B 305 MET cc_start: 0.7002 (mtt) cc_final: 0.6429 (mtt) REVERT: C 82 MET cc_start: 0.8508 (tpt) cc_final: 0.7228 (tpp) REVERT: C 86 TRP cc_start: 0.9384 (m-10) cc_final: 0.8663 (m-90) REVERT: C 99 GLU cc_start: 0.7896 (mm-30) cc_final: 0.6680 (mm-30) REVERT: C 123 MET cc_start: 0.8409 (mmm) cc_final: 0.7935 (mtp) REVERT: C 129 VAL cc_start: 0.8969 (m) cc_final: 0.8662 (t) REVERT: C 140 LEU cc_start: 0.9483 (mm) cc_final: 0.9004 (mt) REVERT: C 149 THR cc_start: 0.9090 (t) cc_final: 0.8885 (p) REVERT: C 289 ILE cc_start: 0.8764 (pt) cc_final: 0.8556 (pt) REVERT: C 305 MET cc_start: 0.8229 (mmm) cc_final: 0.7214 (tpp) REVERT: C 330 ILE cc_start: 0.9391 (mp) cc_final: 0.8781 (mt) REVERT: C 339 VAL cc_start: 0.9525 (m) cc_final: 0.9313 (m) REVERT: C 349 LEU cc_start: 0.9085 (mt) cc_final: 0.8181 (mp) REVERT: C 364 GLU cc_start: 0.8200 (tp30) cc_final: 0.7680 (tp30) REVERT: D 79 TRP cc_start: 0.7544 (m100) cc_final: 0.7195 (m100) REVERT: D 82 MET cc_start: 0.8222 (tpt) cc_final: 0.7222 (tpp) REVERT: D 133 TYR cc_start: 0.8673 (t80) cc_final: 0.8351 (t80) REVERT: D 176 MET cc_start: 0.7633 (tpt) cc_final: 0.7106 (tpt) REVERT: D 211 ASP cc_start: 0.7608 (t0) cc_final: 0.7277 (t0) REVERT: D 240 TYR cc_start: 0.8188 (t80) cc_final: 0.7564 (t80) REVERT: D 330 ILE cc_start: 0.9155 (tp) cc_final: 0.8947 (mp) REVERT: E 267 TYR cc_start: 0.7062 (t80) cc_final: 0.6773 (t80) REVERT: E 276 HIS cc_start: 0.6381 (p-80) cc_final: 0.5677 (t70) REVERT: G 141 MET cc_start: 0.3947 (ppp) cc_final: 0.3229 (ttt) REVERT: H 72 GLU cc_start: 0.6312 (tt0) cc_final: 0.5761 (tt0) REVERT: H 105 ARG cc_start: 0.7416 (ttm110) cc_final: 0.7120 (ttm110) REVERT: H 149 LYS cc_start: 0.5898 (mtmm) cc_final: 0.5642 (ptpt) REVERT: I 117 LEU cc_start: 0.8508 (mm) cc_final: 0.8267 (mm) REVERT: J 113 MET cc_start: 0.7248 (mtm) cc_final: 0.6597 (ttp) REVERT: J 194 TYR cc_start: 0.8590 (t80) cc_final: 0.8223 (t80) REVERT: J 268 LEU cc_start: 0.9155 (tp) cc_final: 0.8819 (tp) REVERT: J 490 ASN cc_start: 0.8870 (t0) cc_final: 0.8346 (t0) REVERT: J 568 ASN cc_start: 0.9078 (p0) cc_final: 0.8706 (p0) REVERT: K 237 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7759 (ptp-170) REVERT: K 313 ILE cc_start: 0.9029 (pt) cc_final: 0.8690 (mp) REVERT: K 351 LYS cc_start: 0.8095 (mttp) cc_final: 0.7813 (mttm) REVERT: K 357 MET cc_start: 0.8797 (tpp) cc_final: 0.8480 (mmm) REVERT: K 371 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7143 (mt-10) REVERT: K 378 THR cc_start: 0.8723 (p) cc_final: 0.8228 (m) REVERT: K 380 GLU cc_start: 0.9161 (mp0) cc_final: 0.8840 (mp0) REVERT: K 424 THR cc_start: 0.9397 (p) cc_final: 0.9135 (p) REVERT: K 466 GLU cc_start: 0.8355 (tt0) cc_final: 0.7916 (tt0) REVERT: K 479 ASN cc_start: 0.9262 (m-40) cc_final: 0.8455 (m-40) REVERT: K 526 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7557 (mttm) REVERT: K 535 GLU cc_start: 0.7902 (pt0) cc_final: 0.7642 (pt0) REVERT: K 536 GLU cc_start: 0.7944 (tt0) cc_final: 0.7292 (tt0) REVERT: K 694 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.7603 (mtt90) REVERT: K 799 MET cc_start: 0.6074 (mtp) cc_final: 0.5812 (mtp) REVERT: L 72 ILE cc_start: 0.7578 (tt) cc_final: 0.7354 (tt) REVERT: M 84 LEU cc_start: 0.8643 (mt) cc_final: 0.8341 (mp) REVERT: M 110 MET cc_start: 0.6736 (ttp) cc_final: 0.6225 (ttp) REVERT: M 118 MET cc_start: 0.4267 (tmm) cc_final: 0.3867 (tmm) REVERT: M 144 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8283 (mm-30) REVERT: M 171 GLU cc_start: 0.6971 (tp30) cc_final: 0.6558 (tp30) outliers start: 3 outliers final: 0 residues processed: 696 average time/residue: 0.1896 time to fit residues: 212.4584 Evaluate side-chains 523 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 180 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 350 optimal weight: 0.0170 chunk 345 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 355 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 231 optimal weight: 0.5980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN B 296 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 87 HIS D 225 ASN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 482 ASN K 654 ASN L 125 ASN ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.107618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094114 restraints weight = 87303.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096034 restraints weight = 51292.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097768 restraints weight = 33363.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.098229 restraints weight = 21103.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098353 restraints weight = 17112.675| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31251 Z= 0.145 Angle : 0.641 11.866 42138 Z= 0.329 Chirality : 0.043 0.249 4612 Planarity : 0.005 0.055 5470 Dihedral : 5.507 57.914 4208 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.10 % Rotamer: Outliers : 0.09 % Allowed : 2.03 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % 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: 0.19 (0.14), residues: 3817 helix: 1.03 (0.12), residues: 1813 sheet: -0.12 (0.26), residues: 394 loop : -0.80 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG J 108 TYR 0.024 0.002 TYR A 306 PHE 0.021 0.001 PHE A 90 TRP 0.078 0.002 TRP B 86 HIS 0.010 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (31251) covalent geometry : angle 0.64115 / 0.33 (42138) hydrogen bonds : bond 0.04504 / 3.05 ( 1538) hydrogen bonds : angle 4.55830 / 3.14 ( 4287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 668 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8509 (ttm) cc_final: 0.8130 (ttp) REVERT: A 123 MET cc_start: 0.8332 (mmm) cc_final: 0.7759 (mmm) REVERT: A 132 MET cc_start: 0.7739 (ppp) cc_final: 0.7412 (ppp) REVERT: A 176 MET cc_start: 0.9011 (mmm) cc_final: 0.8544 (mmm) REVERT: A 279 TYR cc_start: 0.8649 (t80) cc_final: 0.8445 (t80) REVERT: A 330 ILE cc_start: 0.8765 (mm) cc_final: 0.8526 (mm) REVERT: B 79 TRP cc_start: 0.8524 (m100) cc_final: 0.8022 (m100) REVERT: B 84 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7925 (mtmt) REVERT: B 149 THR cc_start: 0.9175 (p) cc_final: 0.8657 (p) REVERT: B 167 GLU cc_start: 0.7270 (tp30) cc_final: 0.6582 (tp30) REVERT: B 222 ASP cc_start: 0.8394 (t0) cc_final: 0.8133 (m-30) REVERT: B 288 ASP cc_start: 0.8694 (m-30) cc_final: 0.8438 (m-30) REVERT: B 290 ARG cc_start: 0.8528 (mtt180) cc_final: 0.8061 (mtt-85) REVERT: B 305 MET cc_start: 0.6904 (mtt) cc_final: 0.6335 (mtt) REVERT: C 82 MET cc_start: 0.8444 (tpt) cc_final: 0.8234 (tpp) REVERT: C 86 TRP cc_start: 0.9396 (m-10) cc_final: 0.9099 (m-10) REVERT: C 123 MET cc_start: 0.8420 (mmm) cc_final: 0.8011 (mtp) REVERT: C 140 LEU cc_start: 0.9492 (mm) cc_final: 0.9071 (mt) REVERT: C 149 THR cc_start: 0.9105 (t) cc_final: 0.8793 (p) REVERT: C 167 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8530 (mp0) REVERT: C 227 MET cc_start: 0.8375 (tpp) cc_final: 0.8084 (tpp) REVERT: C 296 ASN cc_start: 0.8397 (t0) cc_final: 0.8088 (t0) REVERT: C 305 MET cc_start: 0.8152 (mmm) cc_final: 0.7215 (tpp) REVERT: C 330 ILE cc_start: 0.9348 (mp) cc_final: 0.8856 (mt) REVERT: C 349 LEU cc_start: 0.9073 (mt) cc_final: 0.8012 (mt) REVERT: C 364 GLU cc_start: 0.8047 (tp30) cc_final: 0.7518 (tp30) REVERT: D 82 MET cc_start: 0.8072 (tpt) cc_final: 0.7643 (tpt) REVERT: D 123 MET cc_start: 0.8633 (mmm) cc_final: 0.8282 (mmm) REVERT: D 133 TYR cc_start: 0.8646 (t80) cc_final: 0.8439 (t80) REVERT: D 176 MET cc_start: 0.7551 (tpt) cc_final: 0.6609 (tpp) REVERT: D 211 ASP cc_start: 0.7430 (t0) cc_final: 0.7103 (t0) REVERT: D 240 TYR cc_start: 0.8062 (t80) cc_final: 0.7506 (t80) REVERT: D 330 ILE cc_start: 0.9198 (tp) cc_final: 0.8586 (tt) REVERT: E 267 TYR cc_start: 0.7090 (t80) cc_final: 0.6733 (t80) REVERT: E 276 HIS cc_start: 0.6105 (p-80) cc_final: 0.5830 (t70) REVERT: F 281 MET cc_start: 0.4675 (ppp) cc_final: 0.4407 (ppp) REVERT: G 8 MET cc_start: 0.5022 (ttm) cc_final: 0.4208 (ttm) REVERT: H 72 GLU cc_start: 0.6268 (tt0) cc_final: 0.5825 (tt0) REVERT: H 105 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6997 (ttm110) REVERT: H 149 LYS cc_start: 0.5787 (mtmm) cc_final: 0.5529 (ptpt) REVERT: I 117 LEU cc_start: 0.8496 (mm) cc_final: 0.8226 (mm) REVERT: J 25 GLU cc_start: 0.7312 (mp0) cc_final: 0.7069 (mp0) REVERT: J 194 TYR cc_start: 0.8559 (t80) cc_final: 0.8137 (t80) REVERT: J 268 LEU cc_start: 0.9182 (tp) cc_final: 0.8779 (tp) REVERT: J 344 GLU cc_start: 0.7505 (pp20) cc_final: 0.7107 (pp20) REVERT: J 490 ASN cc_start: 0.8894 (t0) cc_final: 0.8539 (t0) REVERT: J 508 TRP cc_start: 0.8720 (t-100) cc_final: 0.8463 (t-100) REVERT: J 568 ASN cc_start: 0.9100 (p0) cc_final: 0.8748 (p0) REVERT: J 659 MET cc_start: 0.8718 (mmm) cc_final: 0.8226 (mmt) REVERT: J 699 LEU cc_start: 0.8356 (tp) cc_final: 0.7929 (tp) REVERT: K 31 PHE cc_start: 0.9053 (t80) cc_final: 0.8614 (t80) REVERT: K 122 CYS cc_start: 0.8757 (p) cc_final: 0.8533 (p) REVERT: K 266 TYR cc_start: 0.8841 (m-80) cc_final: 0.8521 (m-80) REVERT: K 313 ILE cc_start: 0.9091 (pt) cc_final: 0.8778 (mp) REVERT: K 349 MET cc_start: 0.7905 (mpp) cc_final: 0.7478 (mpp) REVERT: K 357 MET cc_start: 0.8770 (tpp) cc_final: 0.8532 (mmm) REVERT: K 378 THR cc_start: 0.8544 (p) cc_final: 0.8103 (m) REVERT: K 380 GLU cc_start: 0.9199 (mp0) cc_final: 0.8916 (mp0) REVERT: K 424 THR cc_start: 0.9382 (p) cc_final: 0.9130 (p) REVERT: K 466 GLU cc_start: 0.8399 (tt0) cc_final: 0.7808 (tt0) REVERT: K 475 GLN cc_start: 0.8639 (mp10) cc_final: 0.7941 (mp10) REVERT: K 479 ASN cc_start: 0.9172 (m-40) cc_final: 0.8277 (m-40) REVERT: K 522 ASP cc_start: 0.8620 (m-30) cc_final: 0.8254 (m-30) REVERT: K 526 LYS cc_start: 0.8343 (mmtp) cc_final: 0.7792 (mmtp) REVERT: K 536 GLU cc_start: 0.7958 (tt0) cc_final: 0.6876 (tt0) REVERT: K 538 CYS cc_start: 0.8677 (m) cc_final: 0.8317 (m) REVERT: K 694 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7653 (mtt90) REVERT: L 72 ILE cc_start: 0.7088 (tt) cc_final: 0.6863 (tt) REVERT: L 118 MET cc_start: 0.5334 (mmp) cc_final: 0.4880 (mmp) REVERT: M 84 LEU cc_start: 0.8649 (mt) cc_final: 0.8369 (mp) REVERT: M 110 MET cc_start: 0.6510 (ttp) cc_final: 0.6074 (ttp) REVERT: M 118 MET cc_start: 0.4326 (tmm) cc_final: 0.3909 (tmm) REVERT: M 144 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8242 (mm-30) REVERT: M 171 GLU cc_start: 0.6835 (tp30) cc_final: 0.6499 (tp30) outliers start: 3 outliers final: 1 residues processed: 671 average time/residue: 0.1831 time to fit residues: 198.6611 Evaluate side-chains 540 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 539 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 chunk 314 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 289 optimal weight: 0.4980 chunk 209 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 296 ASN C 296 ASN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 482 ASN K 654 ASN ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094208 restraints weight = 88009.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096049 restraints weight = 50682.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097638 restraints weight = 33697.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098021 restraints weight = 21965.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098200 restraints weight = 18161.262| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31251 Z= 0.134 Angle : 0.647 13.930 42138 Z= 0.328 Chirality : 0.044 0.262 4612 Planarity : 0.004 0.081 5470 Dihedral : 5.362 59.330 4208 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 0.03 % Allowed : 1.33 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3817 helix: 1.09 (0.12), residues: 1815 sheet: -0.06 (0.25), residues: 405 loop : -0.78 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 82 TYR 0.020 0.002 TYR B 337 PHE 0.023 0.001 PHE B 90 TRP 0.062 0.002 TRP B 86 HIS 0.007 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (31251) covalent geometry : angle 0.64698 / 0.33 (42138) hydrogen bonds : bond 0.04386 / 2.96 ( 1538) hydrogen bonds : angle 4.52273 / 3.12 ( 4287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 676 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8567 (ttm) cc_final: 0.8172 (ttp) REVERT: A 123 MET cc_start: 0.8320 (mmm) cc_final: 0.7170 (mmm) REVERT: A 132 MET cc_start: 0.7761 (ppp) cc_final: 0.7532 (ppp) REVERT: A 227 MET cc_start: 0.7863 (tpp) cc_final: 0.7432 (tpp) REVERT: A 330 ILE cc_start: 0.8724 (mm) cc_final: 0.8486 (mm) REVERT: B 79 TRP cc_start: 0.8503 (m100) cc_final: 0.7908 (m100) REVERT: B 84 LYS cc_start: 0.8307 (mtmm) cc_final: 0.8004 (mtmt) REVERT: B 149 THR cc_start: 0.9137 (p) cc_final: 0.8737 (p) REVERT: B 167 GLU cc_start: 0.7257 (tp30) cc_final: 0.6591 (tp30) REVERT: B 269 MET cc_start: 0.8093 (mmm) cc_final: 0.7851 (mmt) REVERT: B 288 ASP cc_start: 0.8762 (m-30) cc_final: 0.8463 (m-30) REVERT: B 290 ARG cc_start: 0.8410 (mtt180) cc_final: 0.7938 (mtt-85) REVERT: B 315 LYS cc_start: 0.9232 (pptt) cc_final: 0.8933 (ttpp) REVERT: B 325 MET cc_start: 0.7757 (mmm) cc_final: 0.7556 (mmm) REVERT: C 61 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8319 (mmtp) REVERT: C 82 MET cc_start: 0.8181 (tpt) cc_final: 0.7092 (tpp) REVERT: C 86 TRP cc_start: 0.8981 (m-10) cc_final: 0.8583 (m-90) REVERT: C 140 LEU cc_start: 0.9463 (mm) cc_final: 0.8975 (mt) REVERT: C 149 THR cc_start: 0.9153 (t) cc_final: 0.8711 (p) REVERT: C 296 ASN cc_start: 0.8422 (t160) cc_final: 0.8036 (t0) REVERT: C 305 MET cc_start: 0.8213 (mmm) cc_final: 0.7266 (tpp) REVERT: C 345 ILE cc_start: 0.9397 (tp) cc_final: 0.9011 (mm) REVERT: C 349 LEU cc_start: 0.9051 (mt) cc_final: 0.8015 (mt) REVERT: C 364 GLU cc_start: 0.8068 (tp30) cc_final: 0.7536 (tp30) REVERT: D 79 TRP cc_start: 0.7364 (m100) cc_final: 0.7142 (m100) REVERT: D 176 MET cc_start: 0.7664 (tpt) cc_final: 0.6781 (tpp) REVERT: D 240 TYR cc_start: 0.8086 (t80) cc_final: 0.7505 (t80) REVERT: D 330 ILE cc_start: 0.9187 (tp) cc_final: 0.8986 (mp) REVERT: E 267 TYR cc_start: 0.7074 (t80) cc_final: 0.6706 (t80) REVERT: G 8 MET cc_start: 0.5151 (ttm) cc_final: 0.4215 (ttm) REVERT: G 97 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7760 (mm-30) REVERT: H 72 GLU cc_start: 0.6555 (tt0) cc_final: 0.6281 (tt0) REVERT: H 149 LYS cc_start: 0.5777 (mtmm) cc_final: 0.5571 (ptpt) REVERT: I 117 LEU cc_start: 0.8566 (mm) cc_final: 0.8278 (mm) REVERT: J 194 TYR cc_start: 0.8520 (t80) cc_final: 0.8060 (t80) REVERT: J 235 THR cc_start: 0.9137 (p) cc_final: 0.8559 (t) REVERT: J 236 VAL cc_start: 0.8790 (m) cc_final: 0.8546 (p) REVERT: J 268 LEU cc_start: 0.9165 (tp) cc_final: 0.8763 (tp) REVERT: J 441 THR cc_start: 0.9437 (p) cc_final: 0.9174 (t) REVERT: J 490 ASN cc_start: 0.8898 (t0) cc_final: 0.8511 (t0) REVERT: J 508 TRP cc_start: 0.8843 (t-100) cc_final: 0.8486 (t-100) REVERT: J 568 ASN cc_start: 0.9090 (p0) cc_final: 0.8728 (p0) REVERT: J 659 MET cc_start: 0.8610 (mmm) cc_final: 0.8409 (mmm) REVERT: K 31 PHE cc_start: 0.9017 (t80) cc_final: 0.8666 (t80) REVERT: K 122 CYS cc_start: 0.8735 (p) cc_final: 0.8520 (p) REVERT: K 248 ILE cc_start: 0.9039 (tp) cc_final: 0.8821 (tp) REVERT: K 266 TYR cc_start: 0.8775 (m-80) cc_final: 0.8554 (m-80) REVERT: K 313 ILE cc_start: 0.9068 (pt) cc_final: 0.8763 (mp) REVERT: K 351 LYS cc_start: 0.8249 (mttp) cc_final: 0.7986 (mttm) REVERT: K 357 MET cc_start: 0.8817 (tpp) cc_final: 0.8541 (mmm) REVERT: K 378 THR cc_start: 0.8662 (p) cc_final: 0.8266 (m) REVERT: K 380 GLU cc_start: 0.9183 (mp0) cc_final: 0.8873 (mp0) REVERT: K 424 THR cc_start: 0.9402 (p) cc_final: 0.9171 (p) REVERT: K 466 GLU cc_start: 0.8291 (tt0) cc_final: 0.7640 (tt0) REVERT: K 479 ASN cc_start: 0.9241 (m-40) cc_final: 0.8362 (m-40) REVERT: K 522 ASP cc_start: 0.8471 (m-30) cc_final: 0.8043 (m-30) REVERT: K 525 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8343 (tm-30) REVERT: K 526 LYS cc_start: 0.8085 (mmtp) cc_final: 0.7721 (mmtp) REVERT: K 534 LEU cc_start: 0.8298 (tp) cc_final: 0.7579 (tp) REVERT: K 536 GLU cc_start: 0.7958 (tt0) cc_final: 0.6832 (tt0) REVERT: K 538 CYS cc_start: 0.8596 (m) cc_final: 0.8249 (m) REVERT: K 694 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7593 (mtt90) REVERT: K 799 MET cc_start: 0.5877 (mtp) cc_final: 0.5469 (mtp) REVERT: L 72 ILE cc_start: 0.7058 (tt) cc_final: 0.6772 (tt) REVERT: L 118 MET cc_start: 0.5447 (mmp) cc_final: 0.4779 (mmp) REVERT: M 84 LEU cc_start: 0.8565 (mt) cc_final: 0.8311 (mp) REVERT: M 110 MET cc_start: 0.6639 (ttp) cc_final: 0.6190 (ttp) REVERT: M 118 MET cc_start: 0.4359 (tmm) cc_final: 0.3911 (tmm) REVERT: M 144 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8230 (mm-30) REVERT: M 171 GLU cc_start: 0.6771 (tp30) cc_final: 0.6456 (tp30) outliers start: 1 outliers final: 0 residues processed: 677 average time/residue: 0.1790 time to fit residues: 196.2260 Evaluate side-chains 547 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 249 optimal weight: 0.0030 chunk 356 optimal weight: 4.9990 chunk 333 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 377 optimal weight: 2.9990 chunk 309 optimal weight: 0.6980 chunk 285 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN B 296 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 482 ASN K 80 ASN K 482 ASN K 654 ASN L 90 GLN ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095243 restraints weight = 87061.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097148 restraints weight = 52243.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098577 restraints weight = 34848.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099160 restraints weight = 22979.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099243 restraints weight = 18563.412| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31251 Z= 0.141 Angle : 0.647 11.066 42138 Z= 0.328 Chirality : 0.044 0.260 4612 Planarity : 0.005 0.144 5470 Dihedral : 5.328 59.681 4208 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 0.03 % Allowed : 0.67 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3817 helix: 1.08 (0.12), residues: 1828 sheet: -0.04 (0.26), residues: 402 loop : -0.73 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG L 82 TYR 0.025 0.002 TYR D 133 PHE 0.028 0.001 PHE D 223 TRP 0.041 0.002 TRP B 86 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (31251) covalent geometry : angle 0.64693 / 0.33 (42138) hydrogen bonds : bond 0.04371 / 2.96 ( 1538) hydrogen bonds : angle 4.51179 / 3.11 ( 4287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 678 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8544 (ttm) cc_final: 0.8198 (ttp) REVERT: A 123 MET cc_start: 0.8424 (mmm) cc_final: 0.7893 (mmm) REVERT: A 132 MET cc_start: 0.7856 (ppp) cc_final: 0.7527 (ppp) REVERT: A 330 ILE cc_start: 0.8718 (mm) cc_final: 0.8489 (mm) REVERT: B 79 TRP cc_start: 0.8266 (m100) cc_final: 0.7838 (m100) REVERT: B 84 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7997 (mtmt) REVERT: B 167 GLU cc_start: 0.7429 (tp30) cc_final: 0.6786 (tp30) REVERT: B 244 ASP cc_start: 0.8673 (p0) cc_final: 0.8279 (p0) REVERT: B 269 MET cc_start: 0.8094 (mmm) cc_final: 0.7829 (mmt) REVERT: B 288 ASP cc_start: 0.8757 (m-30) cc_final: 0.8462 (m-30) REVERT: B 290 ARG cc_start: 0.8398 (mtt180) cc_final: 0.7921 (mtt-85) REVERT: B 305 MET cc_start: 0.7080 (mtt) cc_final: 0.6467 (mtt) REVERT: B 336 LYS cc_start: 0.9333 (mtpt) cc_final: 0.8962 (mtpp) REVERT: C 82 MET cc_start: 0.8210 (tpt) cc_final: 0.7086 (tpp) REVERT: C 86 TRP cc_start: 0.8978 (m-10) cc_final: 0.8386 (m-90) REVERT: C 140 LEU cc_start: 0.9459 (mm) cc_final: 0.9152 (mt) REVERT: C 149 THR cc_start: 0.9149 (t) cc_final: 0.8742 (p) REVERT: C 227 MET cc_start: 0.8465 (tpp) cc_final: 0.8125 (tpp) REVERT: C 296 ASN cc_start: 0.8494 (t0) cc_final: 0.8079 (t0) REVERT: C 305 MET cc_start: 0.8182 (mmm) cc_final: 0.7289 (tpp) REVERT: C 345 ILE cc_start: 0.9362 (tp) cc_final: 0.9057 (mm) REVERT: C 364 GLU cc_start: 0.7998 (tp30) cc_final: 0.7460 (tp30) REVERT: D 61 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8104 (mtmt) REVERT: D 79 TRP cc_start: 0.7469 (m100) cc_final: 0.7201 (m100) REVERT: D 82 MET cc_start: 0.8187 (tpp) cc_final: 0.7024 (tpp) REVERT: D 176 MET cc_start: 0.7598 (tpt) cc_final: 0.6772 (tpp) REVERT: D 240 TYR cc_start: 0.8230 (t80) cc_final: 0.7494 (t80) REVERT: D 306 TYR cc_start: 0.8644 (m-10) cc_final: 0.8372 (m-10) REVERT: D 330 ILE cc_start: 0.9167 (tp) cc_final: 0.8960 (mp) REVERT: F 281 MET cc_start: 0.5500 (ppp) cc_final: 0.5218 (ppp) REVERT: G 8 MET cc_start: 0.4931 (ttm) cc_final: 0.3966 (ttm) REVERT: I 117 LEU cc_start: 0.8516 (mm) cc_final: 0.8230 (mm) REVERT: J 194 TYR cc_start: 0.8501 (t80) cc_final: 0.8081 (t80) REVERT: J 235 THR cc_start: 0.9089 (p) cc_final: 0.8576 (t) REVERT: J 268 LEU cc_start: 0.9115 (tp) cc_final: 0.8742 (tp) REVERT: J 357 MET cc_start: 0.8092 (mmm) cc_final: 0.6834 (mmm) REVERT: J 441 THR cc_start: 0.9443 (p) cc_final: 0.9179 (t) REVERT: J 508 TRP cc_start: 0.8923 (t-100) cc_final: 0.8572 (t-100) REVERT: J 568 ASN cc_start: 0.9103 (p0) cc_final: 0.8755 (p0) REVERT: J 655 LEU cc_start: 0.9049 (tp) cc_final: 0.8803 (tt) REVERT: J 659 MET cc_start: 0.8604 (mmm) cc_final: 0.8366 (mmm) REVERT: J 699 LEU cc_start: 0.8442 (tp) cc_final: 0.7960 (tp) REVERT: K 31 PHE cc_start: 0.9004 (t80) cc_final: 0.8635 (t80) REVERT: K 248 ILE cc_start: 0.9063 (tp) cc_final: 0.8832 (tp) REVERT: K 266 TYR cc_start: 0.8779 (m-80) cc_final: 0.8541 (m-80) REVERT: K 313 ILE cc_start: 0.9095 (pt) cc_final: 0.8820 (mp) REVERT: K 378 THR cc_start: 0.8800 (p) cc_final: 0.8462 (m) REVERT: K 380 GLU cc_start: 0.9205 (mp0) cc_final: 0.8927 (mp0) REVERT: K 424 THR cc_start: 0.9405 (p) cc_final: 0.9163 (p) REVERT: K 466 GLU cc_start: 0.8305 (tt0) cc_final: 0.7769 (tt0) REVERT: K 475 GLN cc_start: 0.8647 (mp10) cc_final: 0.7906 (mp10) REVERT: K 479 ASN cc_start: 0.9275 (m-40) cc_final: 0.8425 (m-40) REVERT: K 522 ASP cc_start: 0.8482 (m-30) cc_final: 0.8152 (m-30) REVERT: K 525 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8303 (tm-30) REVERT: K 526 LYS cc_start: 0.7995 (mmtp) cc_final: 0.7694 (mmtp) REVERT: K 535 GLU cc_start: 0.7704 (pt0) cc_final: 0.7451 (pt0) REVERT: K 538 CYS cc_start: 0.8670 (m) cc_final: 0.8111 (m) REVERT: K 694 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7626 (mtt90) REVERT: L 72 ILE cc_start: 0.7002 (tt) cc_final: 0.6674 (tt) REVERT: L 118 MET cc_start: 0.5356 (mmp) cc_final: 0.4672 (mmp) REVERT: M 84 LEU cc_start: 0.8557 (mt) cc_final: 0.8291 (mp) REVERT: M 110 MET cc_start: 0.6812 (ttp) cc_final: 0.6381 (ttp) REVERT: M 118 MET cc_start: 0.4442 (tmm) cc_final: 0.3993 (tmm) REVERT: M 144 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8292 (mm-30) REVERT: M 171 GLU cc_start: 0.6808 (tp30) cc_final: 0.6479 (tp30) outliers start: 1 outliers final: 0 residues processed: 679 average time/residue: 0.1704 time to fit residues: 187.5233 Evaluate side-chains 538 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 221 optimal weight: 3.9990 chunk 341 optimal weight: 0.9980 chunk 311 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 289 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 360 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 296 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 482 ASN K 654 ASN ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092860 restraints weight = 88489.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094553 restraints weight = 52408.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096194 restraints weight = 35190.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096668 restraints weight = 22133.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096671 restraints weight = 18421.775| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31251 Z= 0.154 Angle : 0.666 11.099 42138 Z= 0.339 Chirality : 0.044 0.271 4612 Planarity : 0.005 0.057 5470 Dihedral : 5.324 57.922 4208 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.98 % Favored : 94.97 % Rotamer: Outliers : 0.03 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % 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 (0.14), residues: 3817 helix: 1.04 (0.12), residues: 1826 sheet: -0.02 (0.26), residues: 400 loop : -0.74 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 105 TYR 0.025 0.002 TYR C 166 PHE 0.021 0.001 PHE D 223 TRP 0.077 0.003 TRP D 86 HIS 0.009 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (31251) covalent geometry : angle 0.66627 / 0.34 (42138) hydrogen bonds : bond 0.04394 / 2.98 ( 1538) hydrogen bonds : angle 4.54938 / 3.13 ( 4287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 661 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8266 (mm) cc_final: 0.7858 (mm) REVERT: A 119 MET cc_start: 0.8567 (ttm) cc_final: 0.8224 (ttp) REVERT: A 123 MET cc_start: 0.8323 (mmm) cc_final: 0.7796 (mmm) REVERT: A 132 MET cc_start: 0.7875 (ppp) cc_final: 0.7537 (ppp) REVERT: B 79 TRP cc_start: 0.8129 (m100) cc_final: 0.7927 (m100) REVERT: B 149 THR cc_start: 0.9172 (p) cc_final: 0.8785 (p) REVERT: B 167 GLU cc_start: 0.7392 (tp30) cc_final: 0.6841 (tp30) REVERT: B 244 ASP cc_start: 0.8717 (p0) cc_final: 0.8422 (p0) REVERT: B 269 MET cc_start: 0.8056 (mmm) cc_final: 0.7797 (mmt) REVERT: B 287 ILE cc_start: 0.9251 (tt) cc_final: 0.8783 (tt) REVERT: B 288 ASP cc_start: 0.8779 (m-30) cc_final: 0.8456 (m-30) REVERT: B 290 ARG cc_start: 0.8474 (mtt180) cc_final: 0.7989 (mtt-85) REVERT: B 325 MET cc_start: 0.7671 (mmm) cc_final: 0.7377 (mmt) REVERT: B 336 LYS cc_start: 0.9353 (mtpt) cc_final: 0.9063 (mtpp) REVERT: C 99 GLU cc_start: 0.7943 (mm-30) cc_final: 0.6767 (mm-30) REVERT: C 140 LEU cc_start: 0.9473 (mm) cc_final: 0.9205 (mt) REVERT: C 149 THR cc_start: 0.9178 (t) cc_final: 0.8660 (p) REVERT: C 227 MET cc_start: 0.8583 (tpp) cc_final: 0.8250 (tpp) REVERT: C 305 MET cc_start: 0.8125 (mmm) cc_final: 0.7269 (tpp) REVERT: C 364 GLU cc_start: 0.8014 (tp30) cc_final: 0.7498 (tp30) REVERT: D 10 CYS cc_start: 0.8309 (t) cc_final: 0.8038 (t) REVERT: D 50 LYS cc_start: 0.7527 (mmmm) cc_final: 0.7260 (mmmm) REVERT: D 79 TRP cc_start: 0.7534 (m100) cc_final: 0.7195 (m100) REVERT: D 137 GLN cc_start: 0.7115 (mt0) cc_final: 0.6851 (mp10) REVERT: D 176 MET cc_start: 0.7664 (tpt) cc_final: 0.6781 (tpp) REVERT: D 240 TYR cc_start: 0.8244 (t80) cc_final: 0.7539 (t80) REVERT: D 330 ILE cc_start: 0.9144 (tp) cc_final: 0.8657 (tt) REVERT: E 267 TYR cc_start: 0.6942 (t80) cc_final: 0.6680 (t80) REVERT: F 281 MET cc_start: 0.5506 (ppp) cc_final: 0.5198 (ppp) REVERT: G 8 MET cc_start: 0.5056 (ttm) cc_final: 0.3982 (ttm) REVERT: I 117 LEU cc_start: 0.8538 (mm) cc_final: 0.8242 (mm) REVERT: J 87 ILE cc_start: 0.8183 (mm) cc_final: 0.7820 (mm) REVERT: J 194 TYR cc_start: 0.8516 (t80) cc_final: 0.8149 (t80) REVERT: J 235 THR cc_start: 0.9019 (p) cc_final: 0.8668 (t) REVERT: J 268 LEU cc_start: 0.9065 (tp) cc_final: 0.8729 (tp) REVERT: J 344 GLU cc_start: 0.7678 (pp20) cc_final: 0.7397 (pp20) REVERT: J 357 MET cc_start: 0.8459 (mmm) cc_final: 0.7660 (mmm) REVERT: J 568 ASN cc_start: 0.9086 (p0) cc_final: 0.8736 (p0) REVERT: J 699 LEU cc_start: 0.8412 (tp) cc_final: 0.8185 (tp) REVERT: K 31 PHE cc_start: 0.9014 (t80) cc_final: 0.8582 (t80) REVERT: K 248 ILE cc_start: 0.9081 (tp) cc_final: 0.8825 (tp) REVERT: K 313 ILE cc_start: 0.9109 (pt) cc_final: 0.8809 (mp) REVERT: K 380 GLU cc_start: 0.9155 (mp0) cc_final: 0.8931 (mp0) REVERT: K 442 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7598 (tpt-90) REVERT: K 479 ASN cc_start: 0.9226 (m-40) cc_final: 0.8446 (m-40) REVERT: K 522 ASP cc_start: 0.8389 (m-30) cc_final: 0.7945 (m-30) REVERT: K 525 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8248 (tm-30) REVERT: K 526 LYS cc_start: 0.8123 (mmtp) cc_final: 0.7770 (mmtp) REVERT: K 535 GLU cc_start: 0.7531 (pt0) cc_final: 0.7288 (pt0) REVERT: K 536 GLU cc_start: 0.8016 (pp20) cc_final: 0.7604 (pp20) REVERT: K 538 CYS cc_start: 0.8740 (m) cc_final: 0.8123 (m) REVERT: K 694 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.7549 (mtt90) REVERT: K 756 TYR cc_start: 0.7929 (p90) cc_final: 0.7501 (p90) REVERT: L 72 ILE cc_start: 0.6792 (tt) cc_final: 0.6436 (tt) REVERT: L 118 MET cc_start: 0.5459 (mmp) cc_final: 0.4767 (mmp) REVERT: M 110 MET cc_start: 0.6694 (ttp) cc_final: 0.6375 (ttp) REVERT: M 118 MET cc_start: 0.4431 (tmm) cc_final: 0.3972 (tmm) REVERT: M 144 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8292 (mm-30) outliers start: 1 outliers final: 0 residues processed: 662 average time/residue: 0.1698 time to fit residues: 183.1607 Evaluate side-chains 518 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 228 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 208 optimal weight: 0.0170 chunk 181 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN B 296 ASN B 353 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 482 ASN ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095768 restraints weight = 86036.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097694 restraints weight = 51991.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099238 restraints weight = 34406.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099716 restraints weight = 22829.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099785 restraints weight = 18983.080| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31251 Z= 0.146 Angle : 0.670 13.661 42138 Z= 0.341 Chirality : 0.044 0.320 4612 Planarity : 0.005 0.090 5470 Dihedral : 5.314 57.531 4208 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3817 helix: 1.02 (0.12), residues: 1819 sheet: -0.05 (0.26), residues: 414 loop : -0.78 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 123 TYR 0.025 0.002 TYR C 166 PHE 0.043 0.002 PHE J 468 TRP 0.090 0.003 TRP B 86 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (31251) covalent geometry : angle 0.66985 / 0.34 (42138) hydrogen bonds : bond 0.04403 / 2.98 ( 1538) hydrogen bonds : angle 4.57778 / 3.15 ( 4287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 649 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8302 (mm) cc_final: 0.7841 (mm) REVERT: A 119 MET cc_start: 0.8546 (ttm) cc_final: 0.8179 (ttp) REVERT: A 123 MET cc_start: 0.8372 (mmm) cc_final: 0.7854 (mmm) REVERT: A 132 MET cc_start: 0.7873 (ppp) cc_final: 0.7497 (ppp) REVERT: A 176 MET cc_start: 0.8948 (mmm) cc_final: 0.8572 (mmm) REVERT: A 330 ILE cc_start: 0.8729 (mm) cc_final: 0.8520 (mm) REVERT: B 149 THR cc_start: 0.9172 (p) cc_final: 0.8587 (p) REVERT: B 167 GLU cc_start: 0.7598 (tp30) cc_final: 0.6720 (tp30) REVERT: B 244 ASP cc_start: 0.8717 (p0) cc_final: 0.8422 (p0) REVERT: B 269 MET cc_start: 0.8099 (mmm) cc_final: 0.7854 (mmt) REVERT: B 287 ILE cc_start: 0.9228 (tt) cc_final: 0.8770 (tt) REVERT: B 288 ASP cc_start: 0.8762 (m-30) cc_final: 0.8435 (m-30) REVERT: B 290 ARG cc_start: 0.8413 (mtt180) cc_final: 0.7919 (mtt-85) REVERT: B 325 MET cc_start: 0.7705 (mmm) cc_final: 0.7358 (mmt) REVERT: C 82 MET cc_start: 0.8103 (tpp) cc_final: 0.7472 (tpp) REVERT: C 86 TRP cc_start: 0.9030 (m-10) cc_final: 0.8654 (m-90) REVERT: C 99 GLU cc_start: 0.7933 (mm-30) cc_final: 0.6781 (mm-30) REVERT: C 140 LEU cc_start: 0.9461 (mm) cc_final: 0.9207 (mt) REVERT: C 227 MET cc_start: 0.8545 (tpp) cc_final: 0.8208 (tpp) REVERT: C 296 ASN cc_start: 0.8397 (t0) cc_final: 0.8124 (t0) REVERT: C 305 MET cc_start: 0.8182 (mmm) cc_final: 0.7319 (tpp) REVERT: C 364 GLU cc_start: 0.7942 (tp30) cc_final: 0.7423 (tp30) REVERT: D 10 CYS cc_start: 0.8212 (t) cc_final: 0.8006 (t) REVERT: D 50 LYS cc_start: 0.7501 (mmmm) cc_final: 0.7156 (mmmm) REVERT: D 176 MET cc_start: 0.7585 (tpt) cc_final: 0.6765 (tpp) REVERT: D 240 TYR cc_start: 0.8282 (t80) cc_final: 0.7572 (t80) REVERT: F 281 MET cc_start: 0.5515 (ppp) cc_final: 0.5203 (ppp) REVERT: G 8 MET cc_start: 0.4992 (ttm) cc_final: 0.4008 (ttm) REVERT: H 149 LYS cc_start: 0.5608 (mtmm) cc_final: 0.5381 (ptpt) REVERT: I 117 LEU cc_start: 0.8166 (mm) cc_final: 0.7922 (mm) REVERT: J 194 TYR cc_start: 0.8495 (t80) cc_final: 0.8074 (t80) REVERT: J 268 LEU cc_start: 0.9084 (tp) cc_final: 0.8734 (tp) REVERT: J 344 GLU cc_start: 0.7701 (pp20) cc_final: 0.7478 (pp20) REVERT: J 357 MET cc_start: 0.8203 (mmm) cc_final: 0.7210 (mmm) REVERT: J 441 THR cc_start: 0.9439 (p) cc_final: 0.9182 (t) REVERT: J 537 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8183 (mm-30) REVERT: J 568 ASN cc_start: 0.9094 (p0) cc_final: 0.8768 (p0) REVERT: J 655 LEU cc_start: 0.9262 (tt) cc_final: 0.9035 (tp) REVERT: K 31 PHE cc_start: 0.9001 (t80) cc_final: 0.8627 (t80) REVERT: K 248 ILE cc_start: 0.9095 (tp) cc_final: 0.8848 (tp) REVERT: K 313 ILE cc_start: 0.9069 (pt) cc_final: 0.8792 (mp) REVERT: K 380 GLU cc_start: 0.9145 (mp0) cc_final: 0.8919 (mp0) REVERT: K 442 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7661 (ttt-90) REVERT: K 479 ASN cc_start: 0.9278 (m-40) cc_final: 0.8558 (m-40) REVERT: K 522 ASP cc_start: 0.8563 (m-30) cc_final: 0.7447 (m-30) REVERT: K 535 GLU cc_start: 0.7617 (pt0) cc_final: 0.7410 (pt0) REVERT: K 536 GLU cc_start: 0.8047 (pp20) cc_final: 0.7749 (pp20) REVERT: K 538 CYS cc_start: 0.8681 (m) cc_final: 0.8282 (m) REVERT: K 694 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7465 (mtt90) REVERT: K 756 TYR cc_start: 0.7807 (p90) cc_final: 0.7583 (p90) REVERT: L 72 ILE cc_start: 0.6711 (tt) cc_final: 0.6358 (tt) REVERT: L 118 MET cc_start: 0.5270 (mmp) cc_final: 0.4611 (mmp) REVERT: M 82 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7521 (ttm-80) REVERT: M 118 MET cc_start: 0.4469 (tmm) cc_final: 0.4054 (tmm) REVERT: M 144 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8315 (mm-30) outliers start: 1 outliers final: 0 residues processed: 650 average time/residue: 0.1773 time to fit residues: 185.6373 Evaluate side-chains 513 residues out of total 3297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 277 optimal weight: 1.9990 chunk 353 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 184 optimal weight: 0.7980 chunk 340 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 324 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 296 ASN B 353 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 482 ASN K 654 ASN ** M 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095004 restraints weight = 87415.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096974 restraints weight = 52862.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097969 restraints weight = 35243.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098349 restraints weight = 28993.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098680 restraints weight = 23051.488| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31251 Z= 0.156 Angle : 0.679 11.213 42138 Z= 0.346 Chirality : 0.044 0.307 4612 Planarity : 0.005 0.170 5470 Dihedral : 5.352 56.013 4208 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.05 % 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: 0.17 (0.14), residues: 3817 helix: 0.98 (0.12), residues: 1825 sheet: -0.07 (0.26), residues: 404 loop : -0.81 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 82 TYR 0.024 0.002 TYR C 166 PHE 0.024 0.001 PHE J 473 TRP 0.085 0.003 TRP B 86 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (31251) covalent geometry : angle 0.67877 / 0.35 (42138) hydrogen bonds : bond 0.04457 / 3.00 ( 1538) hydrogen bonds : angle 4.58688 / 3.14 ( 4287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5328.43 seconds wall clock time: 93 minutes 9.13 seconds (5589.13 seconds total)